Incorportate batch of logging support changes

.gitignore

@@ -3,4 +3,4 @@
 /.gradle/
 /build/
 .metadata
-.idea
+.idea

.project

@@ -20,4 +20,4 @@
 		<nature>org.eclipse.jdt.core.javanature</nature>
 		<nature>org.eclipse.buildship.core.gradleprojectnature</nature>
 	</natures>
-</projectDescription>
+</projectDescription>

gradlew

@@ -241,4 +241,4 @@ eval "set -- $(
         tr '\n' ' '
     )" '"$@"'
 
-exec "$JAVACMD" "$@"
+exec "$JAVACMD" "$@"

gradlew.bat

@@ -89,4 +89,4 @@ exit /b %EXIT_CODE%
 :mainEnd
 if "%OS%"=="Windows_NT" endlocal
 
-:omega
+:omega

src/main/java/scriptmanager/cli/BAM_Format_Converter/BAMtoBEDCLI.java

@@ -9,6 +9,7 @@
 
 import java.io.File;
 import java.io.IOException;
+import java.io.PrintStream;
 
 import scriptmanager.objects.ToolDescriptions;
 import scriptmanager.util.ExtensionFileFilter;
@@ -115,11 +116,11 @@ private String validateInput() throws IOException {
 		}
 		//set default output filename
 		if(output==null &&  !stdout){
-			if(STRAND==0){ output = new File( bamFile.getName().split("\\.")[0] + "_READ1.bed" ); }
-			else if(STRAND==1){ output = new File( bamFile.getName().split("\\.")[0] + "_READ2.bed" ); }
-			else if(STRAND==2){ output = new File( bamFile.getName().split("\\.")[0] + "_COMBINED.bed" ); }
-			else if(STRAND==3){ output = new File( bamFile.getName().split("\\.")[0] + "_MIDPOINT.bed" ); }
-			else if(STRAND==4){ output = new File( bamFile.getName().split("\\.")[0] + "_FRAGMENT.bed" ); }
+			if (STRAND==0) { output = new File( ExtensionFileFilter.stripExtensionIgnoreGZ(bamFile) + "_READ1.bed" + (gzOutput ? ".gz" : "")); }
+			else if (STRAND==1) { output = new File( ExtensionFileFilter.stripExtensionIgnoreGZ(bamFile) + "_READ2.bed" + (gzOutput ? ".gz" : "")); }
+			else if (STRAND==2) { output = new File( ExtensionFileFilter.stripExtensionIgnoreGZ(bamFile) + "_COMBINED.bed" + (gzOutput ? ".gz" : "")); }
+			else if (STRAND==3) { output = new File( ExtensionFileFilter.stripExtensionIgnoreGZ(bamFile) + "_MIDPOINT.bed" + (gzOutput ? ".gz" : "")); }
+			else if (STRAND==4) { output = new File( ExtensionFileFilter.stripExtensionIgnoreGZ(bamFile) + "_FRAGMENT.bed" + (gzOutput ? ".gz" : "")); }
 			else { r += "(!)Somehow invalid STRAND!This error should never print. Check code if it does.\n"; }
 		//check stdout and output not both selected
 		}else if(stdout){
@@ -143,4 +144,27 @@ private String validateInput() throws IOException {
 
 		return(r);
 	}
+	public static String getCLIcommand(File BAM, File output, int strand, int pair, int min, int max) {
+		String command = "java -jar $SCRIPTMANAGER bam-format-converter bam-to-bed";
+		command += " " + BAM.getAbsolutePath();
+		command += " -o " + output.getAbsolutePath();
+		if (strand == 0) {
+			command += " -1 ";
+		} else if (strand == 1) {
+			command += " -2 ";
+		} else if (strand == 2) {
+			command += " -a ";
+		} else if (strand == 3 )  {
+			command += " -m ";
+		} else if (strand == 4)  {
+			command += " -f ";
+		}
+		command += pair != 0 ? " -p" : "";
+		if (min != -9999) {
+			command += " -n " + min;
+		} else if (max != -9999) {
+			command += " -x " + max;
+		}
+		return command;
+	}
 }

src/main/java/scriptmanager/cli/BAM_Format_Converter/BAMtoGFFCLI.java

@@ -9,6 +9,7 @@
 
 import java.io.File;
 import java.io.IOException;
+import java.io.PrintStream;
 
