Fixing annotate_pvcf_cov

I wasn't preserving variants

Author: ACEnglish

variants/diversity/mk_convert_cmds.sh

@@ -1,10 +1,11 @@
+in_files=$@
 mkdir -p jobs
 mkdir -p utmos_files
-for i in ../data/parts/*.bcf.gz
+for i in $in_files
 do
     bname=$(basename $i)
-    job_name=jobs/${bname%.bcf.gz}_cvt.sh
+    job_name=jobs/${bname%.vcf.gz}_cvt.sh
     echo "#!/bin/bash" > ${job_name}
-    echo "bcftools view -i \"SVLEN == '.'\" $i | bcftools filter -S . -e \"FT == 'F'\" | utmos convert --lowmem /dev/stdin utmos_files/${bname}_utmos_small.jl" >> ${job_name}
-    echo "bcftools view -i \"SVLEN != '.'\" $i | bcftools filter -S . -e \"FT == 'F'\" | utmos convert --lowmem /dev/stdin utmos_files/${bname}_utmos_big.jl" >> ${job_name}
+    echo "bcftools view -i \"SVLEN == '.'\" $i | bcftools filter -S . -e \"FT == 'FAIL'\" | utmos convert --lowmem /dev/stdin utmos_files/${bname}_utmos_small.jl" >> ${job_name}
+    echo "bcftools view -i \"SVLEN != '.'\" $i | bcftools filter -S . -e \"FT == 'FAIL'\" | utmos convert --lowmem /dev/stdin utmos_files/${bname}_utmos_big.jl" >> ${job_name}
 done

variants/scripts/annotate_pvcf_cov.py

@@ -51,11 +51,14 @@
         is_single2 = u_cov2 == 1 and d_cov2 == 1
         if is_single1 and is_single2:
             entry.samples[sample]["FT"] = 'PASS'
+            gt1, gt2 = entry.samples[sample]["GT"]
+            gt1 = 0 if gt1 is None else gt1
+            gt2 = 0 if gt2 is None else gt2
         else:
             entry.samples[sample]["FT"] = 'FAIL'
+            gt1 = 0 if u_cov1 >= 1 and d_cov1 >= 1 else None
+            gt2 = 0 if u_cov2 >= 1 and u_cov2 >= 1 else None
         # Set the genotype
-        gt1 = 0 if u_cov1 >= 1 and d_cov1 >= 1 else None
-        gt2 = 0 if u_cov2 >= 1 and u_cov2 >= 1 else None
         entry.samples[sample]["GT"] = (gt1, gt2)
         entry.samples[sample]["AD"] = (max(u_cov1, d_cov1), max(u_cov2, d_cov2))
     out.write(entry)