feat: bump and fix Mehari for SVs in varfish_export (#444)

bihealth · Sep 18, 2023 · 0ca23f6 · 0ca23f6
1 parent 98825db
commit 0ca23f6
Show file tree

Hide file tree

Showing 2 changed files with 6 additions and 1 deletion.
diff --git a/snappy_wrappers/wrappers/mehari/annotate_strucvars/wrapper.py b/snappy_wrappers/wrappers/mehari/annotate_strucvars/wrapper.py
@@ -80,6 +80,11 @@
         --output-vcf $TMPDIR/fixed_bnd_to_inv_unsorted.$num.vcf
     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
+    # Fixup MELT header
+    sed -i -e "s/seperated by '..'/separated by '\\\\\\\\|'/" $TMPDIR/fixed_bnd_to_inv_unsorted.$num.vcf
+
     # Add the missing "GT" tag
     echo '##FORMAT=<ID=GT,Number=1,Type=String,Description="Genotype">' \
     > $TMPDIR/header.gt.txt

diff --git a/snappy_wrappers/wrappers/mehari/environment.yaml b/snappy_wrappers/wrappers/mehari/environment.yaml
@@ -5,7 +5,7 @@ dependencies:
   - bcftools >=1.9
   - htslib >=1.9
   - samtools >=1.9
-  - mehari ==0.6.2
+  - mehari ==0.7.0
   - jq
   - vcfpy
   - pysam