diff --git a/RUN.sh b/RUN.sh
index afc2eca..3975f5d 100755
--- a/RUN.sh
+++ b/RUN.sh
@@ -1,18 +1,17 @@
 #!/bin/bash
 function printVersion {
-    printf "Spliceogen 1.0 1-March-2019\n"
+    printf "Spliceogen 2.0 1-October-2019\n"
 }
 function printHelp {
     cat <<-END
 Usage:
 ------
 3 required args:
-1)  -inputVCF path/to/VCF/input(s).VCF
-        OR
-    -inputBED path/to/input(s).BED 
-        Note: wildcard matching of multiple files is allowed
-2)  -gtf path/to/annotation.GTF
-3)  -fasta path/to/genome.fasta
+1)  -input path/to/VCF/input/file(s).VCF
+        Note: multiple input files are accepted "eg. -input *.vcf"
+        Note: deprecated v1.0 tags "inputVCF" and "inputBED" are still accepted
+2)  -gtf path/to/annotation.gtf
+3)  -fasta path/to/genome.fa
 optional arg:
 4)  -branchpointer hgXX
         OR
@@ -22,8 +21,6 @@ END
 }
 #set default parameters
 POSITIONAL=()
-INPUTVCF="FALSE"
-INPUTBED="FALSE"
 INPUTFILES=""
 USEBP=""
 USEBPINDELS=""
@@ -43,8 +40,16 @@ case $key in
     printVersion
     exit 0
     ;;
+    -input)
+    INPUTFILES="$2"
+    shift
+    shift
+    while [ "$1" ] && [[ ! $1 == *-* ]]; do
+        INPUTFILES="$INPUTFILES $1"
+        shift
+    done
+    ;;
     -inputVCF)
-    INPUTVCF="TRUE"
     INPUTFILES="$2"
     shift
     shift
@@ -54,7 +59,6 @@ case $key in
     done
     ;;
     -inputBED)
-    INPUTBED="TRUE"
     INPUTFILES="$2"
     shift
     shift
@@ -97,36 +101,26 @@ elif [ ! -f "$ANNOTATION" ]; then
     echo "GTF annotation file not found: use -gtf path/to/gencodeXX.gtf\nExiting..."
     exit 1
 fi
-checkGzip=$( file --mime-type "$FASTAPATH" "$ANNOTATION" "$INPUTFILES" | grep gzip)
-if [ ! "$checkGzip" = "" ]; then
-    echo "Error: Input FASTA and GTF files must be unzipped. Exiting..."
-    exit 1
-fi
-#check input files for consistenty in "chr" nomenlature
-gtfChr=$(head "$ANNOTATION" | tail -1 | awk '{print $1}' | grep chr)
-fastaChr=$(head -1 "$FASTAPATH" | awk '{print $1}' | grep chr)
-firstInputFile=$(echo "$INPUTFILES" | awk '{print $1}')
-inputChr=$(tail -1 "$firstInputFile" | awk '{print $1}' | grep chr)
-warningChr="Warning: it appears the provided gtf, fasta, and input files use inconsistent Chromosome nomenclature. Eg. \"chr1\" vs \"1\". This will likely cause issues. Please edit them for consistency"
-if [ "$gtfChr" == "" ]; then
+#check input gtf/fasta "chr" nomenclature
+gtfChr=$(zcat -f "$ANNOTATION" | grep -v '^GL000' | tail -1 | awk '{print $1}' | grep chr)
+fastaChr=$(cat "$FASTAPATH" | head -1 | awk '{print $1}' | grep chr)
+    gtfChrAdd=""
+    gtfChrRemove="UnmatchedString"
     if [ "$fastaChr" != "" ]; then
-        echo "$warningChr"
-    elif [ "$inputChr" != "" ]; then
-        echo "$warningChr"
+        if [ "$gtfChr" == "" ]; then
+            gtfChrAdd="chr"
+        fi        
+    elif [ "$fastaChr" == "" ]; then
+        if [ "$gtfChr" != "" ]; then
+            gtfChrRemove="chr"
+        fi        
     fi
-else
-    if [ "$fastaChr" == "" ]; then
-        echo "$warningChr"
-    elif [ "$inputChr" == "" ]; then
-        echo "$warningChr"
-    fi
-fi
 #prepare splice site intervals from annotation.gtf
 gtfBasename=$(basename $ANNOTATION)
 if [ ! -f data/"$gtfBasename"_SpliceSiteIntervals.txt ] || [[ "$ANNOTATION" -nt data/"$gtfBasename"_SpliceSiteIntervals.txt ]] ; then
     echo "Preparing splice site annotation..."
-    grep '[[:blank:]]gene[[:blank:]]\|[[:blank:]]transcript[[:blank:]]\|[[:blank:]]exon[[:blank:]]' "$ANNOTATION" | grep -v '^GL000' |
-    java -cp bin getSpliceSiteIntervalsFromGTF > data/"$gtfBasename"_SpliceSiteIntervals.txt
+    zcat -f "$ANNOTATION" | grep '[[:blank:]]gene[[:blank:]]\|[[:blank:]]transcript[[:blank:]]\|[[:blank:]]exon[[:blank:]]' | grep -v '^GL000' | 
+    sed "s/$gtfChrRemove//" | awk -v var="$gtfChrAdd" '{print var$0}' | java -cp bin getSpliceSiteIntervalsFromGTF > data/"$gtfBasename"_SpliceSiteIntervals.txt
 fi
 #for each input VCF/BED file
 for FILE in $INPUTFILES; do
@@ -139,9 +133,39 @@ for FILE in $INPUTFILES; do
     echo "Input file: $fileID"
     #remove temp files from any previous run
     rm temp/"$fileID"* 2> /dev/null
+    #check input file type
+    FILETYPE=""
+    nFields=$(zcat -f $FILE | tail -1 | wc -w)
+    vcfHeader=$(zcat -f $FILE | head -1 | grep VCF)
+    if [ "$nFields" -eq 4 ]; then
+        FILETYPE="TSV"
+    elif [ ! -z "$vcfHeader" ]; then
+        FILETYPE="VCF"
+    else
+        FILETYPE="BED"
+    fi
+    echo "File type: $FILETYPE"
+    #correct mismatches in "chr" nomenclature among input files
+    inputChr=$(zcat -f "$FILE" | tail -1 | awk '{print $1}' | grep chr)
+    inputChrAdd=""
+    inputChrRemove="UnmatchedString"
+    if [ "$fastaChr" != "" ]; then
+        if [ "$inputChr" == "" ]; then
+            inputChrAdd="chr"
+        fi        
+    elif [ "$fastaChr" == "" ]; then
+        if [ "$inputChr" != "" ]; then
+            inputChrRemove="chr"
+        fi        
+    fi
     #sort body of input file
-    grep "^#" "$FILE" > temp/"$fileID"_sorted
-    grep -v "^#" "$FILE" | sort -k1,1 -k2,2n >> temp/"$fileID"_sorted
+        zcat -f "$FILE" | grep "^#" > temp/"$fileID"_sorted
+        if [ "$FILETYPE" == "TSV" ]; then
+            zcat -f "$FILE" | grep -v "^#" | sort -k1,1 -k2,2n | sed "s/$inputChrRemove//" | awk -v OFS="\\t" -v var=$inputChrAdd '{print var$1, $2, $2, "x", "1", ".", $3, $4}' >> temp/"$fileID"_sorted
+        else 
+            #zcat -f "$FILE" | grep -v "^#" | sort -k1,1 -k2,2n | sed "s/$inputChrRemove//" | sed "/^/$inputChrAdd/" >> temp/"$fileID"_sorted
+            zcat -f "$FILE" | grep -v "^#" | sort -k1,1 -k2,2n | sed "s/$inputChrRemove//" | awk -v OFS="\\t" -v var=$inputChrAdd '{print var$0}' >> temp/"$fileID"_sorted
+        fi
     #check bedtools is installed
     bedtoolsLocation=$(which bedtools);
     if [ "$bedtoolsLocation" == "" ]; then
@@ -157,7 +181,7 @@ for FILE in $INPUTFILES; do
     fi
     #bedtools intersect to get strand info
     echo "Retrieving strand info..."
-    grep '[[:blank:]]gene[[:blank:]]' "$ANNOTATION" | sort -k1,1 -k4,4n | grep -v '^GL000' | bedtools intersect -a temp/"$fileID"_sorted -b stdin -wa -wb -sorted  > temp/"$fileID"unstrandedInput.txt 
+    zcat -f "$ANNOTATION" | grep '[[:blank:]]gene[[:blank:]]' | sort -k1,1 -k4,4n | grep -v '^GL000' | awk -v var="$gtfChrAdd" -v OFS="\\t" '{print var$0}' | sed "s/$gtfChrRemove//" | bedtools intersect -a temp/"$fileID"_sorted -b stdin -wa -wb -sorted  > temp/"$fileID"unstrandedInput.txt 
     if [ $? -ne 0 ]; then
         echo "Warning. Bedtools intersect returned non-zero exit status. Intersection failed between provided variant VCF/BED file and provided GTF. See above error message for more details"
     fi
@@ -166,10 +190,10 @@ for FILE in $INPUTFILES; do
         exit 1
     fi
     #generate flanking intervals.bed for bedtools getfasta and branchpointer input
-    if [ "$INPUTVCF" = "TRUE" ]; then
+    if [ "$FILETYPE" = "VCF" ]; then
         grep '[[:blank:]]+[[:blank:]]' temp/"$fileID"unstrandedInput.txt | awk -v OFS="\\t" '{print ".", $1, $2, "+", $4, $5}' | ( [[ "$USEBP" ]] && tee temp/"$fileID"bpInput.txt || cat ) | java -cp bin getFastaIntervals > temp/"$fileID"fastaIntervals.bed
         grep '[[:blank:]]-[[:blank:]]' temp/"$fileID"unstrandedInput.txt | awk -v OFS="\\t" '{print ".", $1, $2, "-", $4, $5}' | ( [[ "$USEBP" ]] && tee -a temp/"$fileID"bpInput.txt || cat ) | java -cp bin getFastaIntervals >> temp/"$fileID"fastaIntervals.bed
-    elif [ "$INPUTBED" = "TRUE" ]; then
+    elif [ "$FILETYPE" = "TSV" ] || [ "$FILETYPE" = "BED" ] ; then
         grep '[[:blank:]]+[[:blank:]]' temp/"$fileID"unstrandedInput.txt | awk -v OFS="\\t" '{print ".", $1, $2, "+", $7, $8}' | ( [[ "$USEBP" ]] && tee temp/"$fileID"bpInput.txt || cat ) | java -cp bin getFastaIntervals > temp/"$fileID"fastaIntervals.bed
         grep '[[:blank:]]-[[:blank:]]' temp/"$fileID"unstrandedInput.txt | awk -v OFS="\\t" '{print ".", $1, $2, "-", $7, $8}' | ( [[ "$USEBP" ]] && tee -a temp/"$fileID"bpInput.txt || cat ) | java -cp bin getFastaIntervals >> temp/"$fileID"fastaIntervals.bed
     fi
@@ -185,25 +209,42 @@ for FILE in $INPUTFILES; do
     fi
     #seqScan: generates input strings for maxentscan and genesplicer as well as ESRseq scores
     echo "Scanning for motifs..."
-    rm output/mesOmmitted/"$fileID" 2> /dev/null
+    rm output/"$fileID"mesOmmitted.txt 2> /dev/null
+    rm output/"$fileID"refMismatch.txt 2> /dev/null
     java -cp bin seqScan temp/"$fileID"seqToScan.FASTA -useESR $fileID 1>&2
+    if [ -s output/"$fileID"refMismatch.txt ]; then
+        refMismatchCount=$(wc -l output/"$fileID"refMismatch.txt | awk '{print $1}')
+        echo "Note: $refMismatchCount variants were excluded because the provided Reference allele does not match the nucleotide(s) in the provided FASTA. IDs of excluded variant(s) are outputted here: Spliceogen/output/""$fileID""refMismatch.txt"
+    fi
+    if [ -s output/"$fileID"mesOmmitted.txt ]; then
+        mesOmmittedCount=$(wc -l output/"$fileID"mesOmmitted.txt | awk '{print $1}')
+        echo "Note: $mesOmmittedCount variants were excluded from MaxEntScan because their flanking FASTA sequence contains invalid characters (most commonly \"n\"), which cannot be processed by MaxEntScan. IDs of ommitted variant(s) are listed in: Spliceogen/output/""$fileID""mesOmmitted.txt"
+    fi
     #run maxEntScan and confirm non-zero exit, since invalid inputs cause it to exit early
-    echo "Running MaxEntScan..."
-    perl score5.pl temp/"$fileID"mesDonorInput.txt | java -cp bin processScoresMES > temp/"$fileID"mesDonorScores.txt
-    retVal=( ${PIPESTATUS[0]} )
-    if [ $retVal -ne 0 ]; then
-        echo "MaxEntScan returned non-zero exit status. It is likely not all variants were processed. Exiting..."
-    exit $retVal
-    fi
-    perl score3.pl temp/"$fileID"mesAcceptorInput.txt | java -cp bin processScoresMES > temp/"$fileID"mesAcceptorScores.txt
-    retVal=( ${PIPESTATUS[0]} )
-    if [ $retVal -ne 0 ]; then
-        echo "MaxEntScan returned non-zero exit status. It is likely not all variants were processed. Exiting..."
-    exit $retVal
+    if [ -s temp/"$fileID"mesDonorInput.txt ] || [ -s temp/"$fileID"mesAcceptorInput.txt ] ; then
+        echo "Running MaxEntScan..."
+        perl score5.pl temp/"$fileID"mesDonorInput.txt | java -cp bin processScoresMES > temp/"$fileID"mesDonorScores.txt
+        retVal=( ${PIPESTATUS[0]} )
+        if [ $retVal -ne 0 ]; then
+            echo "MaxEntScan returned non-zero exit status. It is likely not all variants were processed. Exiting..."
+        exit $retVal
+        fi
+        perl score3.pl temp/"$fileID"mesAcceptorInput.txt | java -cp bin processScoresMES > temp/"$fileID"mesAcceptorScores.txt
+        retVal=( ${PIPESTATUS[0]} )
+        if [ $retVal -ne 0 ]; then
+            echo "MaxEntScan returned non-zero exit status. It is likely not all variants were processed. Exiting..."
+        exit $retVal
+        fi
+    else
+        echo "No input for MaxEntScan"
     fi
     #run genesplicer
-    echo "Running GeneSplicer..."
-    bin/linux/genesplicerAdapted temp/"$fileID"gsInput.FASTA human > temp/"$fileID"gsScores.txt
+    if [ -s temp/"$fileID"gsInput.FASTA ] ; then
+        echo "Running GeneSplicer..."
+        bin/linux/genesplicerAdapted temp/"$fileID"gsInput.FASTA human > temp/"$fileID"gsScores.txt
+    else
+        echo "No input for GeneSplicer"
+    fi
     #run branchpointer SNPs
     if [ "$USEBP" = "TRUE" -a "$USEBPINDELS" = "FALSE" ]; then
         echo "Running Branchpointer..."
@@ -226,25 +267,35 @@ for FILE in $INPUTFILES; do
         #awk -v OFS=\\t '{print $2, $3, $4, $8, $9, $15, $16, $22, $23, $24, $25}' output/"$fileID"bpOutputSNPs.txt" > output/bpSNPsSummarised.txt
     fi
     #merge scores into one line
-    echo "Processing scores..."
-    cat temp/"$fileID"mesDonorScores.txt temp/"$fileID"mesAcceptorScores.txt temp/"$fileID"gsScores.txt temp/"$fileID"ESRoutput.txt data/"$gtfBasename"_SpliceSiteIntervals.txt sources/terminatingMergeLine.txt |
-    sort -k1,1 -k 2,2n -k 3 -k 4 -s | java -cp bin mergeOutput "$fileID"
-    #sort predictions
-    if [ -s temp/"$fileID"_donorCreating_unsorted.txt ]; then
-        sort -gr -k11,11 temp/"$fileID"_donorCreating_unsorted.txt >> output/"$fileID"_donorCreating.txt
-    else
-        rm output/"$fileID"_donorCreating.txt
-    fi 
-    if [ -s temp/"$fileID"_acceptorCreating_unsorted.txt ]; then
-        sort -gr -k11,11 temp/"$fileID"_acceptorCreating_unsorted.txt >> output/"$fileID"_acceptorCreating.txt
+    scoresToMerge=""
+    if [ -s temp/"$fileID"gsScores.txt ] ; then
+        scoresToMerge="temp/"$fileID"gsScores.txt"
+    fi
+    if [ -s temp/"$fileID"mesDonorScores.txt ] ; then
+        scoresToMerge="$scoresToMerge temp/"$fileID"mesDonorScores.txt"
+    fi
+    if [ -s temp/"$fileID"mesAcceptorScores.txt ] ; then
+        scoresToMerge="$scoresToMerge temp/"$fileID"mesAcceptorScores.txt"
+    fi
+    if [ -s temp/"$fileID"ESRoutput.txt ] ; then
+        scoresToMerge="$scoresToMerge temp/"$fileID"ESRoutput.txt"
+    fi
+    checkScoresExist=$(echo "$scoresToMerge" | grep "temp")
+    if [ -z "$checkScoresExist" ]; then
+        echo "No MaxEntScan/GeneSplicer/ESRseq scores to process"
     else
-        rm output/"$fileID"_acceptorCreating.txt
+        echo "Processing scores..."
+        cat $(echo "$scoresToMerge") data/"$gtfBasename"_SpliceSiteIntervals.txt sources/terminatingMergeLine.txt | sort -k1,1 -k 2,2n -k 3 -k 4 -s | java -cp bin mergeOutput "$fileID"
+    fi
+    #sort predictions
+    if [ -s temp/"$fileID"_gain_unsorted.txt ]; then
+        echo -e "#CHR\tSTART\tREF\tALT\tGENE\tdonGainP\taccGainP" > output/"$fileID"_ssGain.txt
+        sort -gr -k8,8 temp/"$fileID"_gain_unsorted.txt | cut -f1-7 >> output/"$fileID"_ssGain.txt
     fi 
-    if [ -s temp/"$fileID"_withinSS_unsorted.txt ]; then
-        sort -gr -k17,17 temp/"$fileID"_withinSS_unsorted.txt | cut -f1-15 >> output/"$fileID"_withinSS.txt
-    else
-        rm output/"$fileID"_withinSS.txt
+    if [ -s temp/"$fileID"_loss_unsorted.txt ]; then
+        echo -e "#CHR\tSTART\tREF\tALT\tGENE\twithinSS\tdonGainP\taccGainP" > output/"$fileID"_withinSS.txt
+        sort -gr -k9,9 temp/"$fileID"_loss_unsorted.txt | cut -f1-8 >> output/"$fileID"_withinSS.txt
     fi 
     #clean up temp files
-    rm temp/"$fileID"* 2> /dev/null
+    #rm temp/"$fileID"* 2> /dev/null
 done
diff --git a/bin/mergeOutput.class b/bin/mergeOutput.class
index 79c45b5..8a12440 100644
Binary files a/bin/mergeOutput.class and b/bin/mergeOutput.class differ
diff --git a/bin/mergeOutput.java b/bin/mergeOutput.java
index 585c66a..ec17cbe 100644
--- a/bin/mergeOutput.java
+++ b/bin/mergeOutput.java
@@ -6,19 +6,17 @@
 import java.text.DecimalFormat;
 public class mergeOutput {
 