 import scriptmanager.objects.ToolDescriptions;
 import scriptmanager.util.ExtensionFileFilter;
@@ -115,11 +116,11 @@ private String validateInput() throws IOException {
 		}
 		//set default output filename
 		if(output==null &&  !stdout){
-			if(STRAND==0){ output = new File( bamFile.getName().split("\\.")[0] + "_READ1.gff" ); }
-			else if(STRAND==1){ output = new File( bamFile.getName().split("\\.")[0] + "_READ2.gff" ); }
-			else if(STRAND==2){ output = new File( bamFile.getName().split("\\.")[0] + "_COMBINED.gff" ); }
-			else if(STRAND==3){ output = new File( bamFile.getName().split("\\.")[0] + "_MIDPOINT.gff" ); }
-			else if(STRAND==4){ output = new File( bamFile.getName().split("\\.")[0] + "_FRAGMENT.gff" ); }
+			if (STRAND==0) { output = new File( ExtensionFileFilter.stripExtensionIgnoreGZ(bamFile) + "_READ1.gff" + (gzOutput ? ".gz" : "")); }
+			else if (STRAND==1) { output = new File( ExtensionFileFilter.stripExtensionIgnoreGZ(bamFile) + "_READ2.gff" + (gzOutput ? ".gz" : "")); }
+			else if (STRAND==2) { output = new File( ExtensionFileFilter.stripExtensionIgnoreGZ(bamFile) + "_COMBINED.gff" + (gzOutput ? ".gz" : "")); }
+			else if (STRAND==3) { output = new File( ExtensionFileFilter.stripExtensionIgnoreGZ(bamFile) + "_MIDPOINT.gff" + (gzOutput ? ".gz" : "")); }
+			else if (STRAND==4) { output = new File( ExtensionFileFilter.stripExtensionIgnoreGZ(bamFile) + "_FRAGMENT.gff" + (gzOutput ? ".gz" : "")); }
 			else { r += "(!)Somehow invalid STRAND!This error should never print. Check code if it does.\n"; }
 		//check stdout and output not both selected
 		}else if(stdout){
@@ -143,4 +144,27 @@ private String validateInput() throws IOException {
 
 		return(r);
 	}
+	public static String getCLIcommand(File BAM, File output, int strand, int pair, int min, int max) {
+		String command = "java -jar $SCRIPTMANAGER bam-format-converter bam-to-gff";
+		command += " " + BAM.getAbsolutePath();
+		command += " -o " + output.getAbsolutePath();
+		if (strand == 0) {
+			command += " -1 ";
+		} else if (strand == 1) {
+			command += " -2 ";
+		} else if (strand == 2) {
+			command += " -a ";
+		} else if (strand == 3 )  {
+			command += " -m ";
+		} else if (strand == 4)  {
+			command += " -f ";
+		}
+		command += pair != 0 ? " -p" : "";
+		if (min != -9999) {
+			command += " -n " + min;
+		} else if (max != -9999) {
+			command += " -x " + max;
+		}
+		return command;
+	}
 }

src/main/java/scriptmanager/cli/BAM_Format_Converter/BAMtobedGraphCLI.java

@@ -9,6 +9,7 @@
 
 import java.io.File;
 import java.io.IOException;
+import java.io.PrintStream;
 
 import scriptmanager.objects.ToolDescriptions;
 import scriptmanager.util.ExtensionFileFilter;
@@ -138,4 +139,25 @@ private String validateInput() throws IOException {
 
 		return(r);
 	}
+	public static String getCLIcommand(File BAM, File output, int strand, int pair, int min, int max){
+		String command = "java -jar $SCRIPTMANAGER bam-format-converter bam-to-bedgraph";
+		command += " " + BAM.getAbsolutePath();
+		command += " -o " + output.getAbsolutePath();
+		if (strand == 0) {
+			command += " -1 ";
+		} else if (strand == 1) {
+			command += " -2 ";
+		} else if (strand == 2) {
+			command += " -a ";
+		} else if (strand == 3 )  {
+			command += " -m ";
+		}
+		command += pair != 0 ? " -p" : "";
+		if (min != -9999) {
+			command += " -n " + min;
+		} else if (max != -9999) {
+			command += " -x " + max;
+		}
+		return command;
+	}
 }

src/main/java/scriptmanager/cli/BAM_Format_Converter/BAMtoscIDXCLI.java

@@ -9,6 +9,7 @@
 
 import java.io.File;
 import java.io.IOException;
+import java.io.PrintStream;
 
