rm flag 0x1 for singleEnd

wbaopaul · Nov 9, 2022 · a381e9d · a381e9d
1 parent 4564c50
commit a381e9d
Showing 1 changed file with 4 additions and 9 deletions.
diff --git a/scripts/mapping.sh b/scripts/mapping.sh
@@ -47,21 +47,16 @@ rm ${mapRes_dir}/${OUTPUT_PREFIX}.positionsort0.bam
 ${SAMTOOLS_PATH}/samtools index -@ $ncore ${mapRes_dir}/${OUTPUT_PREFIX}.positionsort.bam 
 
 
-
 ## filtering low quality and/or deplicates for downstreame analysis
-flag0=0x2
 if [ ${isSingleEnd} = 'TRUE' ]; then
-    flag0=0x1
+    ${SAMTOOLS_PATH}/samtools view -b -h -q $MAPQ -@ $ncore ${mapRes_dir}/${OUTPUT_PREFIX}.positionsort.bam -o ${mapRes_dir}/${OUTPUT_PREFIX}.positionsort.MAPQ${MAPQ}.bam 
+else
+     ${SAMTOOLS_PATH}/samtools view -f 0x2 -b -h -q $MAPQ -@ $ncore ${mapRes_dir}/${OUTPUT_PREFIX}.positionsort.bam -o ${mapRes_dir}/${OUTPUT_PREFIX}.positionsort.MAPQ${MAPQ}.bam 
 fi
 
-${SAMTOOLS_PATH}/samtools view -f $flag0 -b -h -q 30 -@ $ncore ${mapRes_dir}/${OUTPUT_PREFIX}.positionsort.bam -o ${mapRes_dir}/${OUTPUT_PREFIX}.positionsort.MAPQ30.bam 
-${SAMTOOLS_PATH}/samtools index -@ $ncore ${mapRes_dir}/${OUTPUT_PREFIX}.positionsort.MAPQ30.bam 
+${SAMTOOLS_PATH}/samtools index -@ $ncore ${mapRes_dir}/${OUTPUT_PREFIX}.positionsort.MAPQ${MAPQ}.bam 
 
 
-if [ $MAPQ -ne 30 ]; then
-     ${SAMTOOLS_PATH}/samtools view -f $flag0 -b -h -q $MAPQ -@ $ncore ${mapRes_dir}/${OUTPUT_PREFIX}.positionsort.bam -o ${mapRes_dir}/${OUTPUT_PREFIX}.positionsort.MAPQ${MAPQ}.bam 
-fi
-
 
 ## mapping stats
 echo "Summarizing mapping stats ..."