correct a bug in process_with_bam module

wbaopaul · Feb 17, 2022 · db30e00 · db30e00
1 parent b951aa5
commit db30e00
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Showing 2 changed files with 20 additions and 8 deletions.
diff --git a/complete_update_history.md b/complete_update_history.md
@@ -1,7 +1,8 @@
 ## Complete Update History
 - Version 1.4.2 released
     * correct bugs in processing single-end sequencing data
-    * correct minor underestimate of overall FrIP in the qc report
+    * correct minor underestimate of overall FrIP in the qc *report*
+    * correst a bug in *process_with_bam* module
 - Version 1.4.1 released
     * *qc_per_barcode*: add tss enrichment score per cell into the QC metrics
     * update tutorial

diff --git a/scripts/bam2qc.sh b/scripts/bam2qc.sh
@@ -14,8 +14,15 @@ mapRes_dir="${OUTPUT_DIR}/mapping_result"
 mkdir -p $mapRes_dir
 curr_dir=`dirname $0`
 
+## if input bam not under default scatac-pro output file path,
+## create a soft link for it
+position_sort_bam=${mapRes_dir}/${OUTPUT_PREFIX}.positionsort.bam
+if [[ ! -f $position_sort_bam ]]; then
+    ln -s $bam_file $position_sort_bam
+fi
+
 ## check whether the bam file is position sorted or not
-isort=`samtools view $bam_file -H | grep HD | cut -f3`
+isort=`samtools view $position_sort_bam -H | grep HD | cut -f3`
 ncore=$(nproc --all)
 ncore=$(($ncore - 1))
  ## if the input is position sorted, suppose it's duplicates marked
@@ -37,21 +44,25 @@ if [[ "$isort" != "SO:coordinate"  ]]; then
     ## mark duplicates
     ${SAMTOOLS_PATH}/samtools markdup -@ $ncore ${mapRes_dir}/${OUTPUT_PREFIX}.positionsort0.bam ${mapRes_dir}/${OUTPUT_PREFIX}.positionsort.bam
     rm ${mapRes_dir}/${OUTPUT_PREFIX}.positionsort0.bam
-    position_sort_bam=${mapRes_dir}/${OUTPUT_PREFIX}.positionsort.bam
-else
-    position_sort_bam=$bam_file
 fi
 
-${SAMTOOLS_PATH}/samtools index -@ $ncore $position_sort_bam 
+if [[ ! -f ${position_sort_bam}.bai ]];then
+    ${SAMTOOLS_PATH}/samtools index -@ $ncore $position_sort_bam
+fi
 
 
 ## filtering low quality and/or deplicates for downstreame analysis
-${SAMTOOLS_PATH}/samtools view -f 0x2 -b -h -q 30 -@ $ncore $position_sort_bam -o ${mapRes_dir}/${OUTPUT_PREFIX}.positionsort.MAPQ30.bam 
+flag0=0x2
+if [ ${isSingleEnd} = 'TRUE' ]; then
+    flag0=0x1
+fi
+
+${SAMTOOLS_PATH}/samtools view -f $flag0 -b -h -q 30 -@ $ncore $position_sort_bam -o ${mapRes_dir}/${OUTPUT_PREFIX}.positionsort.MAPQ30.bam 
 ${SAMTOOLS_PATH}/samtools index -@ $ncore ${mapRes_dir}/${OUTPUT_PREFIX}.positionsort.MAPQ30.bam 
 
 
 if [ $MAPQ -ne 30 ]; then
-     ${SAMTOOLS_PATH}/samtools view -f 0x2 -b -h -q $MAPQ -@ $ncore $position_sort_bam -o ${mapRes_dir}/${OUTPUT_PREFIX}.positionsort.MAPQ${MAPQ}.bam 
+     ${SAMTOOLS_PATH}/samtools view -f $flag0 -b -h -q $MAPQ -@ $ncore $position_sort_bam -o ${mapRes_dir}/${OUTPUT_PREFIX}.positionsort.MAPQ${MAPQ}.bam 
 fi