Merge pull request #7 from GruA/master

Update mapq0_vcf_filter.sh

mapq0_vcf_filter.sh

@@ -1,29 +1,30 @@
 #!/bin/bash
 set -e
 
-outvcf=$1
+# arguments
+outdir=$1
 vcf=$2
 bam=$3
 mapq0perc=$4
 sample_name=$5
-outdir=$(dirname "$outvcf")
 
-count=0;
+# for each variant
+# define number of reads with MAPQ=0 
 zgrep -v "^#" "$vcf" | cut -f 1,2 | while read chr pos;do
     pysamstats --type mapq --chromosome $chr --start $pos --end $((pos+1)) "$bam"  | grep $pos | cut -f 1,2,5 >>$outdir/mapq0counts
-    count=$((count+1))
 done
 
 
-if [[ $count -eq 0 ]];then
+if [[ ! -z $outdir/mapq0counts ]];then
+    #process each line, add MQ0 and MQ0PERC values to the right sample, and add MAPQ0 filter when needed
+    python3 /usr/bin/add_mq0_and_filter.py $vcf $outdir/mapq0counts $sample_name $mapq0perc $outdir/mapq_filtered.vcf.gz
+else
     #no sites to process, just make a copy of the (empty) vcf.
     #handle both gzipped and unzipped vcfs
+    echo "There is no variant to process. The input VCF file will be copied."
     if [[ ${vcf: -3} == ".gz" ]];then 
         cp $vcf $outdir/mapq_filtered.vcf.gz
     else
         gzip -c $vcf > $outdir/mapq_filtered.vcf.gz
     fi
-else 
-    #process each line, add MQ0 and MQ0PERC values to the right sample, and add MAPQ0 filter when needed
-    python3 /usr/bin/add_mq0_and_filter.py $vcf mapq0counts $sample_name mapq0perc $outdir/mapq_filtered.vcf.gz
 fi