-	//store output lines in buffers to minimise I/O
+    //store output lines in buffers to minimise I/O
     public static String[] avBuffer = new String[30000];
-    public static String[] donBuffer = new String[30000];
-    public static String[] accBuffer = new String[30000];
+    public static String[] gainBuffer = new String[30000];
     public static String[] ssBuffer = new String[30000];
+    public static int gainBufferIndex = 0;
     public static int avBufferIndex = 0;
-    public static int donBufferIndex = 0;
-    public static int accBufferIndex = 0;
     public static int ssBufferIndex = 0;
 
     public static void main (String[] args) {
         if (args.length < 1) {
-            System.out.println("must provide vcf/bed file name as command line argument");
+            System.out.println("Must provide input filename arg...exiting");
             System.exit(1);
         }
         String fileName=args[0];
@@ -43,238 +41,317 @@ public static void main (String[] args) {
         try {
             BufferedReader in = new BufferedReader(new InputStreamReader(System.in));
             while ((s = in.readLine()) != null && s.length() != 0) {
-            String[] split = s.split("\\s+");
-            String chr = split[0];
-            int start = Integer.parseInt(split[1]);
-            String ref = split[2].toUpperCase();
-            String alt = split[3].toUpperCase();
-            String type = split[4];
-            //check if current line is next variant
-            boolean nextVariant = false;
-            if (!(chr.equals(prevID[0])&&start==Integer.parseInt(prevID[1]))) {
-                nextVariant = true;
-            } else
-            if (!(ref.equals(prevID[2])&&alt.equals(prevID[3]))) {
-                nextVariant = true;
-            } else
-            if (chr.equals("xxx")) {
-                nextVariant = true;
-            }
-            //print scores of previous variant, if current line is next variant and previous line wasn't a gene annotation
-            if(nextVariant && !prevID[4].equals("GENE")) {
-            	//update overlapping genes and splice sites
-            	geneID = updateOverlappingGenes(geneID, prevID);
-            	String withinSS = checkForOverlappingSpliceSite(prevID, donNames, accNames, donStart, accStart, donEnd, accEnd);
-            	//format output columns
-                String[] out = new String[21];
-                out[0] = prevID[0]; out[1] = Integer.toString(Integer.parseInt(prevID[1]));
-                out[3] = prevID[2]; out[4] = prevID[3]; out[5] = geneID[1]; out[6] = withinSS;
-                //adjust end value for indels
-                int endPos = Integer.parseInt(prevID[1])+prevID[2].length()-1;
-                if (prevID[3].equals("*")) {
-                    endPos++;
-                }
-                out[2]= Integer.toString(endPos);
-                //fill scores
-                for (int i=0; i<12; i++) {
-                    if (scores[i]==-99 || scores[i]==0) {
-                        out[i+7]=".";
-                    } else {
-                        out[i+7]=Double.toString(scores[i]);
+                String[] split = s.split("\\s+");
+                String chr = split[0];
+                int start = Integer.parseInt(split[1]);
+                String ref = split[2].toUpperCase();
+                String alt = split[3].toUpperCase();
+                String type = split[4];
+                //check if current line is next variant
+                boolean nextVariant = false;
+                if (!(chr.equals(prevID[0])&&start==Integer.parseInt(prevID[1]))) {
+                    nextVariant = true;
+                } else
+                    if (!(ref.equals(prevID[2])&&alt.equals(prevID[3]))) {
+                        nextVariant = true;
+                    } else
+                        if (chr.equals("xxx")) {
+                            nextVariant = true;
+                        }
+                //print scores of previous variant, if current line is next variant and previous line wasn't a gene annotation
+                if(nextVariant && !prevID[4].equals("GENE")) {
+                    //update overlapping genes and splice sites
+                    geneID = updateOverlappingGenes(geneID, prevID);
+                    String withinSS = checkForOverlappingSpliceSite(prevID, donNames, accNames, donStart, accStart, donEnd, accEnd);
+                    //format output columns
+                    String[] out = new String[23];
+                    out[0] = prevID[0]; out[1] = Integer.toString(Integer.parseInt(prevID[1]));
+                    out[3] = prevID[2]; out[4] = prevID[3]; out[5] = geneID[1]; out[6] = withinSS;
+                    //adjust end value for indels
+                    int endPos = Integer.parseInt(prevID[1])+prevID[2].length()-1;
+                    if (prevID[3].equals("*")) {
+                        endPos++;
                     }
-                }
-                //calculate donor/acceptor creating logistic regression scores
-                String[] lrScores = calculateLogRegScores(scores).split("\\s+");
-                if (!out[6].contains("ENSE")) {
-                    out[19]= lrScores[0];                
+                    out[2]= Integer.toString(endPos);
+                    //fill scores
+                    for (int i=0; i<12; i++) {
+                        if (scores[i]==-99 || scores[i]==0) {
+                            out[i+7]=".";
+                        } else {
+                            out[i+7]=Double.toString(scores[i]);
+                        }
+                    }
+                    //calculate donor/acceptor creating logistic regression scores
+                    String[] lrScores = calculateLogRegScores(scores, out[6]).split("\\s+");
+                    out[19]= lrScores[0];
                     out[20]= lrScores[1];
-                } else {
-                    out[19]= ".";                
-                    out[20]= ".";
+                    out[21]= lrScores[2];
+                    out[22]= lrScores[3];
+
+                    //add output line to file buffers
+                    outputVariantToBuffers(out);
+                    //reset scores
+                    Arrays.fill(scores, -99.0);
+                    //append to file and empty buffers every ~25000 lines
+                    if (avBufferIndex > 25000) {
+                        appendToFiles(fileName);
+                        resetOutputArrays();
+                    }                
                 }
-                //add output line to file buffers
-                outputVariantToBuffers(out);
-                //reset scores
-                Arrays.fill(scores, -99.0);
-                //append to file and empty buffers every ~25000 lines
-                if (avBufferIndex > 25000) {
-                    appendToFiles(fileName);
-                    resetOutputArrays();
-                }                
-            }
-        //MaxEntScan
-    if (type.equals("MESDON")) {
-        scores[0]=Double.parseDouble(split[5]);
-        scores[1]=Double.parseDouble(split[6]);
-    } else
-    if(type.equals("MESACC")){
-        scores[2]=Double.parseDouble(split[5]);
-        scores[3]=Double.parseDouble(split[6]);
-    } else
-    //GeneSplicer
-    if (type.equals("GSREF")) {
-        if (split[6].equals("donor")) {
-            scores[4]=Double.parseDouble(split[5]);
-        } else
-        if (split[6].equals("acceptor")) {
-            scores[6]=Double.parseDouble(split[5]);
-        } 
-    } else   
-    if (type.equals("GSALT")) {
-        if (split[6].equals("donor")) {
-            scores[5]=Double.parseDouble(split[5]);
-        } else
-        if (split[6].equals("acceptor")) {
-            scores[7]=Double.parseDouble(split[5]);
-        } 
-    } else
-    //ESR
-        if (type.equals("ESR")) {
-            scores[8]=Double.parseDouble(split[5]);
-            scores[9]=Double.parseDouble(split[6]);
-            scores[10]=Double.parseDouble(split[7]);
-            scores[11]=Double.parseDouble(split[8]);
-        }
-        //GENE
-        if (type.equals("GENE")) {
-            //overlapping gene annotations
-        	if (ifGenesOverlap(geneID, chr, start)) {
-                geneID[1] = geneID[1].concat(";").concat(split[3]);
-                geneID[2] = geneID[2].concat(";").concat(split[2]);
-                geneID[0] = split[0];
-                if (split.length>11) {
-                    //update splice site pos/name arrays with info from new overlapping gene
-                    String[] donStartStr=split[6].split(",");
-                    String[] donEndStr=split[7].split(",");
-                    String[] accStartStr=split[8].split(",");
-                    String[] accEndStr=split[9].split(",");
-                    String[] donNamesStr=split[10].split(",");
-                    String[] accNamesStr=split[11].split(",");
-                    int accIndex = 0;
-                    int donIndex = 0;
-                    while (donStart[donIndex]>0) {
-                        donIndex++;
-                    }
-                    while (accStart[accIndex]>0) {
-                        accIndex++;
-                    }
-                    for (int k = 0; k < donStartStr.length; k++) {
-                        donStart[donIndex+k] = Integer.parseInt(donStartStr[k]);
-                        donEnd[donIndex+k] = Integer.parseInt(donEndStr[k]);
-                        donNames[donIndex+k] = donNamesStr[k];
-                    }
-                    for (int k = 0; k < accStartStr.length; k++) {
-                        accStart[accIndex+k] = Integer.parseInt(accStartStr[k]);
-                        accEnd[accIndex+k] = Integer.parseInt(accEndStr[k]);
-                        accNames[accIndex+k] = accNamesStr[k];
+                //MaxEntScan
+                if (type.equals("MESDON")) {
+                    scores[0]=Double.parseDouble(split[5]);
+                    scores[1]=Double.parseDouble(split[6]);
+                } else
+                    if(type.equals("MESACC")){
+                        scores[2]=Double.parseDouble(split[5]);
+                        scores[3]=Double.parseDouble(split[6]);
+                    } else
+                        //GeneSplicer
+                        if (type.equals("GSREF")) {
+                            if (split[6].equals("donor")) {
+                                scores[4]=Double.parseDouble(split[5]);
+                            } else
+                                if (split[6].equals("acceptor")) {
+                                    scores[6]=Double.parseDouble(split[5]);
+                                } 
+                        } else   
+                            if (type.equals("GSALT")) {
+                                if (split[6].equals("donor")) {
+                                    scores[5]=Double.parseDouble(split[5]);
+                                } else
+                                    if (split[6].equals("acceptor")) {
+                                        scores[7]=Double.parseDouble(split[5]);
+                                    } 
+                            } else
+                                //ESR
+                                if (type.equals("ESR")) {
+                                    scores[8]=Double.parseDouble(split[5]);
+                                    scores[9]=Double.parseDouble(split[6]);
+                                    scores[10]=Double.parseDouble(split[7]);
+                                    scores[11]=Double.parseDouble(split[8]);
+                                }
+                //GENE
+                if (type.equals("GENE")) {
+                    //overlapping gene annotations
+                    if (ifGenesOverlap(geneID, chr, start)) {
+                        geneID[1] = geneID[1].concat(";").concat(split[3]);
+                        geneID[2] = geneID[2].concat(";").concat(split[2]);
+                        geneID[0] = split[0];
+                        if (split.length>11) {
+                            //update splice site pos/name arrays with info from new overlapping gene
+                            String[] donStartStr=split[6].split(",");
+                            String[] donEndStr=split[7].split(",");
+                            String[] accStartStr=split[8].split(",");
+                            String[] accEndStr=split[9].split(",");
+                            String[] donNamesStr=split[10].split(",");
+                            String[] accNamesStr=split[11].split(",");
+                            int accIndex = 0;
+                            int donIndex = 0;
+                            while (donStart[donIndex]>0) {
+                                donIndex++;
+                            }
+                            while (accStart[accIndex]>0) {
+                                accIndex++;
+                            }
+                            for (int k = 0; k < donStartStr.length; k++) {
+                                donStart[donIndex+k] = Integer.parseInt(donStartStr[k]);
+                                donEnd[donIndex+k] = Integer.parseInt(donEndStr[k]);
+                                donNames[donIndex+k] = donNamesStr[k];
+                            }
+                            for (int k = 0; k < accStartStr.length; k++) {
+                                accStart[accIndex+k] = Integer.parseInt(accStartStr[k]);
+                                accEnd[accIndex+k] = Integer.parseInt(accEndStr[k]);
+                                accNames[accIndex+k] = accNamesStr[k];
+                            }
+                        }
+                        //non-overlapping genes
+                    } else {
+                        //reset arrays
+                        Arrays.fill(donStart, 0);
+                        Arrays.fill(donEnd, 0);
+                        Arrays.fill(accStart, 0);
+                        Arrays.fill(accEnd, 0);
+                        Arrays.fill(donNames, null);
+                        Arrays.fill(accNames, null);
+                        geneID[1] = split[3];
+                        geneID[2] = split[2];
+                        geneID[0] = split[0];
+                        if (split.length>11) {
+                            //reset and update splice site pos/name arrays
+                            String[] donStartStr=split[6].split(",");
+                            String[] donEndStr=split[7].split(",");
+                            String[] accStartStr=split[8].split(",");
+                            String[] accEndStr=split[9].split(",");
+                            String[] donNamesStr=split[10].split(",");
+                            String[] accNamesStr=split[11].split(",");
+                            for (int k=0; k<donStartStr.length; k++) {
+                                donStart[k]=Integer.parseInt(donStartStr[k]);
+                                donEnd[k]=Integer.parseInt(donEndStr[k]);
+                                donNames[k]=donNamesStr[k];
+                            }
+                            for (int k=0; k<accStartStr.length; k++) {
+                                accStart[k]=Integer.parseInt(accStartStr[k]);
+                                accEnd[k]=Integer.parseInt(accEndStr[k]);
+                                accNames[k]=accNamesStr[k];
+                            }
+                        }        	            	
                     }
                 }
-        //non-overlapping genes
-        } else {
-        	//reset arrays
-            Arrays.fill(donStart, 0);
-            Arrays.fill(donEnd, 0);
-            Arrays.fill(accStart, 0);
-            Arrays.fill(accEnd, 0);
-            Arrays.fill(donNames, null);
-            Arrays.fill(accNames, null);
-            geneID[1] = split[3];
-            geneID[2] = split[2];
-            geneID[0] = split[0];
-            if (split.length>11) {
-                //reset and update splice site pos/name arrays
-                String[] donStartStr=split[6].split(",");
-                String[] donEndStr=split[7].split(",");
-                String[] accStartStr=split[8].split(",");
-                String[] accEndStr=split[9].split(",");
-                String[] donNamesStr=split[10].split(",");
-                String[] accNamesStr=split[11].split(",");
-                for (int k=0; k<donStartStr.length; k++) {
-                    donStart[k]=Integer.parseInt(donStartStr[k]);
-                    donEnd[k]=Integer.parseInt(donEndStr[k]);
-                    donNames[k]=donNamesStr[k];
-                }
-                for (int k=0; k<accStartStr.length; k++) {
-                    accStart[k]=Integer.parseInt(accStartStr[k]);
-                    accEnd[k]=Integer.parseInt(accEndStr[k]);
-                    accNames[k]=accNamesStr[k];
-                }
-            }        	            	
-            }
-        }
                 //update info for comparison with next line
                 prevID[0] = chr;
                 prevID[1] = Integer.toString(start);
                 prevID[2] = ref;
                 prevID[3] = alt;
                 prevID[4] = type;
+            }
+            //final append to file
+            if (avBufferIndex > 0) {
+                appendToFiles(fileName);
+            }
+        } catch (Exception e) {
+            e.printStackTrace();
         }
-        //final append to file
-        if (avBufferIndex > 0) {
-            appendToFiles(fileName);
-        }
-} catch (Exception e) {
-	e.printStackTrace();
+    }
+    /*
+       public static String calculateLogRegScores (double[] s) {
+//impute missing values
+//maxEntScan
+for (int i=0; i<4; i++) {
+if (s[i]==-99.0 | s[i]==0.0) {
+s[i] = -20.0;
+}
+}                    
+//gsDonRef
+if (s[4]==-99.0 | s[4]==0.0) {
+if (s[5]==-99.0 | s[5]==0.0) {
+s[4]=0.0;
+s[5]=0.0;
+} else {
+s[4]=-3.0;
 }
+} else
+//gsDonAlt
+if (s[7]==-99.0 | s[7]==0.0) {
+s[7]=-3.0;
+}
+//gsAccRef
+if (s[6]==-99.0 | s[6]==0.0) {
+if (s[7]==-99.0 | s[7]==0.0) {
+s[6]=0.0;
+s[7]=0.0;
+} else {
+s[6]=-3.0;
+}
+} else
+//gsAccAlt
+if (s[7]==-99.0 | s[7]==0.0) {
+s[7]=-3.0;
+}
+double mesDonChange = s[1] - s[0];
+double mesAccChange = s[3] - s[2];
+double gsDonChange = s[5] - s[4];
+double gsAccChange = s[7] - s[6];
+// calculate p = 1/(1+e^-(a + b1X1 + b2X2 + ... + bnXn))
+double pDon = 1/(1 + Math.exp(-(-0.9865 + (mesDonChange * 0.1129) + (gsDonChange * 0.01151) + (s[1] * 0.2076) + (s[5] * 0.4350) )));
+double pAcc = 1/(1 + Math.exp(-(-1.665 + (mesAccChange * 0.3323) + (gsAccChange * 0.05084) + (s[3] * 0.1877) + (s[7] * 0.1730) )));
+String pDonStr = Double.toString(pDon);
+String pAccStr = Double.toString(pAcc);
+//round scores to 2 decimal places
+try {
+pDonStr = String.format("%.02f",pDon);
+pAccStr = String.format("%.02f",pAcc);
+} catch (Exception e) {}
+String ret = pDonStr + "\t" + pAccStr;
+return ret;
+}
+     */
+
+public static String calculateLogRegScores (double[] s, String withinSS) {
+    //impute missing values
+    //maxEntScan
+    for (int i=0; i<4; i++) {
+        if (s[i]==-99.0 | s[i]==0.0) {
+            s[i] = -20.0;
+        }
     }
-        
-    public static String calculateLogRegScores (double[] s) {
-        //impute missing values
-        //maxEntScan
-        for (int i=0; i<4; i++) {
-            if (s[i]==-99.0 | s[i]==0.0) {
-                s[i] = -20.0;
-            }
-        }                    
-        //gsDonRef
-        if (s[4]==-99.0 | s[4]==0.0) {
-            if (s[5]==-99.0 | s[5]==0.0) {
-                s[4]=0.0;
-                s[5]=0.0;
-            } else {
-                s[4]=-3.0;
-            }
-        } else
+    //gsDonRef
+    if (s[4]==-99.0 | s[4]==0.0) {
+        if (s[5]==-99.0 | s[5]==0.0) {
+            s[4]=0.0;
+            s[5]=0.0;
+        } else {
+            s[4]=-3.0;
+        }
+    } else
         //gsDonAlt
         if (s[7]==-99.0 | s[7]==0.0) {
             s[7]=-3.0;
         }
-        //gsAccRef
-        if (s[6]==-99.0 | s[6]==0.0) {
-            if (s[7]==-99.0 | s[7]==0.0) {
-                s[6]=0.0;
-                s[7]=0.0;
-            } else {
-                s[6]=-3.0;
-            }
-        } else
+    //gsAccRef
+    if (s[6]==-99.0 | s[6]==0.0) {
+        if (s[7]==-99.0 | s[7]==0.0) {
+            s[6]=0.0;
+            s[7]=0.0;
+        } else {
+            s[6]=-3.0;
+        }
+    } else
         //gsAccAlt
         if (s[7]==-99.0 | s[7]==0.0) {
             s[7]=-3.0;
         }
-        double mesDonChange = s[1] - s[0];
-        double mesAccChange = s[3] - s[2];
-        double gsDonChange = s[5] - s[4];
-        double gsAccChange = s[7] - s[6];
-        // calculate p = 1/(1+e^-(a + b1X1 + b2X2 + ... + bnXn))
-        double pDon = 1/(1 + Math.exp(-(-0.9865 + (mesDonChange * 0.1129) + (gsDonChange * 0.01151) + (s[1] * 0.2076) + (s[5] * 0.4350) )));
-        double pAcc = 1/(1 + Math.exp(-(-1.665 + (mesAccChange * 0.3323) + (gsAccChange * 0.05084) + (s[3] * 0.1877) + (s[7] * 0.1730) )));
-        String pDonStr = Double.toString(pDon);
-        String pAccStr = Double.toString(pAcc);
-        //round scores to 2 decimal places
-        try {
-            pDonStr = String.format("%.02f",pDon);
-            pAccStr = String.format("%.02f",pAcc);
-        } catch (Exception e) {}
-        String ret = pDonStr + "\t" + pAccStr;
-        return ret;
+    double mesDonChange = s[1] - s[0];
+    double mesAccChange = s[3] - s[2];
+    double gsDonChange = s[5] - s[4];
+    double gsAccChange = s[7] - s[6];
+    double pDonGain = -1; double pAccGain = -1; double pDonLoss = -1; double pAccLoss = -1;
+    // using within/outside splice site logistic regression models, calculate p = 1/(1+e^-(a + b1X1 + b2X2 + ... + bnXn))
+    if (!withinSS.contains("ENSE")) {
+        pDonGain = 1/(1 + Math.exp(-(-0.9865 + (mesDonChange * 0.1129) + (gsDonChange * 0.01151) + (s[1] * 0.2076) + (s[5] * 0.4350) )));
+        pAccGain = 1/(1 + Math.exp(-(-1.665 + (mesAccChange * 0.3323) + (gsAccChange * 0.05084) + (s[3] * 0.1877) + (s[7] * 0.1730) )));
+    }
+    if (withinSS.contains("donor")){
+        //pDonLoss = 1/(1 + Math.exp(-(-1.6678 + (mesDonChange * -0.6752) )));
+        pDonLoss = 1/(1 + Math.exp(-(-1.1028 + (mesDonChange * -0.4240) )));
+    }
+    if (withinSS.contains("acceptor")){
+        //pAccLoss = 1/(1 + Math.exp(-(-0.6209 + (mesAccChange * -0.5100) )));
+        pAccLoss = 1/(1 + Math.exp(-(-0.2355 + (mesAccChange * -0.2283) )));
+    }
+    String pDonGainStr = Double.toString(pDonGain);
+    String pAccGainStr = Double.toString(pAccGain);
+    String pDonLossStr = Double.toString(pDonLoss);
+    String pAccLossStr = Double.toString(pAccLoss);
+    //round scores to 2 decimal places
+    try {
+        pDonGainStr = String.format("%.02f",pDonGain);
+        pAccGainStr = String.format("%.02f",pAccGain);
+        pDonLossStr = String.format("%.02f",pDonLoss);
+        pAccLossStr = String.format("%.02f",pAccLoss);
+    } catch (Exception e) {
+        //use unrounded score
+    }
+    if (pDonGainStr.equals("-1.00")) {
+        pDonGainStr = ".";
+    }
+    if (pAccGainStr.equals("-1.00")) {
+        pAccGainStr = ".";
     }
+    if (pDonLossStr.equals("-1.00")) {
+        pDonLossStr = ".";
+    }
+    if (pAccLossStr.equals("-1.00")) {
+        pAccLossStr = ".";
+    }
+    String ret = pDonGainStr + "\t" + pAccGainStr + "\t" + pDonLossStr + "\t" + pAccLossStr;
+    return ret;
+}
 
