From 0ca23f645d38130ac08f85b1861ae795f62f96b2 Mon Sep 17 00:00:00 2001
From: Manuel Holtgrewe <manuel.holtgrewe@bih-charite.de>
Date: Mon, 18 Sep 2023 15:46:47 +0200
Subject: [PATCH] feat: bump and fix Mehari for SVs in varfish_export (#444)

---
 .../wrappers/mehari/annotate_strucvars/wrapper.py            | 5 +++++
 snappy_wrappers/wrappers/mehari/environment.yaml             | 2 +-
 2 files changed, 6 insertions(+), 1 deletion(-)

diff --git a/snappy_wrappers/wrappers/mehari/annotate_strucvars/wrapper.py b/snappy_wrappers/wrappers/mehari/annotate_strucvars/wrapper.py
index 671048469..7b5f9386f 100644
--- 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
index 8461e28b2..58ca64f7a 100644
--- 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