[med-svn] [Git][med-team/snippy][master] Work with snpeff >= 5.1

[Andreas Tille (@tille)]

Andreas Tille pushed to branch master at Debian Med / snippy


Commits:
dff0fc3f by Andreas Tille at 2023-12-06T17:16:34+01:00
Work with snpeff >= 5.1

- - - - -


3 changed files:

- debian/changelog
- debian/patches/series
- + debian/patches/snpeff_v5.1+.patch


Changes:

=====================================
debian/changelog
=====================================
@@ -1,3 +1,10 @@
+snippy (4.6.0+dfsg-4) UNRELEASED; urgency=medium
+
+  * Work with snpeff >= 5.1
+    Closes: #1029202
+
+ -- Andreas Tille <tille at debian.org>  Wed, 06 Dec 2023 17:07:28 +0100
+
 snippy (4.6.0+dfsg-3) unstable; urgency=medium
 
   * Restrict autopkgtest to "Architecture: amd64 arm64" since the


=====================================
debian/patches/series
=====================================
@@ -1,2 +1,3 @@
 debian_packaged_libs.patch
 snpeff.config.patch
+snpeff_v5.1+.patch


=====================================
debian/patches/snpeff_v5.1+.patch
=====================================
@@ -0,0 +1,29 @@
+Description: Work with snpeff >= 5.1
+  According to snpEff upstream there is a problem with poorly annotated GFF files
+  You can read more about this in this section of the documentation: https://pcingola.github.io/SnpEff/snpeff/build_db/#step-3-checking-the-database
+  see also snpEff Github issue #455
+Origin: https://github.com/pcingola/SnpEff/issues/455
+Bug-Debian: https://bugs.debian.org/1029202
+Author: Andreas Tille <tille at debian.org>
+Last-Update: Wed, 06 Dec 2023 17:07:28 +0100
+
+--- a/bin/snippy
++++ b/bin/snippy
+@@ -373,7 +373,7 @@ my @cmd = (
+   "ln -sf $refdir/ref.fa.fai .",
+   # snpeff index
+   "mkdir -p $refdir/ref && gzip -c $refdir/ref.gff > $refdir/ref/genes.gff.gz",
+-  ( $nfeat > 0 ? "snpEff build -c $refdir/snpeff.config -dataDir . -gff3 ref" 
++  ( $nfeat > 0 ? "snpEff build -noCheckCds -noCheckProtein -c $refdir/snpeff.config -dataDir . -gff3 ref" 
+                : () ),
+   # make BAM
+   ($bam ? "samtools view -h -O SAM \Q$bam\E" : "bwa mem $bwaopt -t $cpus $refdir/ref.fa @reads")
+@@ -393,7 +393,7 @@ my @cmd = (
+    " | bcftools annotate --remove '$KEEP_VCF_TAGS' > $prefix.filt.vcf",
+ #   " > $prefix.filt.vcf",
+   # call consequences
+-  ( $nfeat > 0 ? "snpEff ann -noLog -noStats -no-downstream -no-upstream -no-utr"
++  ( $nfeat > 0 ? "snpEff ann -noCheckCds -noCheckProtein -noLog -noStats -no-downstream -no-upstream -no-utr"
+                  ." -c $refdir/snpeff.config -dataDir . ref $prefix.filt.vcf > $prefix.vcf" 
+                : "cp $prefix.filt.vcf $prefix.vcf" ),
+   # prepare output files



View it on GitLab: https://salsa.debian.org/med-team/snippy/-/commit/dff0fc3fbbdc9cbe23b2506122b1620949f9f1a3

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View it on GitLab: https://salsa.debian.org/med-team/snippy/-/commit/dff0fc3fbbdc9cbe23b2506122b1620949f9f1a3
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