 public static void appendToFiles (String fileName) {
     String annovar_file = "output/"+fileName+"_out.txt";
-    String acc_fileUnsorted = "temp/"+fileName+"_acceptorCreating_unsorted.txt";
-    String don_fileUnsorted = "temp/"+fileName+"_donorCreating_unsorted.txt";
-    String ss_fileUnsorted = "temp/"+fileName+"_withinSS_unsorted.txt";
+    String gain_file_unsorted = "temp/"+fileName+"_gain_unsorted.txt";
+    String ss_file_unsorted = "temp/"+fileName+"_loss_unsorted.txt";
     try {
         //write to _out
         FileWriter fwAV = new FileWriter(annovar_file, true);
@@ -283,22 +360,15 @@ public static void appendToFiles (String fileName) {
             avWriter.write(avBuffer[i]+"\n");
         }
         avWriter.close();
-        //write to _donorCreating
-        FileWriter fwDon = new FileWriter(don_fileUnsorted, true);
-        BufferedWriter donWriter = new BufferedWriter(fwDon);
-        for (int i=0; i<donBufferIndex; i++) {
-            donWriter.write(donBuffer[i]+"\n");
-        }
-        donWriter.close();
         //write to _acceptorCreating
-        FileWriter fwAcc = new FileWriter(acc_fileUnsorted, true);
-        BufferedWriter accWriter = new BufferedWriter(fwAcc);
-        for (int i=0; i<accBufferIndex; i++) {
-            accWriter.write(accBuffer[i]+"\n");
+        FileWriter fwGain = new FileWriter(gain_file_unsorted, true);
+        BufferedWriter gainWriter = new BufferedWriter(fwGain);
+        for (int i=0; i<gainBufferIndex; i++) {
+            gainWriter.write(gainBuffer[i]+"\n");
         }
-        accWriter.close();
+        gainWriter.close();
         //write to _withinSS
-        FileWriter fwSS = new FileWriter(ss_fileUnsorted, true);
+        FileWriter fwSS = new FileWriter(ss_file_unsorted, true);
         BufferedWriter ssWriter = new BufferedWriter(fwSS);
         for (int i=0; i<ssBufferIndex; i++) {
             ssWriter.write(ssBuffer[i]+"\n");
@@ -311,30 +381,19 @@ public static void appendToFiles (String fileName) {
 
 public static void writeHeaders (String fileName) {
     String annovar_file = "output/"+fileName+"_out.txt";
-    String acc_file = "output/"+fileName+"_acceptorCreating.txt";
-    String don_file = "output/"+fileName+"_donorCreating.txt";
-    String ss_file = "output/"+fileName+"_withinSS.txt";
+    String gain_file = "temp/"+fileName+"_gain_unsorted.txt";
+    String ss_file = "temp/"+fileName+"_loss_unsorted.txt";
     try {
         //write to _out
         FileWriter fwAV = new FileWriter(annovar_file);
         BufferedWriter avWriter = new BufferedWriter(fwAV);
-        avWriter.write("#CHR\tSTART\tEND\tREF\tALT\tGENE\twithinSite\tmesDonRef\tmesDonAlt\tmesAccRef\tmesAccAlt\tgsDonRef\tgsDonAlt\tgsAccRef\tgsAccAlt\tESEmaxRef\tESEmaxAlt\tESSminRef\tESSminAlt\tdonCreateP\taccCreateP"+"\n");
+        avWriter.write("#CHR\tSTART\tEND\tREF\tALT\tGENE\twithinSite\tmesDonRef\tmesDonAlt\tmesAccRef\tmesAccAlt\tgsDonRef\tgsDonAlt\tgsAccRef\tgsAccAlt\tESEmaxRef\tESEmaxAlt\tESSminRef\tESSminAlt\tdonGainP\taccGainP\tdonLossP\taccLossP"+"\n");
         avWriter.close();
-        //write to _donorCreating
-        FileWriter fwDon = new FileWriter(don_file);
-        BufferedWriter donWriter = new BufferedWriter(fwDon);
-        donWriter.write("#CHR\tSTART\tEND\tREF\tALT\tGENE\tmesDonRef\tmesDonAlt\tgsDonRef\tgsDonAlt\tdonCreateP\n");
-        donWriter.close();
-        //write to _acceptorCreating
-        FileWriter fwAcc = new FileWriter(acc_file);
-        BufferedWriter accWriter = new BufferedWriter(fwAcc);
-        accWriter.write("#CHR\tSTART\tEND\tREF\tALT\tGENE\tmesAccRef\tmesAccAlt\tgsAccRef\tgsAccAlt\taccCreateP\n");
-        accWriter.close();
         //write to _withinSS
-        FileWriter fwSS = new FileWriter(ss_file);
-        BufferedWriter ssWriter = new BufferedWriter(fwSS);
-        ssWriter.write("#CHR\tSTART\tEND\tREF\tALT\tGENE\twithinSite\tmesDonRef\tmesDonAlt\tmesAccRef\tmesAccAlt\tgsDonRef\tgsDonAlt\tgsAccRef\tgsAccAlt\n");
-        ssWriter.close();
+        //FileWriter fwSS = new FileWriter(ss_file);
+        //BufferedWriter ssWriter = new BufferedWriter(fwSS);
+        //ssWriter.write("#CHR\tSTART\tEND\tREF\tALT\tGENE\twithinSite\tdonLossP\tAccLossP\n");
+        //ssWriter.close();
     } catch (IOException e) {
         System.out.println(e.getMessage());
     }
@@ -342,16 +401,15 @@ public static void writeHeaders (String fileName) {
 
 public static void resetOutputArrays() {
     avBuffer = new String[30000];
-    donBuffer = new String[30000];
-    accBuffer = new String[30000];
+    gainBuffer = new String[30000];
     ssBuffer = new String[30000];
-    avBufferIndex = 0; donBufferIndex = 0; accBufferIndex = 0; ssBufferIndex = 0;
+    avBufferIndex = 0; gainBufferIndex = 0; ssBufferIndex = 0;
     System.gc();
 }
 
 public static String[] updateOverlappingGenes(String[] geneID, String[] prevID) {
     //check if previous variant falls within an annotated splice site motif
-	//if previous genes overlapped, check individually whether they overlap this variant and update
+    //if previous genes overlapped, check individually whether they overlap this variant and update
     if (geneID[1].contains(";")) {
         String[] geneNameSplit = geneID[1].split(";");
         String[] geneEndSplit = geneID[2].split(";");
@@ -376,7 +434,7 @@ public static String[] updateOverlappingGenes(String[] geneID, String[] prevID)
     return geneID;
 }
 
-	public static String checkForOverlappingSpliceSite( String[] prevID, String[] donNames, String[] accNames, int[] donStart, int[] accStart, int[] donEnd, int[] accEnd) {
+public static String checkForOverlappingSpliceSite( String[] prevID, String[] donNames, String[] accNames, int[] donStart, int[] accStart, int[] donEnd, int[] accEnd) {
     String withinSS="";
     int startPos = Integer.parseInt(prevID[1]);
     int endPos = Integer.parseInt(prevID[1])+prevID[2].length()-1;
@@ -390,9 +448,9 @@ public static String checkForOverlappingSpliceSite( String[] prevID, String[] do
         if (!withinSS.contains(donNames[i])) {
             if (endPos>=donStart[i]&&startPos<=donEnd[i]) {
                 if (!withinSS.equals("")) {
-                        withinSS=withinSS.concat(",");
+                    withinSS=withinSS.concat(",");
                 }
-            withinSS = withinSS.concat(donNames[i]).concat("_donor");
+                withinSS = withinSS.concat(donNames[i]).concat("_donor");
             }
         }
     }
@@ -413,98 +471,91 @@ public static String checkForOverlappingSpliceSite( String[] prevID, String[] do
         withinSS=".";
     }
     return withinSS;
-	}
-	
-	public static void outputVariantToBuffers(String[] out) {	
+}
+
+public static void outputVariantToBuffers(String[] out) {	
     //write full line for annovar
     String avLine = "";
-    for (int i=0; i<20; i++) {
+    for (int i=0; i<22; i++) {
         avLine = avLine+out[i]+"\t";
     }
-    avLine = avLine+out[20];
+    avLine = avLine+out[22];
     avBuffer[avBufferIndex] = avLine;
     avBufferIndex++;
     //write withinSS
     if (out[6].contains("ENSE")) {
-        String ssLine = "";
-        for (int i=0; i<16; i++) {
-            ssLine = ssLine+out[i]+"\t";
-        }
-        double maxScoreDecrease = -99;
-        //if donorSS
-        if (out[6].contains("_donor")) {
-            if (!out[7].equals(".") && !out[8].equals(".")) {
-                maxScoreDecrease = Double.parseDouble(out[7]) - Double.parseDouble(out[8]); 
+        String ssLine = out[0]+"\t"+out[1]+"\t"+out[3]+"\t"+out[4]+"\t"+out[5]+"\t"+out[6]+"\t"+out[21]+"\t"+out[22];
+        Double lossMax = 0.00 ;
+        try {
+            if (!out[21].equals(".")) {
+                lossMax = Double.parseDouble(out[21]);
             }
-        }
-        //if acceptorSS
-        if (out[6].contains("_acceptor")) {
-            if (!out[9].equals(".") && !out[10].equals(".")) {
-                if (maxScoreDecrease < Double.parseDouble(out[9]) - Double.parseDouble(out[10]) ) {
-                    maxScoreDecrease = Double.parseDouble(out[9]) - Double.parseDouble(out[10]); 
+            if (!out[22].equals(".")) {
+                if (lossMax < Double.parseDouble(out[22])) {
+                    lossMax = Double.parseDouble(out[22]);
                 }
             }
-        }
-        ssLine = ssLine+maxScoreDecrease;
+        } catch (Exception e) {}
+        ssLine = ssLine+"\t"+lossMax;
         ssBuffer[ssBufferIndex] = ssLine;
         ssBufferIndex++;
     } else {
-        //write donCreating
-        if (Double.parseDouble(out[19])>=0.7) {
-            String donLine = "";
-            for (int i=0; i<6; i++) {
-                donLine= donLine+out[i]+"\t";
+        //write gain
+        String gainLine = out[0]+"\t"+out[1]+"\t"+out[3]+"\t"+out[4]+"\t"+out[5]+"\t"+out[19]+"\t"+out[20];
+        Double gainMax = 0.00 ;
+        try {
+            if (!out[19].equals(".")) {
+                gainMax = Double.parseDouble(out[19]);
             }
-            donLine = donLine+out[7]+"\t"+out[8]+"\t"+out[11]+"\t"+out[12]+"\t"+out[19];
-            donBuffer[donBufferIndex] = donLine;
-            donBufferIndex++;
-        }
-        //write accCreating
-        if (Double.parseDouble(out[20])>=0.7) {
-            String accLine = "";
-            for (int i=0; i<6; i++) {
-                accLine= accLine+out[i]+"\t";
+            if (!out[20].equals(".")) {
+                if (gainMax < Double.parseDouble(out[20])) {
+                    gainMax = Double.parseDouble(out[20]);
+                }
             }
-            accLine = accLine+out[9]+"\t"+out[10]+"\t"+out[13]+"\t"+out[14]+"\t"+out[20];
-            accBuffer[accBufferIndex] = accLine;
-            accBufferIndex++;
+        } catch (Exception e) {}
+        if (gainMax>=0.7) {
+            gainLine = gainLine+"\t"+Double.toString(gainMax);
+            gainBuffer[gainBufferIndex] = gainLine;
+            gainBufferIndex++;
         }
     }              
 }
-	
-	public static boolean ifGenesOverlap(String[] geneID, String chr, int start) {
-        //check for overlapping genes
-        int overlapTest = 0;
-        //check individually for already overlapping genes
-        if (geneID[1].concat(geneID[2]).contains(";")) {
-            String[] geneEndSplit = geneID[2].split(";");
-            String[] geneNameSplit = geneID[1].split(";");
-            String updatedGeneName = "";
-            String updatedGeneEnd = "";
-            int geneIndex = Math.min(geneEndSplit.length, geneNameSplit.length);
-            for (int i=0; i<geneIndex; i++) {
-                if (Integer.parseInt(geneEndSplit[i]) >= start) {
-                    overlapTest = Integer.parseInt(geneEndSplit[i]);
-                    if (!updatedGeneName.equals("")) {
-                        updatedGeneName = updatedGeneName.concat(";");
-                        updatedGeneEnd = updatedGeneEnd.concat(";");
-                    }
-                    updatedGeneName = updatedGeneName.concat(geneNameSplit[i]);
-                    updatedGeneEnd = updatedGeneEnd.concat(geneEndSplit[i]);
+//            avWriter.write("#CHR\tSTART\tEND\tREF\tALT\tGENE\twithinSite\tmesDonRef\tmesDonAlt\tmesAccRef\tmesAccAlt\tgsDonRef\tgsDonAlt\tgsAccRef\tgsAccAlt\tESEmaxRef\tESEmaxAlt\tESSminRef\tESSminAlt\tdonGainP\taccGainP\tdonLossP\taccLossP"+"\n");
+//       String ret = pDonGainStr + "\t" + pAccGainStr + "\t" + pDonLossStr + "\t" + pAccLossStr;
+
+public static boolean ifGenesOverlap(String[] geneID, String chr, int start) {
+    //check for overlapping genes
+    int overlapTest = 0;
+    //check individually for already overlapping genes
+    if (geneID[1].concat(geneID[2]).contains(";")) {
+        String[] geneEndSplit = geneID[2].split(";");
+        String[] geneNameSplit = geneID[1].split(";");
+        String updatedGeneName = "";
+        String updatedGeneEnd = "";
+        int geneIndex = Math.min(geneEndSplit.length, geneNameSplit.length);
+        for (int i=0; i<geneIndex; i++) {
+            if (Integer.parseInt(geneEndSplit[i]) >= start) {
+                overlapTest = Integer.parseInt(geneEndSplit[i]);
+                if (!updatedGeneName.equals("")) {
+                    updatedGeneName = updatedGeneName.concat(";");
+                    updatedGeneEnd = updatedGeneEnd.concat(";");
                 }
+                updatedGeneName = updatedGeneName.concat(geneNameSplit[i]);
+                updatedGeneEnd = updatedGeneEnd.concat(geneEndSplit[i]);
             }
-            geneID[1] = updatedGeneName;
-            geneID[2] = updatedGeneEnd;
-        } else if (geneID[2].equals(".")) {    
-            overlapTest = 0;
-            geneID[2]="0";
-        } else if (!geneID[2].equals("")) {    
-            overlapTest = Integer.parseInt(geneID[2]);
         }
-        if (start <= overlapTest && geneID[0].equals(chr)) {
-        	return true;
-        }
-        return false;
-	}
+        geneID[1] = updatedGeneName;
+        geneID[2] = updatedGeneEnd;
+    } else if (geneID[2].equals(".")) {    
+        overlapTest = 0;
+        geneID[2]="0";
+    } else if (!geneID[2].equals("")) {    
+        overlapTest = Integer.parseInt(geneID[2]);
+    }
+    if (start <= overlapTest && geneID[0].equals(chr)) {
+        return true;
+    }
+    return false;
+}
 
