[med-svn] [Git][med-team/snippy][master] 2 commits: In the second part of the patch the first line which invalidates

[Andreas Tille (@tille)]

Andreas Tille pushed to branch master at Debian Med / snippy


Commits:
2c96d5ea by Andreas Tille at 2023-12-19T10:44:12+01:00
In the second part of the patch the first line which invalidates
    the resulting vcf file is removed via sed.  This needs further
    discussion with SnpEff upstream (issue #510)

- - - - -
a422d135 by Andreas Tille at 2023-12-19T10:46:54+01:00
Upload to unstable

- - - - -


2 changed files:

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


Changes:

=====================================
debian/changelog
=====================================
@@ -1,14 +1,15 @@
-snippy (4.6.0+dfsg-4) UNRELEASED; urgency=medium
+snippy (4.6.0+dfsg-4) unstable; urgency=medium
 
   * Work with snpeff >= 5.1
     Closes: #1029202
+    In the second part of the patch the first line which invalidates
+    the resulting vcf file is removed via sed.  This needs further
+    discussion with SnpEff upstream (issue #510)
   * Add another test - for the moment just for users local machine in
     examples since its quite some effort for autopkgtest
   * Set upstream metadata fields: Repository.
-  TODO: test_for_working_snpeff_v5.1+ fails in second snpEff call see
-        https://github.com/pcingola/SnpEff/issues/510
 
- -- Andreas Tille <tille at debian.org>  Wed, 06 Dec 2023 17:35:45 +0100
+ -- Andreas Tille <tille at debian.org>  Tue, 19 Dec 2023 10:44:31 +0100
 
 snippy (4.6.0+dfsg-3) unstable; urgency=medium
 


=====================================
debian/patches/snpeff_v5.1+.patch
=====================================
@@ -2,10 +2,17 @@ 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
+  .
+  In the second part of this patch the first line which invalidates the resulting vcf
+  file is removed via sed.  The problem is reported in
+    https://github.com/pcingola/SnpEff/issues/510
+  but upstream has not respondet yet to this issue.
+  FIXME: Check whether upstream mighg have a better solution
+         for issue #510.
 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
+Last-Update: Tue, 19 Dec 2023 10:41:10 +0100
 
 --- a/bin/snippy
 +++ b/bin/snippy
@@ -18,3 +25,12 @@ Last-Update: Wed, 06 Dec 2023 17:07:28 +0100
                 : () ),
    # make BAM
    ($bam ? "samtools view -h -O SAM \Q$bam\E" : "bwa mem $bwaopt -t $cpus $refdir/ref.fa @reads")
+@@ -394,7 +394,7 @@ my @cmd = (
+ #   " > $prefix.filt.vcf",
+   # call consequences
+   ( $nfeat > 0 ? "snpEff ann -noLog -noStats -no-downstream -no-upstream -no-utr"
+-                 ." -c $refdir/snpeff.config -dataDir . ref $prefix.filt.vcf > $prefix.vcf" 
++                 ." -c $refdir/snpeff.config -dataDir . ref $prefix.filt.vcf | sed '1{/^ ann -noLog.*filt.vcf/d}' > $prefix.vcf" 
+                : "cp $prefix.filt.vcf $prefix.vcf" ),
+   # prepare output files
+   "$BINDIR/snippy-vcf_to_tab --gff $refdir/ref.gff --ref $refdir/ref.fa --vcf $prefix.vcf > $prefix.tab",



View it on GitLab: https://salsa.debian.org/med-team/snippy/-/compare/a61bf70dc057968d438daff1f4bffd320db47f56...a422d135aaf06b7a1ee60bd3d7c4d2441f50e5c7

-- 
View it on GitLab: https://salsa.debian.org/med-team/snippy/-/compare/a61bf70dc057968d438daff1f4bffd320db47f56...a422d135aaf06b7a1ee60bd3d7c4d2441f50e5c7
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