[med-svn] [Git][med-team/pbgenomicconsensus][master] Make sure the test will really pass

[Andreas Tille]

Andreas Tille pushed to branch master at Debian Med / pbgenomicconsensus


Commits:
9603d63c by Andreas Tille at 2019-03-28T16:13:27Z
Make sure the test will really pass

- - - - -


1 changed file:

- debian/patches/ignore_warnings.patch


Changes:

=====================================
debian/patches/ignore_warnings.patch
=====================================
@@ -28,23 +28,25 @@ Last-Update: Thu, 28 Mar 2019 13:40:21 +0100
    [WARNING] Some reference contigs aligned against are not found in the reference FASTA.  Will process only those contigs supported by the reference FASTA.
 --- a/tests/cram/quiver-noqvs-test.t
 +++ b/tests/cram/quiver-noqvs-test.t
-@@ -9,7 +9,7 @@ Quiver actually makes one error here, wh
+@@ -9,7 +9,8 @@ Quiver actually makes one error here, wh
  but this data is from a really ancient instrument-software version, so
  I'm not all that surprised.
  
 -  $ quiver -pC2.NoQVsModel -x0 -q0 $INPUT -r $REFERENCE -o v.gff -o v.vcf -o css.fa -o css.fq
-+  $ quiver -pC2.NoQVsModel -x0 -q0 $INPUT -r $REFERENCE -o v.gff -o v.vcf -o css.fa -o css.fq  2>&1 | tee | grep -v -e H5pyDeprecationWarning -e '\[1\]'
++  $ quiver -pC2.NoQVsModel -x0 -q0 $INPUT -r $REFERENCE -o v.gff -o v.vcf -o css.fa -o css.fq  2>&1 | tee | grep -v -e H5pyDeprecationWarning
++  [1]
  
    $ cat v.gff | tr '\t' ' '
    ##gff-version 3
 --- a/tests/cram/plurality-compressed.t
 +++ b/tests/cram/plurality-compressed.t
-@@ -4,7 +4,7 @@ output files are created correctly.
+@@ -4,7 +4,8 @@ output files are created correctly.
    $ export DATA=$TESTDIR/../data
    $ export INPUT=$DATA/hcv/aligned_reads.cmp.h5
    $ export REFERENCE=$DATA/hcv/HCV_Ref_For_187140.fasta
 -  $ variantCaller --algorithm=plurality -q 10 -r $REFERENCE -o variants.gff.gz -o consensus.fq.gz $INPUT
-+  $ variantCaller --algorithm=plurality -q 10 -r $REFERENCE -o variants.gff.gz -o consensus.fq.gz $INPUT 2>&1 | tee | grep -v -e H5pyDeprecationWarning -e '\[1\]'
++  $ variantCaller --algorithm=plurality -q 10 -r $REFERENCE -o variants.gff.gz -o consensus.fq.gz $INPUT 2>&1 | tee | grep -v -e H5pyDeprecationWarning
++  [1]
  
  I like to show the head of the output files inline here so that glaringly obvious changes will
  pop right out, but I verify that the files are exactly correct by looking at the md5 sums.



View it on GitLab: https://salsa.debian.org/med-team/pbgenomicconsensus/commit/9603d63cb5afe2b847176d420b53b6d00b3a1d3e

-- 
View it on GitLab: https://salsa.debian.org/med-team/pbgenomicconsensus/commit/9603d63cb5afe2b847176d420b53b6d00b3a1d3e
You're receiving this email because of your account on salsa.debian.org.

-------------- next part --------------
An HTML attachment was scrubbed...
URL: <http://alioth-lists.debian.net/pipermail/debian-med-commit/attachments/20190328/9068885f/attachment-0001.html>