 }
diff --git a/bin/mergeOutput2.java b/bin/mergeOutput2.java
new file mode 100644
index 0000000..5e78649
--- /dev/null
+++ b/bin/mergeOutput2.java
@@ -0,0 +1,435 @@
+//Description: Merging GeneSplicer, MaxEntScan and ESRseq scores along with annotation information to be outputted together on one line per variant.
+import java.io.*;
+import java.util.Arrays;
+import java.util.jar.Attributes.Name;
+import java.lang.*;
+import java.text.DecimalFormat;
+public class mergeOutput2 {
+
+    //store output lines in buffers to minimise I/O
+    public static String[] avBuffer = new String[30000];
+    public static int avBufferIndex = 0;
+
+    public static void main (String[] args) {
+        if (args.length < 1) {
+            System.out.println("must provide vcf/bed file name as command line argument");
+            System.exit(1);
+        }
+        String fileName=args[0];
+        writeHeaders(fileName);
+        //initialise score tracking variables
+        int[] donStart = new int[10000];
+        int[] donEnd = new int[10000];
+        int[] accStart = new int[10000];
+        int[] accEnd = new int[10000];
+        String[] donNames = new String[10000];
+        String[] accNames = new String[10000];
+        //Note array elements:
+        //scores[]...mesDonRef(0);mesDonAlt(1);mesAccRef(2);mesAccAlt(3);gsDonRef(4);gsDonAlt(5);gsAccRef(6);gsAccAlt(7);ESEmaxRef(8);ESEmaxAlt(9);ESSminRef(10);ESSminAlt(11);
+        //geneID[]...chr(0), name(1), end(2)
+        //prevID[]...chr(0), start(1), ref(2), alt(3), type(4)
+        double[] scores = new double[12];
+        Arrays.fill(scores, -99.0);
+        String[] geneID = { "", ".", ""};
+        String[] prevID = { "", "-99", "", "", "GENE"};
+        String s = "";
+        //process lines
+        try {
+            BufferedReader in = new BufferedReader(new InputStreamReader(System.in));
+            while ((s = in.readLine()) != null && s.length() != 0) {
+                String[] split = s.split("\\s+");
+                String chr = split[0];
+                int start = Integer.parseInt(split[1]);
+                String ref = split[2].toUpperCase();
+                String alt = split[3].toUpperCase();
+                String type = split[4];
+                //check if current line is next variant
+                boolean nextVariant = false;
+                if (!(chr.equals(prevID[0])&&start==Integer.parseInt(prevID[1]))) {
+                    nextVariant = true;
+                } else
+                    if (!(ref.equals(prevID[2])&&alt.equals(prevID[3]))) {
+                        nextVariant = true;
+                    } else
+                        if (chr.equals("xxx")) {
+                            nextVariant = true;
+                        }
+                //print scores of previous variant, if current line is next variant and previous line wasn't a gene annotation
+                if(nextVariant && !prevID[4].equals("GENE")) {
+                    //update overlapping genes and splice sites
+                    geneID = updateOverlappingGenes(geneID, prevID);
+                    String withinSS = checkForOverlappingSpliceSite(prevID, donNames, accNames, donStart, accStart, donEnd, accEnd);
+                    //format output columns
+                    String[] out = new String[23];
+                    out[0] = prevID[0]; out[1] = Integer.toString(Integer.parseInt(prevID[1]));
+                    out[3] = prevID[2]; out[4] = prevID[3]; out[5] = geneID[1]; out[6] = withinSS;
+                    //adjust end value for indels
+                    int endPos = Integer.parseInt(prevID[1])+prevID[2].length()-1;
+                    if (prevID[3].equals("*")) {
+                        endPos++;
+                    }
+                    out[2]= Integer.toString(endPos);
+                    //fill scores
+                    for (int i=0; i<12; i++) {
+                        if (scores[i]==-99 || scores[i]==0) {
+                            out[i+7]=".";
+                        } else {
+                            out[i+7]=Double.toString(scores[i]);
+                        }
+                    }
+                    //calculate donor/acceptor creating logistic regression scores
+                    String[] lrScores = calculateLogRegScores(scores, out[6]).split("\\s+");
+                    out[19]= lrScores[0];                
+                    out[20]= lrScores[1];
+                    out[21]= lrScores[2];                
+                    out[22]= lrScores[3];
+                    //add output line to file buffers
+                    outputVariantToBuffers(out);
+                    //reset scores
+                    Arrays.fill(scores, -99.0);
+                    //append to file and empty buffers every ~25000 lines
+                    if (avBufferIndex > 25000) {
+                        appendToFiles(fileName);
+                        resetOutputArrays();
+                    }                
+                }
+                //MaxEntScan
+                if (type.equals("MESDON")) {
+                    scores[0]=Double.parseDouble(split[5]);
+                    scores[1]=Double.parseDouble(split[6]);
+                } else
+                    if(type.equals("MESACC")){
+                        scores[2]=Double.parseDouble(split[5]);
+                        scores[3]=Double.parseDouble(split[6]);
+                    } else
+                        //GeneSplicer
+                        if (type.equals("GSREF")) {
+                            if (split[6].equals("donor")) {
+                                scores[4]=Double.parseDouble(split[5]);
+                            } else
+                                if (split[6].equals("acceptor")) {
+                                    scores[6]=Double.parseDouble(split[5]);
+                                } 
+                        } else   
+                            if (type.equals("GSALT")) {
+                                if (split[6].equals("donor")) {
+                                    scores[5]=Double.parseDouble(split[5]);
+                                } else
+                                    if (split[6].equals("acceptor")) {
+                                        scores[7]=Double.parseDouble(split[5]);
+                                    } 
+                            } else
+                                //ESR
+                                if (type.equals("ESR")) {
+                                    scores[8]=Double.parseDouble(split[5]);
+                                    scores[9]=Double.parseDouble(split[6]);
+                                    scores[10]=Double.parseDouble(split[7]);
+                                    scores[11]=Double.parseDouble(split[8]);
+                                }
+                //GENE
+                if (type.equals("GENE")) {
+                    //overlapping gene annotations
+                    if (ifGenesOverlap(geneID, chr, start)) {
+                        geneID[1] = geneID[1].concat(";").concat(split[3]);
+                        geneID[2] = geneID[2].concat(";").concat(split[2]);
+                        geneID[0] = split[0];
+                        if (split.length>11) {
+                            //update splice site pos/name arrays with info from new overlapping gene
+                            String[] donStartStr=split[6].split(",");
+                            String[] donEndStr=split[7].split(",");
+                            String[] accStartStr=split[8].split(",");
+                            String[] accEndStr=split[9].split(",");
+                            String[] donNamesStr=split[10].split(",");
+                            String[] accNamesStr=split[11].split(",");
+                            int accIndex = 0;
+                            int donIndex = 0;
+                            while (donStart[donIndex]>0) {
+                                donIndex++;
+                            }
+                            while (accStart[accIndex]>0) {
+                                accIndex++;
+                            }
+                            for (int k = 0; k < donStartStr.length; k++) {
+                                donStart[donIndex+k] = Integer.parseInt(donStartStr[k]);
+                                donEnd[donIndex+k] = Integer.parseInt(donEndStr[k]);
+                                donNames[donIndex+k] = donNamesStr[k];
+                            }
+                            for (int k = 0; k < accStartStr.length; k++) {
+                                accStart[accIndex+k] = Integer.parseInt(accStartStr[k]);
+                                accEnd[accIndex+k] = Integer.parseInt(accEndStr[k]);
+                                accNames[accIndex+k] = accNamesStr[k];
+                            }
+                        }
+                        //non-overlapping genes
+                    } else {
+                        //reset arrays
+                        Arrays.fill(donStart, 0);
+                        Arrays.fill(donEnd, 0);
+                        Arrays.fill(accStart, 0);
+                        Arrays.fill(accEnd, 0);
+                        Arrays.fill(donNames, null);
+                        Arrays.fill(accNames, null);
+                        geneID[1] = split[3];
+                        geneID[2] = split[2];
+                        geneID[0] = split[0];
+                        if (split.length>11) {
+                            //reset and update splice site pos/name arrays
+                            String[] donStartStr=split[6].split(",");
+                            String[] donEndStr=split[7].split(",");
+                            String[] accStartStr=split[8].split(",");
+                            String[] accEndStr=split[9].split(",");
+                            String[] donNamesStr=split[10].split(",");
+                            String[] accNamesStr=split[11].split(",");
+                            for (int k=0; k<donStartStr.length; k++) {
+                                donStart[k]=Integer.parseInt(donStartStr[k]);
+                                donEnd[k]=Integer.parseInt(donEndStr[k]);
+                                donNames[k]=donNamesStr[k];
+                            }
+                            for (int k=0; k<accStartStr.length; k++) {
+                                accStart[k]=Integer.parseInt(accStartStr[k]);
+                                accEnd[k]=Integer.parseInt(accEndStr[k]);
+                                accNames[k]=accNamesStr[k];
+                            }
+                        }        	            	
+                    }
+                }
+                //update info for comparison with next line
+                prevID[0] = chr;
+                prevID[1] = Integer.toString(start);
+                prevID[2] = ref;
+                prevID[3] = alt;
+                prevID[4] = type;
+            }
+            //final append to file
+            if (avBufferIndex > 0) {
+                appendToFiles(fileName);
+            }
+        } catch (Exception e) {
+            e.printStackTrace();
+        }
+    }
+
+    public static String calculateLogRegScores (double[] s, String withinSS) {
+        //impute missing values
+        //maxEntScan
+        for (int i=0; i<4; i++) {
+            if (s[i]==-99.0 | s[i]==0.0) {
+                s[i] = -20.0;
+            }
+        }                    
+        //gsDonRef
+        if (s[4]==-99.0 | s[4]==0.0) {
+            if (s[5]==-99.0 | s[5]==0.0) {
+                s[4]=0.0;
+                s[5]=0.0;
+            } else {
+                s[4]=-3.0;
+            }
+        } else
+            //gsDonAlt
+            if (s[7]==-99.0 | s[7]==0.0) {
+                s[7]=-3.0;
+            }
+        //gsAccRef
+        if (s[6]==-99.0 | s[6]==0.0) {
+            if (s[7]==-99.0 | s[7]==0.0) {
+                s[6]=0.0;
+                s[7]=0.0;
+            } else {
+                s[6]=-3.0;
+            }
+        } else
+            //gsAccAlt
+            if (s[7]==-99.0 | s[7]==0.0) {
+                s[7]=-3.0;
+            }
+        double mesDonChange = s[1] - s[0];
+        double mesAccChange = s[3] - s[2];
+        double gsDonChange = s[5] - s[4];
+        double gsAccChange = s[7] - s[6];
+        double pDonGain = -1; double pAccGain = -1; double pDonLoss = -1; double pAccLoss = -1;
+        // using within/outside splice site logistic regression models, calculate p = 1/(1+e^-(a + b1X1 + b2X2 + ... + bnXn))
+        if (!withinSS.contains("ENSE")) {
+            pDonGain = 1/(1 + Math.exp(-(-0.9865 + (mesDonChange * 0.1129) + (gsDonChange * 0.01151) + (s[1] * 0.2076) + (s[5] * 0.4350) )));
+            pAccGain = 1/(1 + Math.exp(-(-1.665 + (mesAccChange * 0.3323) + (gsAccChange * 0.05084) + (s[3] * 0.1877) + (s[7] * 0.1730) )));
+        }
+        if (withinSS.contains("donor")){
+            //pDonLoss = 1/(1 + Math.exp(-(-1.6678 + (mesDonChange * -0.6752) )));
+            pDonLoss = 1/(1 + Math.exp(-(-1.1028 + (mesDonChange * -0.4240) )));
+        }
+        if (withinSS.contains("acceptor")){
+            //pAccLoss = 1/(1 + Math.exp(-(-0.6209 + (mesAccChange * -0.5100) )));
+            pAccLoss = 1/(1 + Math.exp(-(-0.2355 + (mesAccChange * -0.2283) )));
+        }
+        String pDonGainStr = Double.toString(pDonGain);
+        String pAccGainStr = Double.toString(pAccGain);
+        String pDonLossStr = Double.toString(pDonLoss);
+        String pAccLossStr = Double.toString(pAccLoss);
+        //round scores to 2 decimal places
+        try {
+            pDonGainStr = String.format("%.02f",pDonGain);
+            pAccGainStr = String.format("%.02f",pAccGain);
+            pDonLossStr = String.format("%.02f",pDonLoss);
+            pAccLossStr = String.format("%.02f",pAccLoss);
+        } catch (Exception e) {
+            //use unrounded score
+        }
+        if (pDonGainStr.equals("-1.00")) {
+            pDonGainStr = ".";
+        }
+        if (pAccGainStr.equals("-1.00")) {
+            pAccGainStr = ".";
+        }
+        if (pDonLossStr.equals("-1.00")) {
+            pDonLossStr = ".";
+        }
+        if (pAccLossStr.equals("-1.00")) {
+            pAccLossStr = ".";
+        }
+        String ret = pDonGainStr + "\t" + pAccGainStr + "\t" + pDonLossStr + "\t" + pAccLossStr;
+        return ret;
+    }
+
+    public static void appendToFiles (String fileName) {
+        String annovar_file = "output/"+fileName+"_out.txt";
+        try {
+            //write to _out
+            FileWriter fwAV = new FileWriter(annovar_file, true);
+            BufferedWriter avWriter = new BufferedWriter(fwAV);
+            for (int i=0; i<avBufferIndex; i++) {
+                avWriter.write(avBuffer[i]+"\n");
+            }
+            avWriter.close();
+        } catch (IOException e) {
+            System.out.println(e.getMessage());
+        }
+    }
+
+    public static void writeHeaders (String fileName) {
+        String annovar_file = "output/"+fileName+"_out.txt";
+        try {
+            //write to _out
+            FileWriter fwAV = new FileWriter(annovar_file);
+            BufferedWriter avWriter = new BufferedWriter(fwAV);
+            avWriter.write("#CHR\tSTART\tREF\tALT\tGENE\twithinSite\tESEmaxRef\tESEmaxAlt\tESSminRef\tESSminAlt\tdonGain\taccGain\tdonLoss\taccLoss"+"\n");
+            avWriter.close();
+        } catch (IOException e) {
+            System.out.println(e.getMessage());
+        }
+    } 
+
+    public static void resetOutputArrays() {
+        avBuffer = new String[30000];
+        avBufferIndex = 0;
+        System.gc();
+    }
+
+    public static String[] updateOverlappingGenes(String[] geneID, String[] prevID) {
+        //check if previous variant falls within an annotated splice site motif
+        //if previous genes overlapped, check individually whether they overlap this variant and update
+        if (geneID[1].contains(";")) {
+            String[] geneNameSplit = geneID[1].split(";");
+            String[] geneEndSplit = geneID[2].split(";");
+            geneID[1]="";
+            geneID[2]="";
+            int geneIndex = Math.min(geneEndSplit.length, geneNameSplit.length);
+            for (int i=0; i<geneIndex; i++) {
+                if (Integer.parseInt(geneEndSplit[i]) >= Integer.parseInt(prevID[1])) {
+                    if (!geneID[1].equals("")) {
+                        geneID[1] = geneID[1].concat(";");
+                        geneID[2] = geneID[2].concat(";");
+                    }
+                    geneID[1] = geneID[1].concat(geneNameSplit[i]);
+                    geneID[2] = geneID[2].concat(geneEndSplit[i]);
+                }
+            }
+        }
+        if ( geneID[1].equals("") || !geneID[0].equals(prevID[0])) {
+            geneID[1]= ".";
+            geneID[2]= ".";
+        }
+        return geneID;
+    }
+
+    public static String checkForOverlappingSpliceSite( String[] prevID, String[] donNames, String[] accNames, int[] donStart, int[] accStart, int[] donEnd, int[] accEnd) {
+        String withinSS="";
+        int startPos = Integer.parseInt(prevID[1]);
+        int endPos = Integer.parseInt(prevID[1])+prevID[2].length()-1;
+        if (prevID[3].equals("*")) {
+            endPos++;
+        }
+        for (int i=0; i<donNames.length; i++) {
+            if (donNames[i]==null) {
+                break;
+            }
+            if (!withinSS.contains(donNames[i])) {
+                if (endPos>=donStart[i]&&startPos<=donEnd[i]) {
+                    if (!withinSS.equals("")) {
+                        withinSS=withinSS.concat(",");
+                    }
+                    withinSS = withinSS.concat(donNames[i]).concat("_donor");
+                }
+            }
+        }
+        for (int i=0; i<accNames.length; i++) {
+            if (accNames[i]==null) {
+                break;
+            }
+            if (!withinSS.contains(accNames[i])) {
+                if (endPos>=accStart[i]&&startPos<=accEnd[i]) {
+                    if (!withinSS.equals("")) {
+                        withinSS=withinSS.concat(",");
+                    }
+                    withinSS = withinSS.concat(accNames[i]).concat("_acceptor");
+                }
+            }
+        }
+        if (withinSS.equals("")) {
+            withinSS=".";
+        }
+        return withinSS;
+    }
+
+    public static void outputVariantToBuffers(String[] out) {	
+        //write full line for annovar
+        String avLine = out[0]+"\t"+out[1]+"\t"+out[3]+"\t"+out[4]+"\t"+out[5]+"\t"+out[6]+"\t"+out[15]+"\t"+out[16]+"\t"+out[17]+"\t"+out[18]+"\t"+out[19]+"\t"+out[20]+"\t"+out[21]+"\t"+out[22];
+        avBuffer[avBufferIndex] = avLine;
+        avBufferIndex++;
+    }              
+
+    public static boolean ifGenesOverlap(String[] geneID, String chr, int start) {
+        //check for overlapping genes
+        int overlapTest = 0;
+        //check individually for already overlapping genes
+        if (geneID[1].concat(geneID[2]).contains(";")) {
+            String[] geneEndSplit = geneID[2].split(";");
+            String[] geneNameSplit = geneID[1].split(";");
+            String updatedGeneName = "";
+            String updatedGeneEnd = "";
+            int geneIndex = Math.min(geneEndSplit.length, geneNameSplit.length);
+            for (int i=0; i<geneIndex; i++) {
+                if (Integer.parseInt(geneEndSplit[i]) >= start) {
+                    overlapTest = Integer.parseInt(geneEndSplit[i]);
+                    if (!updatedGeneName.equals("")) {
+                        updatedGeneName = updatedGeneName.concat(";");
+                        updatedGeneEnd = updatedGeneEnd.concat(";");
+                    }
+                    updatedGeneName = updatedGeneName.concat(geneNameSplit[i]);
+                    updatedGeneEnd = updatedGeneEnd.concat(geneEndSplit[i]);
+                }
+            }
+            geneID[1] = updatedGeneName;
+            geneID[2] = updatedGeneEnd;
+        } else if (geneID[2].equals(".")) {    
+            overlapTest = 0;
+            geneID[2]="0";
+        } else if (!geneID[2].equals("")) {    
+            overlapTest = Integer.parseInt(geneID[2]);
+        }
+        if (start <= overlapTest && geneID[0].equals(chr)) {
+            return true;
+        }
+        return false;
+    }
+
+}
diff --git a/bin/refCheck.java b/bin/refCheck.java
new file mode 100644
index 0000000..8bdf9a0
--- /dev/null
+++ b/bin/refCheck.java
@@ -0,0 +1,22 @@
+//Description: for generating bed intervals as input to bedtools getfasta
+import java.io.*;
+
+class refCheck  {
+
+public static void main(String[] args) {	
+    try {
+    BufferedReader in = new BufferedReader(new InputStreamReader(System.in));
+    String s = "";
+    //process lines
+    while ((s = in.readLine()) != null) {
+        String[] split = s.split("\\s+");
+        int prefixStart= Integer.parseInt(split[2]) - 91;
+        int suffixEnd = Integer.parseInt(split[2]) + 89 + split[4].length();
+   	    System.out.println(split[1]+"\t"+Integer.toString(prefixStart)+"\t"+Integer.toString(suffixEnd)+"\t"+split[1]+";"+split[2]+";"+split[4]+";"+split[5]+";"+split[3]+";\t1\t"+split[3]);
+    }
+    in.close();
+    } catch (Exception e) {
+        System.err.println("Error: " + e.getMessage());
+    }
+}
+}
diff --git a/bin/seqScan.class b/bin/seqScan.class
index 31d48fa..cc44b90 100644
Binary files a/bin/seqScan.class and b/bin/seqScan.class differ
diff --git a/bin/seqScan.java b/bin/seqScan.java
index 60f19e4..a6001f7 100644
--- a/bin/seqScan.java
+++ b/bin/seqScan.java
@@ -18,464 +18,482 @@ class seqScan {
     public static double[] ESStable = createESRarrays("data/ESS.txt");
     public static boolean useESR= true;
     public static String fileID="";
-    public static boolean invalidFastaFound = false;
     public static boolean unsplitVCFfound = false;
 
-public static void main(String[] args) {	
-    
-    String header = "";
-    String s = "";
-    if (args.length < 3) {
-        System.out.println("must provide input file and -useESR/skipESR and fileID as command line argument");
-        System.exit(1);
-    }
-    if (args[1]=="-skipESR") {
-        useESR = false;
-    }
-    fileID=args[2];
-    try{
-    fillESRtables();
-    //open input file
-    FileInputStream fstream = new FileInputStream(args[0]);
-    DataInputStream in = new DataInputStream(fstream);
-    BufferedReader br = new BufferedReader(new InputStreamReader(in));
-    //process file 2 lines at a time
-    while ((header = br.readLine()) != null) {
-        s = br.readLine();
-        try {
-	        scanStrings(header, s, args[2]);
+    public static void main(String[] args) {	
+
+        String header = "";
+        String s = "";
+        if (args.length < 3) {
+            System.out.println("must provide input file and -useESR/skipESR and fileID as command line argument");
+            System.exit(1);
         }
-        catch (Exception e){
-            e.printStackTrace();   
-        }    
-    }
-    in.close();
-    }catch (Exception e){
-        System.err.println("Error: " + e.getMessage());
+        if (args[1]=="-skipESR") {
+            useESR = false;
+        }
+        fileID=args[2];
+        try{
+            fillESRtables();
+            //open input file
+            FileInputStream fstream = new FileInputStream(args[0]);
+            DataInputStream in = new DataInputStream(fstream);
+            BufferedReader br = new BufferedReader(new InputStreamReader(in));
+            //process file 2 lines at a time
+            while ((header = br.readLine()) != null) {
+                s = br.readLine();
+                try {
+                    scanStrings(header, s, args[2]);
+                }
+                catch (Exception e){
+                    e.printStackTrace();   
+                }    
+            }
+            in.close();
+        }catch (Exception e){
+            System.err.println("Error: " + e.getMessage());
+        }
+        //write output to files
+        appendToFiles();
     }
-    //write output to files
-    appendToFiles();
-}
 
