From 95b451b1b259b24c29b0f9453a521fcc2f1b92ba Mon Sep 17 00:00:00 2001
From: Manuel Holtgrewe <manuel.holtgrewe@bih-charite.de>
Date: Mon, 27 May 2024 10:23:57 +0200
Subject: [PATCH] fix: bump mehari to v0.25.5 for bugs fixed there (#510)

---
 .../mehari/annotate_seqvars/wrapper.py         | 18 ++++++++++++++----
 .../wrappers/mehari/environment.yaml           |  2 +-
 2 files changed, 15 insertions(+), 5 deletions(-)

diff --git a/snappy_wrappers/wrappers/mehari/annotate_seqvars/wrapper.py b/snappy_wrappers/wrappers/mehari/annotate_seqvars/wrapper.py
index dce342909..ceea699b4 100644
--- a/snappy_wrappers/wrappers/mehari/annotate_seqvars/wrapper.py
+++ b/snappy_wrappers/wrappers/mehari/annotate_seqvars/wrapper.py
@@ -58,21 +58,31 @@
 
 # Run actual tools --------------------------------------------------------------------------------
 
-# Extract around BED file, if given.
+# Extract around BED file, if given.  Otherwise, "just" normalize.
 if [[ -n "{export_config[path_exon_bed]}" ]] && [[ "{export_config[path_exon_bed]}" != "None" ]]; then
     set -e
     bcftools view \
         -R {export_config[path_exon_bed]} \
         {snakemake.input.vcf} \
+    | bcftools norm \
+        -m -any \
+        --force \
+        --fasta-ref {snakemake.config[static_data_config][reference][path]} \
     | bcftools sort -T $TMPDIR \
-    | bcftools norm -d all \
     | bgzip -c \
     > $TMPDIR/tmp.vcf.gz
     tabix -f $TMPDIR/tmp.vcf.gz
 else
     set -e
-    ln -sr {snakemake.input.vcf} $TMPDIR/tmp.vcf.gz
-    ln -sr {snakemake.input.vcf}.tbi $TMPDIR/tmp.vcf.gz.tbi
+    bcftools norm \
+        -m -any \
+        --force \
+        --fasta-ref {snakemake.config[static_data_config][reference][path]} \
+        {snakemake.input.vcf} \
+    | bcftools sort -T $TMPDIR \
+    | bgzip -c \
+    > $TMPDIR/tmp.vcf.gz
+    tabix -f $TMPDIR/tmp.vcf.gz
 fi
 
 # Perform Mehari sequence variant annotation.
diff --git a/snappy_wrappers/wrappers/mehari/environment.yaml b/snappy_wrappers/wrappers/mehari/environment.yaml
index 1682b165a..8fb73b56b 100644
--- a/snappy_wrappers/wrappers/mehari/environment.yaml
+++ b/snappy_wrappers/wrappers/mehari/environment.yaml
@@ -5,7 +5,7 @@ dependencies:
   - bcftools==1.19
   - htslib==1.19.1
   - samtools==1.19.2
-  - mehari==0.21.1
+  - mehari==0.25.5
   - jq==1.7.1
   - vcfpy==0.13.8
   - pysam==0.22.0