 import scriptmanager.objects.ToolDescriptions;
 import scriptmanager.util.ExtensionFileFilter;
@@ -111,11 +112,11 @@ private String validateInput() throws IOException {
 		}
 		//set default output filename
 		if(output==null &&  !stdout){
-			if(STRAND==0){ output = new File( bamFile.getName().split("\\.")[0] + "_READ1.tab" ); }
-			else if(STRAND==1){ output = new File( bamFile.getName().split("\\.")[0] + "_READ2.tab" ); }
-			else if(STRAND==2){ output = new File( bamFile.getName().split("\\.")[0] + "_COMBINED.tab" ); }
-			else if(STRAND==3){ output = new File( bamFile.getName().split("\\.")[0] + "_MIDPOINT.tab" ); }
-			else if(STRAND==4){ output = new File( bamFile.getName().split("\\.")[0] + "_FRAGMENT.tab" ); }
+			if (STRAND==0) { output = new File( ExtensionFileFilter.stripExtensionIgnoreGZ(bamFile) + "_READ1.tab" + (gzOutput ? ".gz" : "")); }
+			else if (STRAND==1) { output = new File( ExtensionFileFilter.stripExtensionIgnoreGZ(bamFile) + "_READ2.tab" + (gzOutput ? ".gz" : "")); }
+			else if (STRAND==2) { output = new File( ExtensionFileFilter.stripExtensionIgnoreGZ(bamFile) + "_COMBINED.tab" + (gzOutput ? ".gz" : "")); }
+			else if (STRAND==3) { output = new File( ExtensionFileFilter.stripExtensionIgnoreGZ(bamFile) + "_MIDPOINT.tab" + (gzOutput ? ".gz" : "")); }
+			else if (STRAND==4) { output = new File( ExtensionFileFilter.stripExtensionIgnoreGZ(bamFile) + "_FRAGMENT.tab" + (gzOutput ? ".gz" : "")); }
 			else { r += "(!)Somehow invalid STRAND!This error should never print. Check code if it does.\n"; }
 		//check stdout and output not both selected
 		}else if(stdout){
@@ -136,7 +137,29 @@ private String validateInput() throws IOException {
 		if( MAX_INSERT<MIN_INSERT && MIN_INSERT!=-9999 && MAX_INSERT!=-9999){ r += "MAX_INSERT must be larger/equal to MIN_INSERT: " + MIN_INSERT + "," + MAX_INSERT + "\n"; }
 		// turn pair status boolean into int
 		PAIR = matePair ? 1 : 0;
-
 		return(r);
 	}
+	public static String getCLIcommand(File BAM, File output, int strand, int pair, int min, int max) {
+		String command = "java -jar $SCRIPTMANAGER bam-format-converter bam-to-scidx";
+		System.out.println(output);
+		System.out.println(BAM);
+		command += " " + BAM.getAbsolutePath();
+		command += " -o " + output.getAbsolutePath();
+		if (strand == 0) {
+			command += " -1 ";
+		} else if (strand == 1) {
+			command += " -2 ";
+		} else if (strand == 2) {
+			command += " -a ";
+		} else if (strand == 3 )  {
+			command += " -m ";
+		}
+		command += pair != 0 ? " -p" : "";
+		if (min != -9999) {
+			command += " -n " + min;
+		} else if (max != -9999) {
+			command += " -x " + max;
+		}
+		return command;
+	}
 }

src/main/java/scriptmanager/cli/BAM_Manipulation/BAIIndexerCLI.java

@@ -3,6 +3,7 @@
 import picocli.CommandLine.Command;
 
 import java.util.concurrent.Callable;
+import java.io.File;
 
 import scriptmanager.objects.ToolDescriptions;
 
@@ -37,4 +38,18 @@ public Integer call() throws Exception {
 		System.exit(1);
 		return(1);
 	}
+
+	/**
+	 * Reconstruct CLI command
+	 * 
+	 * @param input the BAM file to index
+	 * @return command line to execute with formatted inputs
+	 */
+	public static String getCLIcommand(File input) {
+		String command = "java -jar $PICARD BuildBamIndex";
+		command += " INPUT=" + input.getAbsolutePath();
+		command += " OUTPUT=" + input.getAbsolutePath() + ".bai";
+		return command;
+	}
+
 }

src/main/java/scriptmanager/cli/BAM_Manipulation/BAMRemoveDupCLI.java

@@ -25,11 +25,6 @@
 	exitCodeOnExecutionException = 1)
 public class BAMRemoveDupCLI implements Callable<Integer> {
 
-	/**
-	 * Creates a new BAMRemoveDupCLI object
-	 */
-	public BAMRemoveDupCLI(){}
-
 	/**
 	 * Runs when this subcommand is called, running script in respective script package with user defined arguments
 	 * @throws IOException Invalid file or parameters
@@ -44,19 +39,21 @@ public Integer call() throws Exception {
 	}
 