-public static void scanStrings (String header, String s, String fileID) {
-	/* SCANNING EXPLANATION
-        For MaxEntScan, a region of 45bp with variant at middle nucleotide 23 is needed (anywhere ref/alt can contribute to the motif).
-	    Scan for acceptor AG from nucleotide pos 19 to 41, and for donor GT from pos 18 to 26 and generate query strings for scoring
-	    The additional 68bp flanking sequence is necessary for GeneSplicer and filling out MaxEntScan alt strings shortened by deletions.
-	    For indels, alt strings have a different length. Adjustment "correct1" is made so that only ref/alt equivalent positions are scanned.
-        correct1: only needed on ref string in event of deletions on antisense strand, because start value is sense oriented eg. GAT>GT is represented as 5'-GA>G-3' not 3'-TA>T-5'.
-        correct2: adjusts for empty alt strings, arising from deletions denoted for example as ref=A, alt=-or*
-    */
-    int flank = 68;
-    int correct1 = 0;
-    s = s.toLowerCase();
-	String id = header.substring(0, header.indexOf(":"));
-	String[] sep = id.split(";");
-	String chr = sep[0].substring(1);
-	String start = sep[1];
-	String ref = sep[2].toUpperCase();
-	String alt = sep[3].toUpperCase();
-    String strand = sep[4];
-    String mesAdd = "";
-    double maxRefESE = 0;
-    double maxAltESE = 0;
-    double minRefESS = 0;
-    double minAltESS = 0;
-    //ignore deletions larger than flanking region
-    if (ref.length()>35 || alt.length()>35) {
-        return;
-    }
-    if (strand.equals("+")) {
-        strand = "POS";
-    }
-	//index correction for deletions notated as alt="*"
-	String refName = ref;
-    String altName = alt;
-    int correct2=0;
-	if (alt.equals("*")) {
-        alt="";
-        correct2=1;
-    }
-    //catch unsplit VCFs (ie. multiple alt alleles represented on one comma separated line)
-    if (alt.contains(",")) {
-        if (!unsplitVCFfound) {
-            System.out.println("Note: unsplit VCF/BED record(s) were detected, ie. variants with multiple alt alleles represented on a single line. Such records are susceptible to false negatives, so we recommend splitting these records onto multiple lines");
-            unsplitVCFfound = true;
+    public static void scanStrings (String header, String s, String fileID) {
+        /* SCANNING EXPLANATION
+           For MaxEntScan, a region of 45bp with variant at middle nucleotide 23 is needed (anywhere ref/alt can contribute to the motif).
+           Scan for acceptor AG from nucleotide pos 19 to 41, and for donor GT from pos 18 to 26 and generate query strings for scoring
+           The additional 68bp flanking sequence is necessary for GeneSplicer and filling out MaxEntScan alt strings shortened by deletions.
+           For indels, alt strings have a different length. Adjustment "correct1" is made so that only ref/alt equivalent positions are scanned.
+correct1: only needed on ref string in event of deletions on antisense strand, because start value is sense oriented eg. GAT>GT is represented as 5'-GA>G-3' not 3'-TA>T-5'.
+correct2: adjusts for empty alt strings, arising from deletions denoted for example as ref=A, alt=-or*
+         */
+        int flank = 68;
+        int correct1 = 0;
+        s = s.toLowerCase();
+        String id = header.substring(0, header.indexOf(":"));
+        String[] sep = id.split(";");
+        String chr = sep[0].substring(1);
+        String start = sep[1];
+        String ref = sep[2].toUpperCase();
+        String alt = sep[3].toUpperCase();
+        String strand = sep[4];
+        String mesAdd = "";
+        double maxRefESE = 0;
+        double maxAltESE = 0;
+        double minRefESS = 0;
+        double minAltESS = 0;
+        //ignore deletions larger than flanking region
+        if (ref.length()>35 || alt.length()>35) {
+            return;
         }
-        String[] splitAlt = alt.split("");
-        alt = splitAlt[0];
-    }
-	//if negative strand
-	if (strand.equals("-")) {
-		//reverse complement alt
-		id = id.concat("(-)");
-		ref = getRC(ref);
-		alt = getRC(alt);
-        correct1 = ref.length()-1;
-        strand = "NEG";
-	}
-	//generate alt string
-	String altSeq = s.substring(0, 22 + flank) + alt + s.substring(22 + flank + ref.length());		
-	altSeq = altSeq.toLowerCase();
-    //genesplicer fasta strings
-    gsOutput[gsIndex]=">".concat(strand).concat(chr).concat(":").concat(start).concat(":").concat(refName).concat(":").concat(altName).concat(":GSREF");
-    gsIndex++;
-    gsOutput[gsIndex]=s;
-    gsIndex++;
-    gsOutput[gsIndex]=">".concat(strand).concat(chr).concat(":").concat(start).concat(":").concat(refName).concat(":").concat(altName).concat(":GSALT");
-    gsIndex++;
-    gsOutput[gsIndex]=altSeq;
-    gsIndex++;
-    //ESRseq
-    if(useESR) {
-        for (int i=17+flank; i<23+flank; i++) {
-            int refIndex = getESRindex(s.substring(i, i+6));
-            int altIndex = getESRindex(altSeq.substring(i, i+6));
-            if (ESEtable[refIndex]>maxRefESE) {
-                maxRefESE = ESEtable[refIndex];
-            }
-            if (ESEtable[altIndex]>maxAltESE) {
-                maxAltESE = ESEtable[altIndex];
-            }
-            if (ESStable[refIndex]<minRefESS) {
-                minRefESS = ESStable[refIndex];
-            }
-            if (ESStable[altIndex]<minAltESS) {
-                minAltESS = ESStable[altIndex];
+        if (strand.equals("+")) {
+            strand = "POS";
+        }
+        //index correction for deletions notated as alt="*"
+        String refName = ref;
+        String altName = alt;
+        int correct2=0;
+        if (alt.equals("-") || alt.equals(".")) {
+            alt="*";
+        }
+        if (alt.equals("*")) {
+            alt="";
+            correct2=1;
+        }
+        //catch unsplit VCFs (ie. multiple alt alleles represented on one comma separated line)
+        if (alt.contains(",")) {
+            if (!unsplitVCFfound) {
+                System.out.println("Note: unsplit VCF/BED record(s) were detected, ie. variants with multiple alt alleles represented on a single line. Such records are susceptible to false negatives, so we recommend splitting these records onto multiple lines");
+                unsplitVCFfound = true;
             }
-            if (i==22+flank) {
-                //ESR deletions
-                 if (ref.length()>1 || correct2==1) {
-                    int j=1;
-                    do {
-                        refIndex = getESRindex(s.substring(i+j, i+j+6));
-                        if (ESEtable[refIndex]>maxRefESE) {
-                            maxRefESE = ESEtable[refIndex];
-                        }
-                        if (ESStable[refIndex]<minRefESS) {
-                            minRefESS = ESStable[refIndex];
-                        }
-                        j++;
+            String[] splitAlt = alt.split("");
+            alt = splitAlt[0];
+        }
+        //if negative strand
+        if (strand.equals("-")) {
+            //reverse complement alt
+            id = id.concat("(-)");
+            ref = getRC(ref);
+            alt = getRC(alt);
+            correct1 = ref.length()-1;
+            strand = "NEG";
+        }
+        //generate alt string
+        String altSeq = s.substring(0, 22 + flank) + alt + s.substring(22 + flank + ref.length());		
+        altSeq = altSeq.toLowerCase();
+        //retrieve reference allele from fasta to check for mismatch with provided ref allele
+        String fastaRef = s.substring(22 + flank, 22 + flank + ref.length()).toUpperCase();
+        //ignore variants containing invalid fasta chars such as "n" which cause MaxEntScan to exit prematurely
+        String nTest = altSeq.substring(17+flank-correct1-18, 41+flank-correct1+6+alt.length()).concat(ref).toUpperCase();
+        //check fasta reference matches provided ref allele
+        if (!fastaRef.equals(ref)) {
+            appendOmmittedRefMismatch(id);    
+        } else {
+            //genesplicer fasta strings
+            gsOutput[gsIndex]=">".concat(strand).concat(chr).concat(":").concat(start).concat(":").concat(refName).concat(":").concat(altName).concat(":GSREF");
+            gsIndex++;
+            gsOutput[gsIndex]=s;
+            gsIndex++;
+            gsOutput[gsIndex]=">".concat(strand).concat(chr).concat(":").concat(start).concat(":").concat(refName).concat(":").concat(altName).concat(":GSALT");
+            gsIndex++;
+            gsOutput[gsIndex]=altSeq;
+            gsIndex++;
+            //ESRseq
+            if(useESR) {
+                for (int i=17+flank; i<23+flank; i++) {
+                    int refIndex = getESRindex(s.substring(i, i+6));
+                    int altIndex = getESRindex(altSeq.substring(i, i+6));
+                    if (ESEtable[refIndex]>maxRefESE) {
+                        maxRefESE = ESEtable[refIndex];
                     }
-                    while (j<ref.length());
-                }
-                //ESR insertions
-                if (alt.length()>1) {
-                    int j=1;
-                    do {
-                        altIndex = getESRindex(altSeq.substring(i+j, i+j+6));
-                        if (ESEtable[altIndex]>maxAltESE) {
-                            maxAltESE = ESEtable[altIndex];
+                    if (ESEtable[altIndex]>maxAltESE) {
+                        maxAltESE = ESEtable[altIndex];
+                    }
+                    if (ESStable[refIndex]<minRefESS) {
+                        minRefESS = ESStable[refIndex];
+                    }
+                    if (ESStable[altIndex]<minAltESS) {
+                        minAltESS = ESStable[altIndex];
+                    }
+                    if (i==22+flank) {
+                        //ESR deletions
+                        if (ref.length()>1 || correct2==1) {
+                            int j=1;
+                            do {
+                                refIndex = getESRindex(s.substring(i+j, i+j+6));
+                                if (ESEtable[refIndex]>maxRefESE) {
+                                    maxRefESE = ESEtable[refIndex];
+                                }
+                                if (ESStable[refIndex]<minRefESS) {
+                                    minRefESS = ESStable[refIndex];
+                                }
+                                j++;
+                            }
+                            while (j<ref.length());
                         }
-                        if (ESStable[altIndex]<minAltESS) {
-                            minAltESS = ESStable[altIndex];
+                        //ESR insertions
+                        if (alt.length()>1) {
+                            int j=1;
+                            do {
+                                altIndex = getESRindex(altSeq.substring(i+j, i+j+6));
+                                if (ESEtable[altIndex]>maxAltESE) {
+                                    maxAltESE = ESEtable[altIndex];
+                                }
+                                if (ESStable[altIndex]<minAltESS) {
+                                    minAltESS = ESStable[altIndex];
+                                }
+                                j++;
+                            }
+                            while (j<ref.length());
                         }
-                        j++;
                     }
-                    while (j<ref.length());
                 }
             }
-        }
-    }
-    //ignore variants containing invalid fasta chars such as "n" which cause MaxEntScan to exit prematurely
-    String nTest = altSeq.substring(17+flank-correct1-18, 41+flank-correct1+6+alt.length()).concat(ref).toUpperCase();
-    if (containsIllegalFastaChar(nTest, nTest.length())) {
-        if (!invalidFastaFound) {
-            System.out.println("Note: MaxEntScan cannot process FASTA sequences containing invalid characters (most commonly \"n\"). At least one variant has been omitted from MaxEntScan. IDs of ommitted variant(s) are listed in: Spliceogen/output/mesOmmitted/"+fileID);  
-        }
-        invalidFastaFound = true;
-        appendOmmitted(id);
-    }
-    else {
-        //scan ref sequence
-	    for (int i=17+flank-correct1; i<41+flank-correct1+ref.length()-1; i++) {
-		    //if acceptor
-		    if (s.substring(i, i+2).equals("ag") && i!=17+flank-correct1) {
-                //output ref and alt acceptor strings
-			    mesOutputAcc[mesIndexAcc]=s.substring(i-18, i+5).concat(id).concat("ACC").concat("REF");
-                mesIndexAcc++;
-			    mesOutputAcc[mesIndexAcc]=altSeq.substring(i-18, i+5).concat(id).concat("ACC").concat("ALT");
-                mesIndexAcc++;
-                //for indels, output offset alt acceptor string
-                if (ref.length()>1 || correct2==1) {
-                    int j=1;
-                    do {                
-		                mesOutputAcc[mesIndexAcc]=altSeq.substring(i-18-j, i+5-j).concat(id).concat("ACC").concat("ALT");
+            //MaxEntScan
+            if (containsIllegalFastaChar(nTest, nTest.length())) {
+                appendOmmittedInvalidFasta(id);
+            } else {
+                //scan ref sequence
+                for (int i=17+flank-correct1; i<41+flank-correct1+ref.length()-1; i++) {
+                    //if acceptor
+                    if (s.substring(i, i+2).equals("ag") && i!=17+flank-correct1) {
+                        //output ref and alt acceptor strings
+                        mesOutputAcc[mesIndexAcc]=s.substring(i-18, i+5).concat(id).concat("ACC").concat("REF");
                         mesIndexAcc++;
-                        j++;
-                    }
-                    while (j<ref.length()+correct2);
-                } else
-                if (alt.length()>1) {
-                    int j=1;
-                    do {
-		                mesOutputAcc[mesIndexAcc]=altSeq.substring(i-18+j, i+5+j).concat(id).concat("ACC").concat("ALT");
+                        mesOutputAcc[mesIndexAcc]=altSeq.substring(i-18, i+5).concat(id).concat("ACC").concat("ALT");
                         mesIndexAcc++;
-                        j++;
-                    }
-                    while (j<alt.length());
-                }
-		    }	
-		    //if donor
-		    if (s.substring(i, i+2).equals("gt") && i<26+correct1+flank+ref.length()-1) {
-                //output ref and alt donor strings
-			    mesOutputDon[mesIndexDon]=s.substring(i-3, i+6).concat(id).concat("DON").concat("REF");
-                mesIndexDon++;
-		        mesOutputDon[mesIndexDon]=altSeq.substring(i-3, i+6).concat(id).concat("DON").concat("ALT");
-                mesIndexDon++;
-                //for indels, output offset alt donor string
-                if (ref.length()>1 || correct2==1) {
-                    int j=1;
-                    do {                
-		                mesOutputDon[mesIndexDon]=altSeq.substring(i-3-j, i+6-j).concat(id).concat("DON").concat("ALT");
+                        //for indels, output offset alt acceptor string
+                        if (ref.length()>1 || correct2==1) {
+                            int j=1;
+                            do {                
+                                mesOutputAcc[mesIndexAcc]=altSeq.substring(i-18-j, i+5-j).concat(id).concat("ACC").concat("ALT");
+                                mesIndexAcc++;
+                                j++;
+                            }
+                            while (j<ref.length()+correct2);
+                        } else
+                            if (alt.length()>1) {
+                                int j=1;
+                                do {
+                                    mesOutputAcc[mesIndexAcc]=altSeq.substring(i-18+j, i+5+j).concat(id).concat("ACC").concat("ALT");
+                                    mesIndexAcc++;
+                                    j++;
+                                }
+                                while (j<alt.length());
+                            }
+                    }	
+                    //if donor
+                    if (s.substring(i, i+2).equals("gt") && i<26+correct1+flank+ref.length()-1) {
+                        //output ref and alt donor strings
+                        mesOutputDon[mesIndexDon]=s.substring(i-3, i+6).concat(id).concat("DON").concat("REF");
                         mesIndexDon++;
-                        j++;
-                    }
-                    while (j<ref.length()+correct2);
-                } else
-                if (alt.length()>1) {
-                    int j=1;
-                    do {
-		                mesOutputDon[mesIndexDon]=altSeq.substring(i-3+j, i+6+j).concat(id).concat("DON").concat("ALT");
+                        mesOutputDon[mesIndexDon]=altSeq.substring(i-3, i+6).concat(id).concat("DON").concat("ALT");
                         mesIndexDon++;
-                        j++;
-                    }
-                    while (j<alt.length());
-		        }
-            }	
-	    }
-        //scan alt sequence
-	    for (int i=17+flank; i<41+flank+alt.length()-1; i++) {
-		    //if acceptor
-		    if (altSeq.substring(i, i+2).equals("ag") && i!=17+flank) {
-                //output ref and alt acceptor strings
-			    mesOutputAcc[mesIndexAcc]=altSeq.substring(i-18, i+5).concat(id).concat("ACC").concat("ALT");
-                mesIndexAcc++;
-			    mesOutputAcc[mesIndexAcc]=s.substring(i-18, i+5).concat(id).concat("ACC").concat("REF");
-                mesIndexAcc++;
-                //for indels, output offset ref acceptor string
-                if (alt.length()>1) {
-                    int j=1;
-                    do {
-		                mesOutputAcc[mesIndexAcc]=s.substring(i-18-j, i+5-j).concat(id).concat("ACC").concat("REF");
-                        mesIndexAcc++;
-                        j++;
-                    }
-                    while (j<alt.length());
+                        //for indels, output offset alt donor string
+                        if (ref.length()>1 || correct2==1) {
+                            int j=1;
+                            do {                
+                                mesOutputDon[mesIndexDon]=altSeq.substring(i-3-j, i+6-j).concat(id).concat("DON").concat("ALT");
+                                mesIndexDon++;
+                                j++;
+                            }
+                            while (j<ref.length()+correct2);
+                        } else
+                            if (alt.length()>1) {
+                                int j=1;
+                                do {
+                                    mesOutputDon[mesIndexDon]=altSeq.substring(i-3+j, i+6+j).concat(id).concat("DON").concat("ALT");
+                                    mesIndexDon++;
+                                    j++;
+                                }
+                                while (j<alt.length());
+                            }
+                    }	
                 }
-                if (ref.length()>1||correct2==1) {
-                    int j=1;
-                    do {
-		                mesOutputAcc[mesIndexAcc]=s.substring(i-18+j, i+5+j).concat(id).concat("ACC").concat("REF");
+                //scan alt sequence
+                for (int i=17+flank; i<41+flank+alt.length()-1; i++) {
+                    //if acceptor
+                    if (altSeq.substring(i, i+2).equals("ag") && i!=17+flank) {
+                        //output ref and alt acceptor strings
+                        mesOutputAcc[mesIndexAcc]=altSeq.substring(i-18, i+5).concat(id).concat("ACC").concat("ALT");
                         mesIndexAcc++;
-                        j++;
+                        mesOutputAcc[mesIndexAcc]=s.substring(i-18, i+5).concat(id).concat("ACC").concat("REF");
+                        mesIndexAcc++;
+                        //for indels, output offset ref acceptor string
+                        if (alt.length()>1) {
+                            int j=1;
+                            do {
+                                mesOutputAcc[mesIndexAcc]=s.substring(i-18-j, i+5-j).concat(id).concat("ACC").concat("REF");
+                                mesIndexAcc++;
+                                j++;
+                            }
+                            while (j<alt.length());
+                        }
+                        if (ref.length()>1||correct2==1) {
+                            int j=1;
+                            do {
+                                mesOutputAcc[mesIndexAcc]=s.substring(i-18+j, i+5+j).concat(id).concat("ACC").concat("REF");
+                                mesIndexAcc++;
+                                j++;
+                            }
+                            while (j<ref.length()+correct2);
+                        }
                     }
-                    while (j<ref.length()+correct2);
-                }
-		    }
-		    //if donor
-		    if (altSeq.substring(i, i+2).equals("gt") && i<26+correct1+flank+alt.length()-1) {
-                //output ref and alt donor strings
-		        mesOutputDon[mesIndexDon]=altSeq.substring(i-3, i+6).concat(id).concat("DON").concat("ALT");
-                mesIndexDon++;
-		        mesOutputDon[mesIndexDon]=s.substring(i-3, i+6).concat(id).concat("DON").concat("REF");
-                mesIndexDon++;
-                //for indels, output offset ref donor string
-                if (alt.length()>1) {
-                    int j=1;
-                    do {
-		                mesOutputDon[mesIndexDon]=s.substring(i-3-j, i+6-j).concat(id).concat("DON").concat("REF");
+                    //if donor
+                    if (altSeq.substring(i, i+2).equals("gt") && i<26+correct1+flank+alt.length()-1) {
+                        //output ref and alt donor strings
+                        mesOutputDon[mesIndexDon]=altSeq.substring(i-3, i+6).concat(id).concat("DON").concat("ALT");
                         mesIndexDon++;
-                        j++;
-                    }
-                    while (j<alt.length());
-                }
-                if (ref.length()>1 || correct2==1) {
-                    int j=1;
-                    do {
-		                mesOutputDon[mesIndexDon]=s.substring(i-3+j, i+6+j).concat(id).concat("DON").concat("REF");
+                        mesOutputDon[mesIndexDon]=s.substring(i-3, i+6).concat(id).concat("DON").concat("REF");
                         mesIndexDon++;
-                        j++;                    
+                        //for indels, output offset ref donor string
+                        if (alt.length()>1) {
+                            int j=1;
+                            do {
+                                mesOutputDon[mesIndexDon]=s.substring(i-3-j, i+6-j).concat(id).concat("DON").concat("REF");
+                                mesIndexDon++;
+                                j++;
+                            }
+                            while (j<alt.length());
+                        }
+                        if (ref.length()>1 || correct2==1) {
+                            int j=1;
+                            do {
+                                mesOutputDon[mesIndexDon]=s.substring(i-3+j, i+6+j).concat(id).concat("DON").concat("REF");
+                                mesIndexDon++;
+                                j++;                    
+                            }
+                            while (j<ref.length()+correct2);
+                        }
                     }
-                    while (j<ref.length()+correct2);
-               }
-            }
-		}	
-	}
-    //Format ESR scores and ouput
-    String[] ESRoutputScores = { Double.toString(maxRefESE), Double.toString(maxAltESE), Double.toString(minRefESS), Double.toString(minAltESS) };
-    for (int k=0; k<4; k++) {
-        if (ESRoutputScores[k].equals("0.0")) {
-            ESRoutputScores[k]=".";
+                }
+            }	
         }
-    }    
-    ESRoutput[ESRoutputIndex]=chr+"\t"+start+"\t"+refName+"\t"+altName+"\t"+"ESR"+"\t"+Double.toString(maxRefESE)+"\t"+Double.toString(maxAltESE)+"\t"+Double.toString(minRefESS)+"\t"+Double.toString(minAltESS);
-    ESRoutputIndex++;
-    //append arrays to file then reset
-    if (mesIndexAcc > 25000 || mesIndexDon > 9000 ) {
-        appendToFiles();
-        resetOutputArrays();
-    } else
-    if (gsIndex > 13000 || ESRoutputIndex > 3250 ) {
-        appendToFiles();
-        resetOutputArrays();
+        //Format ESR scores and ouput
+        String[] ESRoutputScores = { Double.toString(maxRefESE), Double.toString(maxAltESE), Double.toString(minRefESS), Double.toString(minAltESS) };
+        for (int k=0; k<4; k++) {
+            if (ESRoutputScores[k].equals("0.0")) {
+                ESRoutputScores[k]=".";
+            }
+        }    
+        ESRoutput[ESRoutputIndex]=chr+"\t"+start+"\t"+refName+"\t"+altName+"\t"+"ESR"+"\t"+Double.toString(maxRefESE)+"\t"+Double.toString(maxAltESE)+"\t"+Double.toString(minRefESS)+"\t"+Double.toString(minAltESS);
+        ESRoutputIndex++;
+        //append arrays to file then reset
+        if (mesIndexAcc > 25000 || mesIndexDon > 9000 ) {
+            appendToFiles();
+            resetOutputArrays();
+        } else
+            if (gsIndex > 13000 || ESRoutputIndex > 3250 ) {
+                appendToFiles();
+                resetOutputArrays();
+            }
     }
-}
-
-//get reverse complement
-public static String getRC (String query) {
-	String rc = "";
-	for (int i=query.length()-1; i>-1; i--) {
-		if (query.charAt(i)=='A') {
-			rc = rc.concat("T");
-		}
-		if (query.charAt(i)=='C') {
-			rc = rc.concat("G");
-		}
-		if (query.charAt(i)=='G') {
-			rc = rc.concat("C");
-		}
-		if (query.charAt(i)=='T') {
-			rc = rc.concat("A");
-		}
-	}
-	return rc;
-}
 
-//generate reference arrays for ESRseq scores, with all potential hexamers mapping to a unique index assigned by getESRindex()
-public static double[] createESRarrays (String fileName) {
-    double[] ESRscores = new double[4096];
-    try {
-        File ESRfile = new File(fileName);
-        BufferedReader br = new BufferedReader(new FileReader(ESRfile));
-        String line = "";
-        while ((line = br.readLine()) != null) {
-            String[] split = line.split("\\s+");
-            ESRscores[getESRindex(split[0])]=Double.parseDouble(split[1]);
+    //get reverse complement
+    public static String getRC (String query) {
+        String rc = "";
+        for (int i=query.length()-1; i>-1; i--) {
+            if (query.charAt(i)=='A') {
+                rc = rc.concat("T");
+            }
+            if (query.charAt(i)=='C') {
+                rc = rc.concat("G");
+            }
+            if (query.charAt(i)=='G') {
+                rc = rc.concat("C");
+            }
+            if (query.charAt(i)=='T') {
+                rc = rc.concat("A");
+            }
         }
-        br.close();
-    }catch (Exception e){
-        System.err.println("Error: " + e.getMessage());
+        return rc;
     }
-    return ESRscores;
-}
 
-public static void fillESRtables() {
-    try {
-        //ESE
-        File ESEfile = new File("data/ESE.txt");
-        BufferedReader ESEbr = new BufferedReader(new FileReader(ESEfile));
-        String line = "";
-        while ((line = ESEbr.readLine()) != null) {
-            String[] split = line.split("\\s+");
-            ESEtable[getESRindex(split[0])]=Double.parseDouble(split[1]);
+    //generate reference arrays for ESRseq scores, with all potential hexamers mapping to a unique index assigned by getESRindex()
+    public static double[] createESRarrays (String fileName) {
+        double[] ESRscores = new double[4096];
+        try {
+            File ESRfile = new File(fileName);
+            BufferedReader br = new BufferedReader(new FileReader(ESRfile));
+            String line = "";
+            while ((line = br.readLine()) != null) {
+                String[] split = line.split("\\s+");
+                ESRscores[getESRindex(split[0])]=Double.parseDouble(split[1]);
+            }
+            br.close();
+        }catch (Exception e){
+            System.err.println("Error: " + e.getMessage());
         }
-        ESEbr.close();
-        //ESS
-        File ESSfile = new File("data/ESS.txt");
-        BufferedReader ESSbr = new BufferedReader(new FileReader(ESSfile));
-        line = "";
-        while ((line = ESSbr.readLine()) != null) {
-            String[] split = line.split("\\s+");
-            ESStable[getESRindex(split[0])]=Double.parseDouble(split[1]);
+        return ESRscores;
+    }
+
+    public static void fillESRtables() {
+        try {
+            //ESE
+            File ESEfile = new File("data/ESE.txt");
+            BufferedReader ESEbr = new BufferedReader(new FileReader(ESEfile));
+            String line = "";
+            while ((line = ESEbr.readLine()) != null) {
+                String[] split = line.split("\\s+");
+                ESEtable[getESRindex(split[0])]=Double.parseDouble(split[1]);
+            }
+            ESEbr.close();
+            //ESS
+            File ESSfile = new File("data/ESS.txt");
+            BufferedReader ESSbr = new BufferedReader(new FileReader(ESSfile));
+            line = "";
+            while ((line = ESSbr.readLine()) != null) {
+                String[] split = line.split("\\s+");
+                ESStable[getESRindex(split[0])]=Double.parseDouble(split[1]);
+            }
+            ESSbr.close();
+        }catch (Exception e){
+            System.err.println("Error: " + e.getMessage());
         }
-        ESSbr.close();
-    }catch (Exception e){
-        System.err.println("Error: " + e.getMessage());
     }
-}
 
