fix: mehari wrapper vcf preprocessing does not actually fix info svle…

…n header (#450) (#451)
bihealth · Oct 11, 2023 · 55146c7 · 55146c7
1 parent 46b2303
commit 55146c7
Showing 1 changed file with 2 additions and 2 deletions.
diff --git a/snappy_wrappers/wrappers/mehari/annotate_strucvars/wrapper.py b/snappy_wrappers/wrappers/mehari/annotate_strucvars/wrapper.py
@@ -81,9 +81,9 @@
     bcftools sort -o $TMPDIR/fixed_bnd_to_inv.$num.vcf $TMPDIR/fixed_bnd_to_inv_unsorted.$num.vcf
 
     # Fixup SVLEN=1 to SVLEN=.
-    sed -i -e 's/ID=SVLEN,Number=1/ID=SVLEN,Number=./g' $TMPDIR/fixed_bnd_to_inv_unsorted.$num.vcf
+    sed -i -e 's/ID=SVLEN,Number=1/ID=SVLEN,Number=./g' $TMPDIR/fixed_bnd_to_inv.$num.vcf
     # Fixup MELT header
-    sed -i -e "s/seperated by '..'/separated by '\\\\\\\\|'/" $TMPDIR/fixed_bnd_to_inv_unsorted.$num.vcf
+    sed -i -e "s/seperated by '..'/separated by '\\\\\\\\|'/" $TMPDIR/fixed_bnd_to_inv.$num.vcf
 
     # Add the missing "GT" tag
     echo '##FORMAT=<ID=GT,Number=1,Type=String,Description="Genotype">' \