 	/**
-	 * Returns picard command for generating running MarkDuplicates 
-	 * @param BAM BAM file ot be marked
-	 * @param removeDuplicates If duplicate reads should be removed
-	 * @param OUTPUT Ouput BAM file
-	 * @param METRICS .metricts file for outputting stats
-	 * @return Picard command for running MarkDuplicates 
+	 * Reconstruct CLI command (Picard)
+	 * 
+	 * @param input            the BAM file to mark/remove duplicates for
+	 * @param removeDuplicates whether to remove or just mark duplicates
+	 * @param output           the marked/filtered BAM output file
+	 * @param metrics          the output metrics file with information about the
+	 *                         deduplicates
+	 * @return command line to execute with formatted inputs
 	 */
-	public static String getCLIcommand(File BAM, boolean removeDuplicates, File OUTPUT, File METRICS) {
+	public static String getCLIcommand(File input, boolean removeDuplicates, File output, File metrics) {
 		String command = "java -jar $PICARD MarkDuplicates";
-		command += " INPUT=" + BAM.getAbsolutePath();
-		command += " OUTPUT=" + OUTPUT.getAbsolutePath();
-		command += " METRICS_FILE=" + METRICS.getAbsolutePath();
-		command += removeDuplicates ? "REMOVE_DUPLICATES=true" : "REMOVE_DUPLICATES=false";
+		command += " INPUT=" + input.getAbsolutePath();
+		command += " OUTPUT=" + output.getAbsolutePath();
+		command += " METRICS_FILE=" + metrics.getAbsolutePath();
+		command += removeDuplicates ? " REMOVE_DUPLICATES=true" : " REMOVE_DUPLICATES=false";
 		return(command);
 	}
 }

src/main/java/scriptmanager/cli/BAM_Manipulation/FilterforPIPseqCLI.java

@@ -115,4 +115,22 @@ private String validateInput() throws IOException {
 
 		return (r);
 	}
+
+	/**
+	 * Reconstruct CLI command
+	 * 
+	 * @param BAM    the BAM file to filter
+	 * @param GENOME the genomic FASTA reference file (should match BAM header)
+	 * @param OUTPUT the output BAM file
+	 * @param txtSeq the IUPAC string to filter by
+	 * @return command line to execute with formatted inputs
+	 */
+	public static String getCLIcommand(File BAM, File GENOME, File OUTPUT, String txtSeq) {
+		String command = "java -jar $SCRIPTMANAGER bam-manipulation filter-pip-seq";
+		command += " " + GENOME.getAbsolutePath();
+		command += " " + BAM.getAbsolutePath();
+		command += " -o " + OUTPUT.getAbsolutePath();
+		command += " -f " + txtSeq;
+		return command;
+	}
 }

src/main/java/scriptmanager/cli/BAM_Manipulation/MergeBAMCLI.java

@@ -2,7 +2,9 @@
 
 import picocli.CommandLine.Command;
 
+import java.util.ArrayList;
 import java.util.concurrent.Callable;
+import java.io.File;
 
 import scriptmanager.objects.ToolDescriptions;
 
@@ -38,4 +40,25 @@ public Integer call() throws Exception {
 		System.exit(1);
 		return(1);
 	}
+
+	/**
+	 * Reconstruct CLI command
+	 * 
+	 * @param inputs          the list of input BAM files to merge (corresponds to
+	 *                        several INPUT values)
+	 * @param output          the output file for the merged BAM file (corresponds
+	 *                        to OUTPUT)
+	 * @param useMultipleCpus whether or not to parallelize (corresponds to
+	 *                        USE_THREADING)
+	 * @return command line to execute with formatted inputs
+	 */
+	public static String getCLIcommand(ArrayList<File> inputs, File output, boolean useMultipleCpus) {
+		String command = "java -jar $PICARD MergeSamFiles";
+		for (File in : inputs) {
+			command += " INPUT=" + in.getAbsolutePath();
+		}
+		command += " OUTPUT=" + output.getAbsolutePath();
+		command += useMultipleCpus ? " USE_THREADING=true" : " USE_THREADING=false";
+		return command;
+	}
 }

src/main/java/scriptmanager/cli/BAM_Manipulation/SortBAMCLI.java

@@ -5,6 +5,10 @@
 import java.io.IOException;
 import java.util.concurrent.Callable;
 
+import htsjdk.samtools.SAMFileHeader;
+
+import java.io.File;
+
 import scriptmanager.objects.ToolDescriptions;
 
 /**
@@ -33,4 +37,19 @@ public Integer call() throws Exception {
 		System.exit(1);
 		return(1);
 	}
+
+	/**
+	 * Reconstruct CLI command
+	 * 
+	 * @param input  the BAM file to be sorted (corresponds to INPUT)
+	 * @param output the file to write the sorted BAM to (corresponds to OUTPUT)
+	 * @return command line to execute with formatted inputs
+	 */
+	public static String getCLIcommand(File input, File output) {
+		String command = "java -jar $PICARD SortSam";
+		command += " INPUT=" + input.getAbsolutePath();
+		command += " OUTPUT=" + output.getAbsolutePath();
+		command += " SORT_ORDER=" + SAMFileHeader.SortOrder.coordinate;
+		return(command);
+	}
 }