-//convert hexamer sequence to integer position in ESR reference score array
-public static int getESRindex (String seq) {
-    seq = seq.toUpperCase();
-    double val=0;
-    for (int i=0; i<6; i++) {
-        char c = seq.charAt(i);
-        switch(c) {
-            case 'A': val = val + 0*Math.pow(4,i);
-            break;
-            case 'C': val = val + 1*Math.pow(4,i);
-            break;
-            case 'G': val = val + 2*Math.pow(4,i);
-            break;
-            case 'T': val = val + 3*Math.pow(4,i);
-            break;
+    //convert hexamer sequence to integer position in ESR reference score array
+    public static int getESRindex (String seq) {
+        seq = seq.toUpperCase();
+        double val=0;
+        for (int i=0; i<6; i++) {
+            char c = seq.charAt(i);
+            switch(c) {
+                case 'A': val = val + 0*Math.pow(4,i);
+                          break;
+                case 'C': val = val + 1*Math.pow(4,i);
+                          break;
+                case 'G': val = val + 2*Math.pow(4,i);
+                          break;
+                case 'T': val = val + 3*Math.pow(4,i);
+                          break;
+            }
         }
+        return (int)val;
     }
-    return (int)val;
-}
 
-public static void resetOutputArrays() {
-    mesOutputAcc = new String[40000];
-    mesOutputDon = new String[15000];
-    gsOutput = new String[30000];
-    ESRoutput = new String[10000];
-    gsIndex = 0; mesIndexDon = 0; mesIndexAcc = 0; ESRoutputIndex = 0;
-    System.gc();
-}
+    public static void resetOutputArrays() {
+        mesOutputAcc = new String[40000];
+        mesOutputDon = new String[15000];
+        gsOutput = new String[30000];
+        ESRoutput = new String[10000];
+        gsIndex = 0; mesIndexDon = 0; mesIndexAcc = 0; ESRoutputIndex = 0;
+        System.gc();
+    }
 
-public static boolean containsIllegalFastaChar(String s, int i) {
-    for (int k=0; k<i; k++) {
-        char current = s.toUpperCase().charAt(k);
-        if (current=='N'|| current==',') {
-            return true;
+    public static boolean containsIllegalFastaChar(String s, int i) {
+        for (int k=0; k<i; k++) {
+            char current = s.toUpperCase().charAt(k);
+            if (current=='N'|| current==',') {
+                return true;
+            }
         }
+        return false;
     }
-    return false;
-}
 
-public static void appendToFiles () {
-    String gsName = "temp/"+fileID+"gsInput.FASTA";
-    String mesAccName = "temp/"+fileID+"mesAcceptorInput.txt";
-    String mesDonName = "temp/"+fileID+"mesDonorInput.txt";
-    String ESRname = "temp/"+fileID+"ESRoutput.txt";
-    try {
-        //write GeneSplicer input to file
-        FileWriter fwGS = new FileWriter(gsName, true);
-        BufferedWriter gsWriter = new BufferedWriter(fwGS);
-        for (int i=0; i<gsIndex; i++) {
-            gsWriter.write(gsOutput[i]+"\n");
-        }
-        gsWriter.close();
-        //write maxEntScan Acceptor input to file
-        FileWriter fwMESacc = new FileWriter(mesAccName, true);
-        BufferedWriter mesAccWriter = new BufferedWriter(fwMESacc);
-        for (int i=0; i<mesIndexAcc; i++) {
-            if (!containsIllegalFastaChar(mesOutputAcc[i], 23)) {
-                mesAccWriter.write(mesOutputAcc[i]+"\n");
+    public static void appendToFiles () {
+        String gsName = "temp/"+fileID+"gsInput.FASTA";
+        String mesAccName = "temp/"+fileID+"mesAcceptorInput.txt";
+        String mesDonName = "temp/"+fileID+"mesDonorInput.txt";
+        String ESRname = "temp/"+fileID+"ESRoutput.txt";
+        try {
+            //write GeneSplicer input to file
+            FileWriter fwGS = new FileWriter(gsName, true);
+            BufferedWriter gsWriter = new BufferedWriter(fwGS);
+            for (int i=0; i<gsIndex; i++) {
+                gsWriter.write(gsOutput[i]+"\n");
             }
-        }
-        mesAccWriter.close();
-        //write maxEntScan Donor input to file
-        FileWriter fwMESdon = new FileWriter(mesDonName, true);
-        BufferedWriter mesDonWriter = new BufferedWriter(fwMESdon);
-        for (int i=0; i<mesIndexDon; i++) {
-            if (!containsIllegalFastaChar(mesOutputDon[i], 9)) {
-                mesDonWriter.write(mesOutputDon[i]+"\n");
+            gsWriter.close();
+            //write maxEntScan Acceptor input to file
+            FileWriter fwMESacc = new FileWriter(mesAccName, true);
+            BufferedWriter mesAccWriter = new BufferedWriter(fwMESacc);
+            for (int i=0; i<mesIndexAcc; i++) {
+                if (!containsIllegalFastaChar(mesOutputAcc[i], 23)) {
+                    mesAccWriter.write(mesOutputAcc[i]+"\n");
+                }
             }
+            mesAccWriter.close();
+            //write maxEntScan Donor input to file
+            FileWriter fwMESdon = new FileWriter(mesDonName, true);
+            BufferedWriter mesDonWriter = new BufferedWriter(fwMESdon);
+            for (int i=0; i<mesIndexDon; i++) {
+                if (!containsIllegalFastaChar(mesOutputDon[i], 9)) {
+                    mesDonWriter.write(mesOutputDon[i]+"\n");
+                }
+            }
+            mesDonWriter.close();
+            //write ESR output to file
+            FileWriter fwESR = new FileWriter(ESRname, true);
+            BufferedWriter ESRwriter = new BufferedWriter(fwESR);
+            for (int i=0; i<ESRoutputIndex; i++) {
+                ESRwriter.write(ESRoutput[i]+"\n");
+            }
+            ESRwriter.close();
+        } catch (IOException e) {
+            System.out.println(e.getMessage());
         }
-        mesDonWriter.close();
-        //write ESR output to file
-        FileWriter fwESR = new FileWriter(ESRname, true);
-        BufferedWriter ESRwriter = new BufferedWriter(fwESR);
-        for (int i=0; i<ESRoutputIndex; i++) {
-            ESRwriter.write(ESRoutput[i]+"\n");
+    }
+
+    public static void appendOmmittedInvalidFasta(String id) {
+        try {
+            String fileName = "output/"+fileID+"mesOmmitted.txt";
+            FileWriter fw = new FileWriter(fileName, true);
+            BufferedWriter writer = new BufferedWriter(fw);
+            writer.write(id+"\n");
+            writer.close();
+        } catch (IOException e) {
+            System.out.println(e.getMessage());
         }
-        ESRwriter.close();
-    } catch (IOException e) {
-        System.out.println(e.getMessage());
     }
-}
 
-public static void appendOmmitted(String id) {
-    try {
-        String fileName = "output/mesOmmitted/"+fileID;
-        FileWriter fw = new FileWriter(fileName, true);
-        BufferedWriter writer = new BufferedWriter(fw);
-        writer.write(id+"\n");
-        writer.close();
-    } catch (IOException e) {
-        System.out.println(e.getMessage());
+    public static void appendOmmittedRefMismatch(String id) {
+        try {
+            String fileName = "output/"+fileID+"refMismatch.txt";
+            FileWriter fw = new FileWriter(fileName, true);
+            BufferedWriter writer = new BufferedWriter(fw);
+            writer.write(id+"\n");
+            writer.close();
+        } catch (IOException e) {
+            System.out.println(e.getMessage());
+        }
     }
-}
+
 }
diff --git a/output/mesOmmitted/note.txt b/output/mesOmmitted/note.txt
deleted file mode 100644
index 12862a5..0000000
--- a/output/mesOmmitted/note.txt
+++ /dev/null
@@ -1 +0,0 @@
-#MaxEntScan exits early when it encounters illegal characters in a fasta (usually "N"). Often a small number of variants need to be excluded from maxEntScan for this reason. Lists of excluded variants are outputted to this directory. Do not remove
diff --git a/temp/note.txt b/temp/note.txt
deleted file mode 100644
index 1f6d3b7..0000000
--- a/temp/note.txt
+++ /dev/null
@@ -1 +0,0 @@
-#intermediate files for each input vcf/bed are created in this directory, do not remove
diff --git a/toy/toy.bed b/toy/toy.bed
deleted file mode 100644
index e45b48a..0000000
--- a/toy/toy.bed
+++ /dev/null
@@ -1,4 +0,0 @@
-chr1	65510	65510	x	1	.	C	G
-chr1	66808	66808	x	1	.	T	G
-chr1	67519	67519	x	1	.	A	G
-chr1	69015	69015	x	1	.	C	T
diff --git a/toy/toy.tsv b/toy/toy.tsv
new file mode 100644
index 0000000..4bfb304
--- /dev/null
+++ b/toy/toy.tsv
@@ -0,0 +1,3 @@
+chr1	65510	T	G
+chr1	66808	A	G
+chr1	69015	C	T
diff --git a/toy/toy.vcf b/toy/toy.vcf
index c942bb5..b6bc81a 100644
--- a/toy/toy.vcf
+++ b/toy/toy.vcf
@@ -1,2731 +1,32 @@
-##fileformat=VCFv4.2
-##ALT=<ID=NON_REF,Description="Represents any possible alternative allele at this location">
-##FILTER=<ID=ExcessHet,Description="ExcessHet > 54.69">
-##FILTER=<ID=LowQual,Description="Low quality">
-##FILTER=<ID=PASS,Description="All filters passed">
-##FILTER=<ID=VQSRTrancheINDEL99.90to99.95,Description="Truth sensitivity tranche level for INDEL model at VQS Lod: -7.6741 <= x < -4.5754">
-##FILTER=<ID=VQSRTrancheINDEL99.95to100.00+,Description="Truth sensitivity tranche level for INDEL model at VQS Lod < -83289.7506">
-##FILTER=<ID=VQSRTrancheINDEL99.95to100.00,Description="Truth sensitivity tranche level for INDEL model at VQS Lod: -83289.7506 <= x < -7.6741">
-##FILTER=<ID=VQSRTrancheSNP99.80to99.90,Description="Truth sensitivity tranche level for SNP model at VQS Lod: -6.6497 <= x < -2.6539">
-##FILTER=<ID=VQSRTrancheSNP99.90to99.95,Description="Truth sensitivity tranche level for SNP model at VQS Lod: -15.7199 <= x < -6.6497">
-##FILTER=<ID=VQSRTrancheSNP99.95to100.00+,Description="Truth sensitivity tranche level for SNP model at VQS Lod < -340696.0499">
-##FILTER=<ID=VQSRTrancheSNP99.95to100.00,Description="Truth sensitivity tranche level for SNP model at VQS Lod: -340696.0499 <= x < -15.7199">
-##FORMAT=<ID=AD,Number=R,Type=Integer,Description="Allelic depths for the ref and alt alleles in the order listed">
-##FORMAT=<ID=DP,Number=1,Type=Integer,Description="Approximate read depth (reads with MQ=255 or with bad mates are filtered)">
-##FORMAT=<ID=GQ,Number=1,Type=Integer,Description="Genotype Quality">
-##FORMAT=<ID=GT,Number=1,Type=String,Description="Genotype">
-##FORMAT=<ID=MIN_DP,Number=1,Type=Integer,Description="Minimum DP observed within the GVCF block">
-##FORMAT=<ID=PGT,Number=1,Type=String,Description="Physical phasing haplotype information, describing how the alternate alleles are phased in relation to one another">
-##FORMAT=<ID=PID,Number=1,Type=String,Description="Physical phasing ID information, where each unique ID within a given sample (but not across samples) connects records within a phasing group">
-##FORMAT=<ID=PL,Number=G,Type=Integer,Description="Normalized, Phred-scaled likelihoods for genotypes as defined in the VCF specification">
-##FORMAT=<ID=RGQ,Number=1,Type=Integer,Description="Unconditional reference genotype confidence, encoded as a phred quality -10*log10 p(genotype call is wrong)">
-##FORMAT=<ID=SB,Number=4,Type=Integer,Description="Per-sample component statistics which comprise the Fisher's Exact Test to detect strand bias.">
-##GATKCommandLine=<ID=ApplyVQSR,CommandLine="ApplyVQSR  --recal-file /short/a32/exi569/WGS_GATK/VQSR/all_gatk4_output_INDEL.recal --tranches-file /short/a32/exi569/WGS_GATK/VQSR/all_gatk4_output_INDEL.tranches --output /g/data3/a32/quarterly_x1_10TB/WGS/VCF/VCF_1_platypus/B6/VCF/varFilt/B6_gatk4_all_co_called_INDEL_AVQSR_30052018.vcf.gz --truth-sensitivity-filter-level 99.7 --mode INDEL --variant /g/data3/a32/quarterly_x1_10TB/WGS/VCF/VCF_1_platypus/B6/VCF/varFilt/B6_gatk4_all_co_called_30052018.vcf.gz --create-output-variant-index true  --use-allele-specific-annotations false --ignore-all-filters false --exclude-filtered false --interval-set-rule UNION --interval-padding 0 --interval-exclusion-padding 0 --interval-merging-rule ALL --read-validation-stringency SILENT --seconds-between-progress-updates 10.0 --disable-sequence-dictionary-validation false --create-output-bam-index true --create-output-bam-md5 false --create-output-variant-md5 false --lenient false --add-output-sam-program-record true --add-output-vcf-command-line true --cloud-prefetch-buffer 40 --cloud-index-prefetch-buffer -1 --disable-bam-index-caching false --help false --version false --showHidden false --verbosity INFO --QUIET false --use-jdk-deflater false --use-jdk-inflater false --gcs-max-retries 20 --disable-tool-default-read-filters false",Date="May 31, 2018 10:59:30 AM AEST",Version=4.0.4.0>
-##GATKCommandLine=<ID=SelectVariants,CommandLine="SelectVariants  --output /g/data3/a32/quarterly_x1_10TB/WGS/VCF/VCF_2_VT_split/B6/B6_gatk4_all_co_called_VQSR_normalize_30052018_chr1.vcf.gz --variant /g/data3/a32/quarterly_x1_10TB/WGS/VCF/VCF_2_VT_split/B6/B6_gatk4_all_co_called_VQSR_normalize_30052018.vcf.gz --intervals chr1 --reference /g/data3/a32/References_and_Databases/hg38.noalt.decoy.bwa/GCA_000001405.15_GRCh38_no_alt_plus_hs38d1_analysis_set.fa  --invertSelect false --exclude-non-variants false --exclude-filtered false --preserve-alleles false --remove-unused-alternates false --restrict-alleles-to ALL --keep-original-ac false --keep-original-dp false --mendelian-violation false --invert-mendelian-violation false --mendelian-violation-qual-threshold 0.0 --select-random-fraction 0.0 --remove-fraction-genotypes 0.0 --fully-decode false --max-indel-size 2147483647 --min-indel-size 0 --max-filtered-genotypes 2147483647 --min-filtered-genotypes 0 --max-fraction-filtered-genotypes 1.0 --min-fraction-filtered-genotypes 0.0 --max-nocall-number 2147483647 --max-nocall-fraction 1.0 --set-filtered-gt-to-nocall false --allow-nonoverlapping-command-line-samples false --suppress-reference-path false --interval-set-rule UNION --interval-padding 0 --interval-exclusion-padding 0 --interval-merging-rule ALL --read-validation-stringency SILENT --seconds-between-progress-updates 10.0 --disable-sequence-dictionary-validation false --create-output-bam-index true --create-output-bam-md5 false --create-output-variant-index true --create-output-variant-md5 false --lenient false --add-output-sam-program-record true --add-output-vcf-command-line true --cloud-prefetch-buffer 40 --cloud-index-prefetch-buffer -1 --disable-bam-index-caching false --help false --version false --showHidden false --verbosity INFO --QUIET false --use-jdk-deflater false --use-jdk-inflater false --gcs-max-retries 20 --disable-tool-default-read-filters false",Date="June 26, 2018 12:21:20 AM AEST",Version=4.0.4.0>
-##INFO=<ID=AC,Number=A,Type=Integer,Description="Allele count in genotypes, for each ALT allele, in the same order as listed">
-##INFO=<ID=AF,Number=A,Type=Float,Description="Allele Frequency, for each ALT allele, in the same order as listed">
-##INFO=<ID=AN,Number=1,Type=Integer,Description="Total number of alleles in called genotypes">
-##INFO=<ID=BaseQRankSum,Number=1,Type=Float,Description="Z-score from Wilcoxon rank sum test of Alt Vs. Ref base qualities">
-##INFO=<ID=ClippingRankSum,Number=1,Type=Float,Description="Z-score From Wilcoxon rank sum test of Alt vs. Ref number of hard clipped bases">
-##INFO=<ID=DB,Number=0,Type=Flag,Description="dbSNP Membership">
-##INFO=<ID=DP,Number=1,Type=Integer,Description="Approximate read depth; some reads may have been filtered">
-##INFO=<ID=DS,Number=0,Type=Flag,Description="Were any of the samples downsampled?">
-##INFO=<ID=END,Number=1,Type=Integer,Description="Stop position of the interval">
-##INFO=<ID=ExcessHet,Number=1,Type=Float,Description="Phred-scaled p-value for exact test of excess heterozygosity">
-##INFO=<ID=FS,Number=1,Type=Float,Description="Phred-scaled p-value using Fisher's exact test to detect strand bias">
-##INFO=<ID=InbreedingCoeff,Number=1,Type=Float,Description="Inbreeding coefficient as estimated from the genotype likelihoods per-sample when compared against the Hardy-Weinberg expectation">
-##INFO=<ID=MLEAC,Number=A,Type=Integer,Description="Maximum likelihood expectation (MLE) for the allele counts (not necessarily the same as the AC), for each ALT allele, in the same order as listed">
-##INFO=<ID=MLEAF,Number=A,Type=Float,Description="Maximum likelihood expectation (MLE) for the allele frequency (not necessarily the same as the AF), for each ALT allele, in the same order as listed">
-##INFO=<ID=MQ,Number=1,Type=Float,Description="RMS Mapping Quality">
-##INFO=<ID=MQRankSum,Number=1,Type=Float,Description="Z-score From Wilcoxon rank sum test of Alt vs. Ref read mapping qualities">
-##INFO=<ID=NEGATIVE_TRAIN_SITE,Number=0,Type=Flag,Description="This variant was used to build the negative training set of bad variants">
-##INFO=<ID=OLD_CLUMPED,Number=1,Type=String,Description="BIALLELIC BIALLELIC Original chr:pos:ref:alt encoding">
-##INFO=<ID=OLD_MULTIALLELIC,Number=1,Type=String,Description="MULTIALLELIC MULTIALLELIC Original chr:pos:ref:alt encoding">
-##INFO=<ID=OLD_VARIANT,Number=.,Type=String,Description="Original chr:pos:ref:alt encoding">
-##INFO=<ID=POSITIVE_TRAIN_SITE,Number=0,Type=Flag,Description="This variant was used to build the positive training set of good variants">
-##INFO=<ID=QD,Number=1,Type=Float,Description="Variant Confidence/Quality by Depth">
-##INFO=<ID=RAW_MQ,Number=1,Type=Float,Description="Raw data for RMS Mapping Quality">
-##INFO=<ID=ReadPosRankSum,Number=1,Type=Float,Description="Z-score from Wilcoxon rank sum test of Alt vs. Ref read position bias">
-##INFO=<ID=SOR,Number=1,Type=Float,Description="Symmetric Odds Ratio of 2x2 contingency table to detect strand bias">
-##INFO=<ID=VQSLOD,Number=1,Type=Float,Description="Log odds of being a true variant versus being false under the trained gaussian mixture model">
-##INFO=<ID=culprit,Number=1,Type=String,Description="The annotation which was the worst performing in the Gaussian mixture model, likely the reason why the variant was filtered out">
-##contig=<ID=chr1,assembly=GCA_000001405.15_GRCh38_no_alt_plus_hs38d1_analysis_set.fa,length=248956422>
-##contig=<ID=chr2,assembly=GCA_000001405.15_GRCh38_no_alt_plus_hs38d1_analysis_set.fa,length=242193529>
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-##contig=<ID=chr4,assembly=GCA_000001405.15_GRCh38_no_alt_plus_hs38d1_analysis_set.fa,length=190214555>
-##contig=<ID=chr5,assembly=GCA_000001405.15_GRCh38_no_alt_plus_hs38d1_analysis_set.fa,length=181538259>
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-##contig=<ID=chr9,assembly=GCA_000001405.15_GRCh38_no_alt_plus_hs38d1_analysis_set.fa,length=138394717>
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-##contig=<ID=chrUn_JTFH01001955v1_decoy,assembly=GCA_000001405.15_GRCh38_no_alt_plus_hs38d1_analysis_set.fa,length=2203>
-##contig=<ID=chrUn_JTFH01001956v1_decoy,assembly=GCA_000001405.15_GRCh38_no_alt_plus_hs38d1_analysis_set.fa,length=2197>
-##contig=<ID=chrUn_JTFH01001957v1_decoy,assembly=GCA_000001405.15_GRCh38_no_alt_plus_hs38d1_analysis_set.fa,length=2196>
-##contig=<ID=chrUn_JTFH01001958v1_decoy,assembly=GCA_000001405.15_GRCh38_no_alt_plus_hs38d1_analysis_set.fa,length=2196>
-##contig=<ID=chrUn_JTFH01001959v1_decoy,assembly=GCA_000001405.15_GRCh38_no_alt_plus_hs38d1_analysis_set.fa,length=2179>
-##contig=<ID=chrUn_JTFH01001960v1_decoy,assembly=GCA_000001405.15_GRCh38_no_alt_plus_hs38d1_analysis_set.fa,length=2178>
-##contig=<ID=chrUn_JTFH01001961v1_decoy,assembly=GCA_000001405.15_GRCh38_no_alt_plus_hs38d1_analysis_set.fa,length=2178>
-##contig=<ID=chrUn_JTFH01001962v1_decoy,assembly=GCA_000001405.15_GRCh38_no_alt_plus_hs38d1_analysis_set.fa,length=2172>
-##contig=<ID=chrUn_JTFH01001963v1_decoy,assembly=GCA_000001405.15_GRCh38_no_alt_plus_hs38d1_analysis_set.fa,length=2170>
-##contig=<ID=chrUn_JTFH01001964v1_decoy,assembly=GCA_000001405.15_GRCh38_no_alt_plus_hs38d1_analysis_set.fa,length=2167>
-##contig=<ID=chrUn_JTFH01001965v1_decoy,assembly=GCA_000001405.15_GRCh38_no_alt_plus_hs38d1_analysis_set.fa,length=2167>
-##contig=<ID=chrUn_JTFH01001966v1_decoy,assembly=GCA_000001405.15_GRCh38_no_alt_plus_hs38d1_analysis_set.fa,length=2157>
-##contig=<ID=chrUn_JTFH01001967v1_decoy,assembly=GCA_000001405.15_GRCh38_no_alt_plus_hs38d1_analysis_set.fa,length=2153>
-##contig=<ID=chrUn_JTFH01001968v1_decoy,assembly=GCA_000001405.15_GRCh38_no_alt_plus_hs38d1_analysis_set.fa,length=2151>
-##contig=<ID=chrUn_JTFH01001969v1_decoy,assembly=GCA_000001405.15_GRCh38_no_alt_plus_hs38d1_analysis_set.fa,length=2147>
-##contig=<ID=chrUn_JTFH01001970v1_decoy,assembly=GCA_000001405.15_GRCh38_no_alt_plus_hs38d1_analysis_set.fa,length=2145>
-##contig=<ID=chrUn_JTFH01001971v1_decoy,assembly=GCA_000001405.15_GRCh38_no_alt_plus_hs38d1_analysis_set.fa,length=2142>
-##contig=<ID=chrUn_JTFH01001972v1_decoy,assembly=GCA_000001405.15_GRCh38_no_alt_plus_hs38d1_analysis_set.fa,length=2142>
-##contig=<ID=chrUn_JTFH01001973v1_decoy,assembly=GCA_000001405.15_GRCh38_no_alt_plus_hs38d1_analysis_set.fa,length=2136>
-##contig=<ID=chrUn_JTFH01001974v1_decoy,assembly=GCA_000001405.15_GRCh38_no_alt_plus_hs38d1_analysis_set.fa,length=2130>
-##contig=<ID=chrUn_JTFH01001975v1_decoy,assembly=GCA_000001405.15_GRCh38_no_alt_plus_hs38d1_analysis_set.fa,length=2128>
-##contig=<ID=chrUn_JTFH01001976v1_decoy,assembly=GCA_000001405.15_GRCh38_no_alt_plus_hs38d1_analysis_set.fa,length=2126>
-##contig=<ID=chrUn_JTFH01001977v1_decoy,assembly=GCA_000001405.15_GRCh38_no_alt_plus_hs38d1_analysis_set.fa,length=2126>
-##contig=<ID=chrUn_JTFH01001978v1_decoy,assembly=GCA_000001405.15_GRCh38_no_alt_plus_hs38d1_analysis_set.fa,length=2119>
-##contig=<ID=chrUn_JTFH01001979v1_decoy,assembly=GCA_000001405.15_GRCh38_no_alt_plus_hs38d1_analysis_set.fa,length=2107>
-##contig=<ID=chrUn_JTFH01001980v1_decoy,assembly=GCA_000001405.15_GRCh38_no_alt_plus_hs38d1_analysis_set.fa,length=2091>
-##contig=<ID=chrUn_JTFH01001981v1_decoy,assembly=GCA_000001405.15_GRCh38_no_alt_plus_hs38d1_analysis_set.fa,length=2087>
-##contig=<ID=chrUn_JTFH01001982v1_decoy,assembly=GCA_000001405.15_GRCh38_no_alt_plus_hs38d1_analysis_set.fa,length=2086>
-##contig=<ID=chrUn_JTFH01001983v1_decoy,assembly=GCA_000001405.15_GRCh38_no_alt_plus_hs38d1_analysis_set.fa,length=2083>
-##contig=<ID=chrUn_JTFH01001984v1_decoy,assembly=GCA_000001405.15_GRCh38_no_alt_plus_hs38d1_analysis_set.fa,length=2075>
-##contig=<ID=chrUn_JTFH01001985v1_decoy,assembly=GCA_000001405.15_GRCh38_no_alt_plus_hs38d1_analysis_set.fa,length=2075>
-##contig=<ID=chrUn_JTFH01001986v1_decoy,assembly=GCA_000001405.15_GRCh38_no_alt_plus_hs38d1_analysis_set.fa,length=2072>
-##contig=<ID=chrUn_JTFH01001987v1_decoy,assembly=GCA_000001405.15_GRCh38_no_alt_plus_hs38d1_analysis_set.fa,length=2068>
-##contig=<ID=chrUn_JTFH01001988v1_decoy,assembly=GCA_000001405.15_GRCh38_no_alt_plus_hs38d1_analysis_set.fa,length=2067>
-##contig=<ID=chrUn_JTFH01001989v1_decoy,assembly=GCA_000001405.15_GRCh38_no_alt_plus_hs38d1_analysis_set.fa,length=2055>
-##contig=<ID=chrUn_JTFH01001990v1_decoy,assembly=GCA_000001405.15_GRCh38_no_alt_plus_hs38d1_analysis_set.fa,length=2051>
-##contig=<ID=chrUn_JTFH01001991v1_decoy,assembly=GCA_000001405.15_GRCh38_no_alt_plus_hs38d1_analysis_set.fa,length=2050>
-##contig=<ID=chrUn_JTFH01001992v1_decoy,assembly=GCA_000001405.15_GRCh38_no_alt_plus_hs38d1_analysis_set.fa,length=2033>
-##contig=<ID=chrUn_JTFH01001993v1_decoy,assembly=GCA_000001405.15_GRCh38_no_alt_plus_hs38d1_analysis_set.fa,length=2024>
-##contig=<ID=chrUn_JTFH01001994v1_decoy,assembly=GCA_000001405.15_GRCh38_no_alt_plus_hs38d1_analysis_set.fa,length=2016>
-##contig=<ID=chrUn_JTFH01001995v1_decoy,assembly=GCA_000001405.15_GRCh38_no_alt_plus_hs38d1_analysis_set.fa,length=2011>
-##contig=<ID=chrUn_JTFH01001996v1_decoy,assembly=GCA_000001405.15_GRCh38_no_alt_plus_hs38d1_analysis_set.fa,length=2009>
-##contig=<ID=chrUn_JTFH01001997v1_decoy,assembly=GCA_000001405.15_GRCh38_no_alt_plus_hs38d1_analysis_set.fa,length=2003>
-##contig=<ID=chrUn_JTFH01001998v1_decoy,assembly=GCA_000001405.15_GRCh38_no_alt_plus_hs38d1_analysis_set.fa,length=2001>
-##reference=file:///g/data3/a32/References_and_Databases/hg38.noalt.decoy.bwa/GCA_000001405.15_GRCh38_no_alt_plus_hs38d1_analysis_set.fa
-##source=ApplyVQSR
-##source=SelectVariants
-##INFO=<ID=ANNOVAR_DATE,Number=1,Type=String,Description="Flag the start of ANNOVAR annotation for one alternative allele">
-##INFO=<ID=Func.refGene,Number=.,Type=String,Description="Func.refGene annotation provided by ANNOVAR">
-##INFO=<ID=Gene.refGene,Number=.,Type=String,Description="Gene.refGene annotation provided by ANNOVAR">
-##INFO=<ID=GeneDetail.refGene,Number=.,Type=String,Description="GeneDetail.refGene annotation provided by ANNOVAR">
-##INFO=<ID=ExonicFunc.refGene,Number=.,Type=String,Description="ExonicFunc.refGene annotation provided by ANNOVAR">
-##INFO=<ID=AAChange.refGene,Number=.,Type=String,Description="AAChange.refGene annotation provided by ANNOVAR">
-##INFO=<ID=EHRF_r90,Number=.,Type=String,Description="EHRF_r90 annotation provided by ANNOVAR">
-##INFO=<ID=cytoBand,Number=.,Type=String,Description="cytoBand annotation provided by ANNOVAR">
-##INFO=<ID=genomicSuperDups,Number=.,Type=String,Description="genomicSuperDups annotation provided by ANNOVAR">
-##INFO=<ID=E_AF_POPMAX,Number=.,Type=String,Description="E_AF_POPMAX annotation provided by ANNOVAR">
-##INFO=<ID=E_AF_TOT,Number=.,Type=String,Description="E_AF_TOT annotation provided by ANNOVAR">
-##INFO=<ID=G_AF_POPMAX,Number=.,Type=String,Description="G_AF_POPMAX annotation provided by ANNOVAR">
-##INFO=<ID=G_AF_TOT,Number=.,Type=String,Description="G_AF_TOT annotation provided by ANNOVAR">
-##INFO=<ID=C_AF_TOT,Number=.,Type=String,Description="C_AF_TOT annotation provided by ANNOVAR">
-##INFO=<ID=C_Hom_TOT,Number=.,Type=String,Description="C_Hom_TOT annotation provided by ANNOVAR">
-##INFO=<ID=ExAC_ALL,Number=1,Type=Float,Description="ExAC_ALL annotation provided by ANNOVAR">
-##INFO=<ID=ExAC_AFR,Number=1,Type=Float,Description="ExAC_AFR annotation provided by ANNOVAR">
-##INFO=<ID=ExAC_AMR,Number=1,Type=Float,Description="ExAC_AMR annotation provided by ANNOVAR">
-##INFO=<ID=ExAC_EAS,Number=1,Type=Float,Description="ExAC_EAS annotation provided by ANNOVAR">
-##INFO=<ID=ExAC_FIN,Number=1,Type=Float,Description="ExAC_FIN annotation provided by ANNOVAR">
-##INFO=<ID=ExAC_NFE,Number=1,Type=Float,Description="ExAC_NFE annotation provided by ANNOVAR">
-##INFO=<ID=ExAC_OTH,Number=1,Type=Float,Description="ExAC_OTH annotation provided by ANNOVAR">
-##INFO=<ID=ExAC_SAS,Number=1,Type=Float,Description="ExAC_SASannotation provided by ANNOVAR">
-##INFO=<ID=ExAC_HIGH,Number=1,Type=Float,Description="ExAC_HIGH annotation provided by ANNOVAR">
-##INFO=<ID=ExAC_HOMO,Number=1,Type=Float,Description="ExAC_HOMO annotation provided by ANNOVAR">
-##INFO=<ID=VC_het_cnt,Number=1,Type=Float,Description="VC_het_cnt annotation provided by ANNOVAR">
-##INFO=<ID=VC_hom_cnt,Number=1,Type=Float,Description="VC_hom_cnt annotation provided by ANNOVAR">
-##INFO=<ID=VC_freq,Number=1,Type=Float,Description="VC_freq annotation provided by ANNOVAR">
-##INFO=<ID=VC_Total_freq,Number=1,Type=Float,Description="VC_Total_freq annotation provided by ANNOVAR">
-##INFO=<ID=VC_Total_variant_cnt,Number=1,Type=Float,Description="VC_Total_variant_cnt annotation provided by ANNOVAR">
-##INFO=<ID=VC_Total_allele_cnt,Number=1,Type=Float,Description="VC_Total_allele_cnt annotation provided by ANNOVAR">
-##INFO=<ID=esp6500siv2_all,Number=1,Type=Float,Description="esp6500siv2_all annotation provided by ANNOVAR">
-##INFO=<ID=1000g2015aug_all,Number=1,Type=Float,Description="1000g2015aug_all annotation provided by ANNOVAR">
-##INFO=<ID=clinvar_20150629,Number=.,Type=String,Description="clinvar_20150629 annotation provided by ANNOVAR">
-##INFO=<ID=UK10K,Number=.,Type=String,Description="UK10K annotation provided by ANNOVAR">
-##INFO=<ID=SIFT_score,Number=1,Type=Float,Description="SIFT_score annotation provided by ANNOVAR">
-##INFO=<ID=SIFT_pred,Number=.,Type=String,Description="SIFT_pred annotation provided by ANNOVAR">
-##INFO=<ID=Polyphen2_HDIV_score,Number=1,Type=Float,Description="Polyphen2_HDIV_score annotation provided by ANNOVAR">
-##INFO=<ID=Polyphen2_HDIV_pred,Number=.,Type=String,Description="Polyphen2_HDIV_pred annotation provided by ANNOVAR">
-##INFO=<ID=Polyphen2_HVAR_score,Number=1,Type=Float,Description="Polyphen2_HVAR_score annotation provided by ANNOVAR">
-##INFO=<ID=Polyphen2_HVAR_pred,Number=.,Type=String,Description="Polyphen2_HVAR_pred annotation provided by ANNOVAR">
-##INFO=<ID=LRT_score,Number=.,Type=String,Description="LRT_score annotation provided by ANNOVAR">
-##INFO=<ID=LRT_pred,Number=.,Type=String,Description="LRT_pred annotation provided by ANNOVAR">
-##INFO=<ID=MutationTaster_score,Number=.,Type=String,Description="MutationTaster_score annotation provided by ANNOVAR">
-##INFO=<ID=MutationTaster_pred,Number=.,Type=String,Description="MutationTaster_pred annotation provided by ANNOVAR">
-##INFO=<ID=MutationAssessor_score,Number=.,Type=String,Description="MutationAssessor_score annotation provided by ANNOVAR">
-##INFO=<ID=MutationAssessor_pred,Number=.,Type=String,Description="MutationAssessor_pred annotation provided by ANNOVAR">
-##INFO=<ID=FATHMM_score,Number=.,Type=String,Description="FATHMM_score annotation provided by ANNOVAR">
-##INFO=<ID=FATHMM_pred,Number=.,Type=String,Description="FATHMM_pred annotation provided by ANNOVAR">
-##INFO=<ID=PROVEAN_score,Number=.,Type=String,Description="PROVEAN_score annotation provided by ANNOVAR">
-##INFO=<ID=PROVEAN_pred,Number=.,Type=String,Description="PROVEAN_pred annotation provided by ANNOVAR">
-##INFO=<ID=VEST3_score,Number=.,Type=String,Description="VEST3_score annotation provided by ANNOVAR">
-##INFO=<ID=CADD_raw,Number=1,Type=Float,Description="CADD_raw annotation provided by ANNOVAR">
-##INFO=<ID=CADD_phred,Number=1,Type=Float,Description="CADD_phred annotation provided by ANNOVAR">
-##INFO=<ID=DANN_score,Number=.,Type=String,Description="DANN_score annotation provided by ANNOVAR">
-##INFO=<ID=fathmm-MKL_coding_score,Number=.,Type=String,Description="fathmm-MKL_coding_score annotation provided by ANNOVAR">
-##INFO=<ID=fathmm-MKL_coding_pred,Number=.,Type=String,Description="fathmm-MKL_coding_pred annotation provided by ANNOVAR">
-##INFO=<ID=MetaSVM_score,Number=.,Type=String,Description="MetaSVM_score annotation provided by ANNOVAR">
-##INFO=<ID=MetaSVM_pred,Number=.,Type=String,Description="MetaSVM_pred annotation provided by ANNOVAR">
-##INFO=<ID=MetaLR_score,Number=.,Type=String,Description="MetaLR_score annotation provided by ANNOVAR">
-##INFO=<ID=MetaLR_pred,Number=.,Type=String,Description="MetaLR_pred annotation provided by ANNOVAR">
-##INFO=<ID=integrated_fitCons_score,Number=.,Type=String,Description="integrated_fitCons_score annotation provided by ANNOVAR">
-##INFO=<ID=integrated_confidence_value,Number=.,Type=String,Description="integrated_confidence_value annotation provided by ANNOVAR">
-##INFO=<ID=GERP++_RS,Number=1,Type=Float,Description="GERP++_RS annotation provided by ANNOVAR">
-##INFO=<ID=phyloP7way_vertebrate,Number=.,Type=String,Description="phyloP7way_vertebrate annotation provided by ANNOVAR">
-##INFO=<ID=phyloP20way_mammalian,Number=.,Type=String,Description="phyloP20way_mammalian annotation provided by ANNOVAR">
-##INFO=<ID=phastCons7way_vertebrate,Number=.,Type=String,Description="phastCons7way_vertebrate annotation provided by ANNOVAR">
-##INFO=<ID=phastCons20way_mammalian,Number=.,Type=String,Description="phastCons20way_mammalian annotation provided by ANNOVAR">
-##INFO=<ID=SiPhy_29way_logOdds,Number=.,Type=String,Description="SiPhy_29way_logOdds annotation provided by ANNOVAR">
-##INFO=<ID=avsnp144,Number=.,Type=String,Description="avsnp144 annotation provided by ANNOVAR">
-##INFO=<ID=MCAP,Number=1,Type=Float,Description="MCAP annotation provided by ANNOVAR">
-##INFO=<ID=gwava_ed,Number=1,Type=Float,Description="gwava_ed annotation provided by ANNOVAR">
-##INFO=<ID=BP_numREF,Number=1,Type=Float,Description="BP_numREF annotation provided by ANNOVAR">
-##INFO=<ID=BP_numALT,Number=1,Type=Float,Description="BP_numALT annotation provided by ANNOVAR">
-##INFO=<ID=BP_scoreREF,Number=1,Type=Float,Description="BP_scoreREF annotation provided by ANNOVAR">
-##INFO=<ID=BP_scoreALT,Number=1,Type=Float,Description="BP_scoreALT annotation provided by ANNOVAR">
-##INFO=<ID=BP_U2REF,Number=1,Type=Float,Description="BP_U2REF annotation provided by ANNOVAR">
-##INFO=<ID=BP_U2ALT,Number=1,Type=Float,Description="BP_U2ALT annotation provided by ANNOVAR">
-##INFO=<ID=GS_REF,Number=1,Type=Float,Description="GS_REF annotation provided by ANNOVAR">
-##INFO=<ID=GS_ALT,Number=1,Type=Float,Description="GS_ALT annotation provided by ANNOVAR">
-##INFO=<ID=GS_TYPE,Number=.,Type=String,Description="GS_TYPE annotation provided by ANNOVAR">
-##INFO=<ID=MESaccRef,Number=1,Type=Float,Description="MESaccRef annotation provided by ANNOVAR">
-##INFO=<ID=MESaccAlt,Number=1,Type=Float,Description="MESaccAlt annotation provided by ANNOVAR">
-##INFO=<ID=MESdonRef,Number=1,Type=Float,Description="MESdonRef annotation provided by ANNOVAR">
-##INFO=<ID=MESdonAlt,Number=1,Type=Float,Description="MESdonAlt annotation provided by ANNOVAR">
-##INFO=<ID=spidex_mt,Number=1,Type=Float,Description="spidex_mt annotation provided by ANNOVAR">
-##INFO=<ID=spidex_zs,Number=1,Type=Float,Description="spidex_zs annotation provided by ANNOVAR">
-##INFO=<ID=dbscSNV_ada,Number=1,Type=Float,Description="dbscSNV_ada annotation provided by ANNOVAR">
-##INFO=<ID=dbscSNV_rf,Number=1,Type=Float,Description="dbscSNV_rf annotation provided by ANNOVAR">
-##INFO=<ID=LINSIGHT_score,Number=1,Type=Float,Description="LINSIGHT_score annotation provided by ANNOVAR">
-##INFO=<ID=VARIANT_TYPE,Number=.,Type=String,Description="VARIANT_TYPE annotation provided by ANNOVAR_EDDIE">
-##INFO=<ID=ALLELE_END,Number=0,Type=Flag,Description="Flag the end of ANNOVAR annotation for one alternative allele">
-#CHROM	POS	ID	REF	ALT	QUAL	FILTER	INFO	FORMAT	11182	11194	11195	13245	13530	13531	14225	14226	14227	150790745	152140225	161480689	162100702	162420370	162590491	162590498	162850325	163050830	163050831	163340643	163340842	170370829	170730795	171010857	171010862	172240507	172550744	172790785	172790804	172820818	172820819	37_1	37_2	37_3	39_1	39_2	39_3	46840	46842	46843	46844	47483	7634956	7634962	8181716	F7514182
-chr1	65510	.	C	G	117.57	PASS	AC=1;AF=0.014;AN=70;BaseQRankSum=1.28;ClippingRankSum=0;DP=2027;ExcessHet=6.9804;FS=0;InbreedingCoeff=-0.1494;MLEAC=2;MLEAF=0.029;MQ=8.59;MQRankSum=0.617;NEGATIVE_TRAIN_SITE;QD=4.9;ReadPosRankSum=1.78;SOR=0.976;VQSLOD=-2.904;culprit=MQRankSum;ANNOVAR_DATE=2017-07-17;Func.refGene=intergenic;Gene.refGene=NONE,DDX11L1;GeneDetail.refGene=dist,NONE,dist,1697;ExonicFunc.refGene=-999;AAChange.refGene=-999;EHRF_r90=-999;cytoBand=1p36.33;genomicSuperDups=0.991969,chr15:101906152;E_AF_POPMAX=0;E_AF_TOT=0;G_AF_POPMAX=0.0058064516129;G_AF_TOT=0.00244910454615;C_AF_TOT=0.00244910454615;C_Hom_TOT=7;ExAC_ALL=-999;ExAC_AFR=-999;ExAC_AMR=-999;ExAC_EAS=-999;ExAC_FIN=-999;ExAC_NFE=-999;ExAC_OTH=-999;ExAC_SAS=-999;ExAC_HIGH=-999;ExAC_HOMO=-999;VC_het_cnt=-999;VC_hom_cnt=-999;VC_freq=-999;VC_Total_freq=-999;VC_Total_variant_cnt=-999;VC_Total_allele_cnt=-999;esp6500siv2_all=-999;1000g2015aug_all=-999;clinvar_20150629=-999;UK10K=-999;SIFT_score=-999;SIFT_pred=-999;Polyphen2_HDIV_score=-999;Polyphen2_HDIV_pred=-999;Polyphen2_HVAR_score=-999;Polyphen2_HVAR_pred=-999;LRT_score=-999;LRT_pred=-999;MutationTaster_score=-999;MutationTaster_pred=-999;MutationAssessor_score=-999;MutationAssessor_pred=-999;FATHMM_score=-999;FATHMM_pred=-999;PROVEAN_score=-999;PROVEAN_pred=-999;VEST3_score=-999;CADD_raw=-999;CADD_phred=-999;DANN_score=-999;fathmm-MKL_coding_score=-999;fathmm-MKL_coding_pred=-999;MetaSVM_score=-999;MetaSVM_pred=-999;MetaLR_score=-999;MetaLR_pred=-999;integrated_fitCons_score=-999;integrated_confidence_value=-999;GERP++_RS=-999;phyloP7way_vertebrate=-999;phyloP20way_mammalian=-999;phastCons7way_vertebrate=-999;phastCons20way_mammalian=-999;SiPhy_29way_logOdds=-999;avsnp144=-999;MCAP=-999;gwava_ed=0.49;BP_numREF=-999;BP_numALT=-999;BP_scoreREF=-999;BP_scoreALT=-999;BP_U2REF=-999;BP_U2ALT=-999;GS_REF=-999;GS_ALT=-999;GS_TYPE=-999;MESaccRef=-999;MESaccAlt=-999;MESdonRef=-999;MESdonAlt=-999;spidex_mt=-999;spidex_zs=-999;dbscSNV_ada=-999;dbscSNV_rf=-999;LINSIGHT_score=-999;VARIANT_TYPE=intergenic_._;ALLELE_END	GT:AD:DP:GQ:PL	./.:33,0:33:.:0,0,0	./.:14,0:14:.:0,0,0	0/0:31,0:31:15:0,15,225	0/0:32,0:32:21:0,21,315	0/0:37,0:37:0:0,0,139	0/0:53,0:53:0:0,0,579	0/0:36,0:36:0:0,0,300	0/1:10,14:24:99:126,0,181	0/0:27,0:27:0:0,0,180	0/0:41,0:41:0:0,0,116	0/0:51,0:51:48:0,48,720	0/0:44,0:44:30:0,30,450	./.:53,0:53:.:0,0,0	0/0:55,0:55:42:0,42,630	0/0:38,0:38:0:0,0,344	./.:45,0:45:.:0,0,0	0/0:60,0:60:14:0,14,1203	./.:44,0:44:.:0,0,0	0/0:52,0:52:4:0,4,960	./.:35,0:35:.:0,0,0	./.:42,0:42:.:0,0,0	0/0:55,0:55:5:0,5,995	0/0:44,0:44:0:0,0,293	./.:41,0:41:.:0,0,0	0/0:27,0:27:12:0,12,548	0/0:48,0:48:41:0,41,992	0/0:54,0:54:12:0,12,1098	0/0:39,0:39:0:0,0,13	0/0:36,0:36:0:0,0,648	0/0:30,0:30:0:0,0,262	0/0:25,0:25:0:0,0,266	0/0:62,0:62:0:0,0,706	./.:58,0:58:.:0,0,0	0/0:53,0:53:0:0,0,126	0/0:59,0:59:15:0,15,1099	0/0:50,0:50:37:0,37,1034	0/0:39,0:39:0:0,0,504	0/0:58,0:58:30:0,30,450	0/0:53,0:53:24:0,24,360	0/0:56,0:56:48:0,48,720	0/0:44,0:44:0:0,0,537	0/0:43,0:43:21:0,21,315	./.:53,0:53:.:0,0,0	0/0:51,0:51:39:0,39,585	./.:56,0:56:.:0,0,0	0/0:35,0:35:9:0,9,135
-chr1	66808	rs201752861	T	G	190.06	VQSRTrancheSNP99.95to100.00	AC=1;AF=0.024;AN=42;BaseQRankSum=-0.328;ClippingRankSum=0;DB;DP=1850;ExcessHet=4.7712;FS=0;InbreedingCoeff=0.0386;MLEAC=6;MLEAF=0.143;MQ=3.51;MQRankSum=-0.484;OLD_MULTIALLELIC=chr1:10177:A/*/C;QD=6.13;ReadPosRankSum=-0.652;SOR=0.763;VQSLOD=-18.46;culprit=MQ;ANNOVAR_DATE=2017-07-17;Func.refGene=intergenic;Gene.refGene=NONE,DDX11L1;GeneDetail.refGene=dist,NONE,dist,1697;ExonicFunc.refGene=-999;AAChange.refGene=-999;EHRF_r90=-999;cytoBand=1p36.33;genomicSuperDups=0.991969,chr15:101906152;E_AF_POPMAX=-999;E_AF_TOT=-999;G_AF_POPMAX=-999;G_AF_TOT=-999;C_AF_TOT=-999;C_Hom_TOT=-999;ExAC_ALL=-999;ExAC_AFR=-999;ExAC_AMR=-999;ExAC_EAS=-999;ExAC_FIN=-999;ExAC_NFE=-999;ExAC_OTH=-999;ExAC_SAS=-999;ExAC_HIGH=-999;ExAC_HOMO=-999;VC_het_cnt=-999;VC_hom_cnt=-999;VC_freq=-999;VC_Total_freq=-999;VC_Total_variant_cnt=-999;VC_Total_allele_cnt=-999;esp6500siv2_all=-999;1000g2015aug_all=-999;clinvar_20150629=-999;UK10K=-999;SIFT_score=-999;SIFT_pred=-999;Polyphen2_HDIV_score=-999;Polyphen2_HDIV_pred=-999;Polyphen2_HVAR_score=-999;Polyphen2_HVAR_pred=-999;LRT_score=-999;LRT_pred=-999;MutationTaster_score=-999;MutationTaster_pred=-999;MutationAssessor_score=-999;MutationAssessor_pred=-999;FATHMM_score=-999;FATHMM_pred=-999;PROVEAN_score=-999;PROVEAN_pred=-999;VEST3_score=-999;CADD_raw=-999;CADD_phred=-999;DANN_score=-999;fathmm-MKL_coding_score=-999;fathmm-MKL_coding_pred=-999;MetaSVM_score=-999;MetaSVM_pred=-999;MetaLR_score=-999;MetaLR_pred=-999;integrated_fitCons_score=-999;integrated_confidence_value=-999;GERP++_RS=-999;phyloP7way_vertebrate=-999;phyloP20way_mammalian=-999;phastCons7way_vertebrate=-999;phastCons20way_mammalian=-999;SiPhy_29way_logOdds=-999;avsnp144=-999;MCAP=-999;gwava_ed=0.49;BP_numREF=-999;BP_numALT=-999;BP_scoreREF=-999;BP_scoreALT=-999;BP_U2REF=-999;BP_U2ALT=-999;GS_REF=-999;GS_ALT=-999;GS_TYPE=-999;MESaccRef=-999;MESaccAlt=-999;MESdonRef=-999;MESdonAlt=-999;spidex_mt=-999;spidex_zs=-999;dbscSNV_ada=-999;dbscSNV_rf=-999;LINSIGHT_score=-999;VARIANT_TYPE=intergenic_._;ALLELE_END	GT:AD:DP:GQ:PL	./.:33,0:33:.:0,0,0	./.:14,0:14:.:0,0,0	./.:31,0:31:.:0,0,0	0/0:29,0:29:0:0,0,99	0/0:37,0:37:0:0,0,139	0/0:53,0:53:0:0,0,41	./.:28,0:28:.:0,0,0	0/1:10,14:24:99:126,0,181	0/0:25,0:25:0:0,0,57	0/0:41,0:41:0:0,0,116	0/0:49,0:49:0:0,0,122	./.:34,0:34:.:0,0,0	./.:53,0:53:.:0,0,0	0/0:50,0:50:0:0,0,142	0/0:34,0:34:0:0,0,175	./.:45,0:45:.:0,0,0	0/0:50,0:50:0:0,0,67	./.:44,0:44:.:0,0,0	0/.:4,0:7:36:36,47,126	./.:35,0:35:.:0,0,0	./.:42,0:42:.:0,0,0	./.:45,0:45:.:0,0,0	./.:40,0:40:.:0,0,0	./.:41,0:41:.:0,0,0	./.:24,0:24:.:0,0,0	0/0:47,0:47:0:0,0,8	0/0:48,0:48:0:0,0,231	0/0:39,0:39:0:0,0,13	./.:29,0:29:.:0,0,0	0/0:24,0:24:0:0,0,62	0/0:21,0:21:0:0,0,24	./.:54,0:54:.:0,0,0	./.:58,0:58:.:0,0,0	0/0:53,0:53:0:0,0,126	./.:56,0:56:.:0,0,0	0/0:43,0:43:0:0,0,133	0/0:38,0:38:0:0,0,105	./.:49,0:49:.:0,0,0	./.:46,0:46:.:0,0,0	0/0:45,0:45:0:0,0,216	./.:40,0:40:.:0,0,0	./.:43,0:43:.:0,0,0	./.:53,0:53:.:0,0,0	./.:50,0:50:.:0,0,0	./.:56,0:56:.:0,0,0	0/0:34,0:34:0:0,0,73
-chr1	67519	rs201752861	A	G	190.06	VQSRTrancheSNP99.95to100.00	AC=1;AF=0.024;AN=42;BaseQRankSum=-0.328;ClippingRankSum=0;DB;DP=1850;ExcessHet=4.7712;FS=0;InbreedingCoeff=0.0386;MLEAC=6;MLEAF=0.143;MQ=3.51;MQRankSum=-0.484;OLD_MULTIALLELIC=chr1:10177:A/*/C;QD=6.13;ReadPosRankSum=-0.652;SOR=0.763;VQSLOD=-18.46;culprit=MQ;ANNOVAR_DATE=2017-07-17;Func.refGene=intergenic;Gene.refGene=NONE,DDX11L1;GeneDetail.refGene=dist,NONE,dist,1697;ExonicFunc.refGene=-999;AAChange.refGene=-999;EHRF_r90=-999;cytoBand=1p36.33;genomicSuperDups=0.991969,chr15:101906152;E_AF_POPMAX=-999;E_AF_TOT=-999;G_AF_POPMAX=-999;G_AF_TOT=-999;C_AF_TOT=-999;C_Hom_TOT=-999;ExAC_ALL=-999;ExAC_AFR=-999;ExAC_AMR=-999;ExAC_EAS=-999;ExAC_FIN=-999;ExAC_NFE=-999;ExAC_OTH=-999;ExAC_SAS=-999;ExAC_HIGH=-999;ExAC_HOMO=-999;VC_het_cnt=-999;VC_hom_cnt=-999;VC_freq=-999;VC_Total_freq=-999;VC_Total_variant_cnt=-999;VC_Total_allele_cnt=-999;esp6500siv2_all=-999;1000g2015aug_all=-999;clinvar_20150629=-999;UK10K=-999;SIFT_score=-999;SIFT_pred=-999;Polyphen2_HDIV_score=-999;Polyphen2_HDIV_pred=-999;Polyphen2_HVAR_score=-999;Polyphen2_HVAR_pred=-999;LRT_score=-999;LRT_pred=-999;MutationTaster_score=-999;MutationTaster_pred=-999;MutationAssessor_score=-999;MutationAssessor_pred=-999;FATHMM_score=-999;FATHMM_pred=-999;PROVEAN_score=-999;PROVEAN_pred=-999;VEST3_score=-999;CADD_raw=-999;CADD_phred=-999;DANN_score=-999;fathmm-MKL_coding_score=-999;fathmm-MKL_coding_pred=-999;MetaSVM_score=-999;MetaSVM_pred=-999;MetaLR_score=-999;MetaLR_pred=-999;integrated_fitCons_score=-999;integrated_confidence_value=-999;GERP++_RS=-999;phyloP7way_vertebrate=-999;phyloP20way_mammalian=-999;phastCons7way_vertebrate=-999;phastCons20way_mammalian=-999;SiPhy_29way_logOdds=-999;avsnp144=-999;MCAP=-999;gwava_ed=0.49;BP_numREF=-999;BP_numALT=-999;BP_scoreREF=-999;BP_scoreALT=-999;BP_U2REF=-999;BP_U2ALT=-999;GS_REF=-999;GS_ALT=-999;GS_TYPE=-999;MESaccRef=-999;MESaccAlt=-999;MESdonRef=-999;MESdonAlt=-999;spidex_mt=-999;spidex_zs=-999;dbscSNV_ada=-999;dbscSNV_rf=-999;LINSIGHT_score=-999;VARIANT_TYPE=intergenic_._;ALLELE_END	GT:AD:DP:GQ:PL	./.:33,0:33:.:0,0,0	./.:14,0:14:.:0,0,0	./.:31,0:31:.:0,0,0	0/0:29,0:29:0:0,0,99	0/0:37,0:37:0:0,0,139	0/0:53,0:53:0:0,0,41	./.:28,0:28:.:0,0,0	0/1:10,14:24:99:126,0,181	0/0:25,0:25:0:0,0,57	0/0:41,0:41:0:0,0,116	0/0:49,0:49:0:0,0,122	./.:34,0:34:.:0,0,0	./.:53,0:53:.:0,0,0	0/0:50,0:50:0:0,0,142	0/0:34,0:34:0:0,0,175	./.:45,0:45:.:0,0,0	0/0:50,0:50:0:0,0,67	./.:44,0:44:.:0,0,0	0/.:4,0:7:36:36,47,126	./.:35,0:35:.:0,0,0	./.:42,0:42:.:0,0,0	./.:45,0:45:.:0,0,0	./.:40,0:40:.:0,0,0	./.:41,0:41:.:0,0,0	./.:24,0:24:.:0,0,0	0/0:47,0:47:0:0,0,8	0/0:48,0:48:0:0,0,231	0/0:39,0:39:0:0,0,13	./.:29,0:29:.:0,0,0	0/0:24,0:24:0:0,0,62	0/0:21,0:21:0:0,0,24	./.:54,0:54:.:0,0,0	./.:58,0:58:.:0,0,0	0/0:53,0:53:0:0,0,126	./.:56,0:56:.:0,0,0	0/0:43,0:43:0:0,0,133	0/0:38,0:38:0:0,0,105	./.:49,0:49:.:0,0,0	./.:46,0:46:.:0,0,0	0/0:45,0:45:0:0,0,216	./.:40,0:40:.:0,0,0	./.:43,0:43:.:0,0,0	./.:53,0:53:.:0,0,0	./.:50,0:50:.:0,0,0	./.:56,0:56:.:0,0,0	0/0:34,0:34:0:0,0,73
-chr1	69015	.	C	T	117.57	PASS	AC=1;AF=0.014;AN=70;BaseQRankSum=1.28;ClippingRankSum=0;DP=2027;ExcessHet=6.9804;FS=0;InbreedingCoeff=-0.1494;MLEAC=2;MLEAF=0.029;MQ=8.59;MQRankSum=0.617;NEGATIVE_TRAIN_SITE;QD=4.9;ReadPosRankSum=1.78;SOR=0.976;VQSLOD=-2.904;culprit=MQRankSum;ANNOVAR_DATE=2017-07-17;Func.refGene=intergenic;Gene.refGene=NONE,DDX11L1;GeneDetail.refGene=dist,NONE,dist,1697;ExonicFunc.refGene=-999;AAChange.refGene=-999;EHRF_r90=-999;cytoBand=1p36.33;genomicSuperDups=0.991969,chr15:101906152;E_AF_POPMAX=0;E_AF_TOT=0;G_AF_POPMAX=0.0058064516129;G_AF_TOT=0.00244910454615;C_AF_TOT=0.00244910454615;C_Hom_TOT=7;ExAC_ALL=-999;ExAC_AFR=-999;ExAC_AMR=-999;ExAC_EAS=-999;ExAC_FIN=-999;ExAC_NFE=-999;ExAC_OTH=-999;ExAC_SAS=-999;ExAC_HIGH=-999;ExAC_HOMO=-999;VC_het_cnt=-999;VC_hom_cnt=-999;VC_freq=-999;VC_Total_freq=-999;VC_Total_variant_cnt=-999;VC_Total_allele_cnt=-999;esp6500siv2_all=-999;1000g2015aug_all=-999;clinvar_20150629=-999;UK10K=-999;SIFT_score=-999;SIFT_pred=-999;Polyphen2_HDIV_score=-999;Polyphen2_HDIV_pred=-999;Polyphen2_HVAR_score=-999;Polyphen2_HVAR_pred=-999;LRT_score=-999;LRT_pred=-999;MutationTaster_score=-999;MutationTaster_pred=-999;MutationAssessor_score=-999;MutationAssessor_pred=-999;FATHMM_score=-999;FATHMM_pred=-999;PROVEAN_score=-999;PROVEAN_pred=-999;VEST3_score=-999;CADD_raw=-999;CADD_phred=-999;DANN_score=-999;fathmm-MKL_coding_score=-999;fathmm-MKL_coding_pred=-999;MetaSVM_score=-999;MetaSVM_pred=-999;MetaLR_score=-999;MetaLR_pred=-999;integrated_fitCons_score=-999;integrated_confidence_value=-999;GERP++_RS=-999;phyloP7way_vertebrate=-999;phyloP20way_mammalian=-999;phastCons7way_vertebrate=-999;phastCons20way_mammalian=-999;SiPhy_29way_logOdds=-999;avsnp144=-999;MCAP=-999;gwava_ed=0.49;BP_numREF=-999;BP_numALT=-999;BP_scoreREF=-999;BP_scoreALT=-999;BP_U2REF=-999;BP_U2ALT=-999;GS_REF=-999;GS_ALT=-999;GS_TYPE=-999;MESaccRef=-999;MESaccAlt=-999;MESdonRef=-999;MESdonAlt=-999;spidex_mt=-999;spidex_zs=-999;dbscSNV_ada=-999;dbscSNV_rf=-999;LINSIGHT_score=-999;VARIANT_TYPE=intergenic_._;ALLELE_END	GT:AD:DP:GQ:PL	./.:33,0:33:.:0,0,0	./.:14,0:14:.:0,0,0	0/0:31,0:31:15:0,15,225	0/0:32,0:32:21:0,21,315	0/0:37,0:37:0:0,0,139	0/0:53,0:53:0:0,0,579	0/0:36,0:36:0:0,0,300	0/1:10,14:24:99:126,0,181	0/0:27,0:27:0:0,0,180	0/0:41,0:41:0:0,0,116	0/0:51,0:51:48:0,48,720	0/0:44,0:44:30:0,30,450	./.:53,0:53:.:0,0,0	0/0:55,0:55:42:0,42,630	0/0:38,0:38:0:0,0,344	./.:45,0:45:.:0,0,0	0/0:60,0:60:14:0,14,1203	./.:44,0:44:.:0,0,0	0/0:52,0:52:4:0,4,960	./.:35,0:35:.:0,0,0	./.:42,0:42:.:0,0,0	0/0:55,0:55:5:0,5,995	0/0:44,0:44:0:0,0,293	./.:41,0:41:.:0,0,0	0/0:27,0:27:12:0,12,548	0/0:48,0:48:41:0,41,992	0/0:54,0:54:12:0,12,1098	0/0:39,0:39:0:0,0,13	0/0:36,0:36:0:0,0,648	0/0:30,0:30:0:0,0,262	0/0:25,0:25:0:0,0,266	0/0:62,0:62:0:0,0,706	./.:58,0:58:.:0,0,0	0/0:53,0:53:0:0,0,126	0/0:59,0:59:15:0,15,1099	0/0:50,0:50:37:0,37,1034	0/0:39,0:39:0:0,0,504	0/0:58,0:58:30:0,30,450	0/0:53,0:53:24:0,24,360	0/0:56,0:56:48:0,48,720	0/0:44,0:44:0:0,0,537	0/0:43,0:43:21:0,21,315	./.:53,0:53:.:0,0,0	0/0:51,0:51:39:0,39,585	./.:56,0:56:.:0,0,0	0/0:35,0:35:9:0,9,135
+##fileformat=VCFv4.0
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+#CHROM	POS	ID	REF	ALT	QUAL	FILTER	INFO
+chr1	65510	.	T	G	117.57	PASS	.
+chr1	66808	.	A	G	117.57	PASS	.
+chr1	69015	.	C	T	117.57	PASS	.