[med-svn] [Git][med-team/minimac4][master] 3 commits: Run both tests

[Andreas Tille (@tille)]

Andreas Tille pushed to branch master at Debian Med / minimac4


Commits:
12b0c579 by Andreas Tille at 2023-01-24T19:52:06+01:00
Run both tests

- - - - -
5c4568b0 by Andreas Tille at 2023-01-24T20:01:45+01:00
Restrictions: allow-stderr

- - - - -
1074eebd by Andreas Tille at 2023-01-24T20:03:13+01:00
Upload to unstable

- - - - -


3 changed files:

- debian/changelog
- debian/tests/control
- debian/tests/run-unit-test


Changes:

=====================================
debian/changelog
=====================================
@@ -1,4 +1,4 @@
-minimac4 (4.1.2-1) UNRELEASED; urgency=medium
+minimac4 (4.1.2-1) unstable; urgency=medium
 
   * Team upload.
   * New upstream version
@@ -9,7 +9,7 @@ minimac4 (4.1.2-1) UNRELEASED; urgency=medium
   * Build-Depends bcftools needed for build tests
   * Adapt autopkgtest to build time test
 
- -- Andreas Tille <tille at debian.org>  Thu, 22 Sep 2022 09:28:59 +0200
+ -- Andreas Tille <tille at debian.org>  Tue, 24 Jan 2023 20:01:52 +0100
 
 minimac4 (4.0.3-1) unstable; urgency=medium
 


=====================================
debian/tests/control
=====================================
@@ -1,2 +1,3 @@
 Tests: run-unit-test
 Depends: @, bcftools
+Restrictions: allow-stderr


=====================================
debian/tests/run-unit-test
=====================================
@@ -1,6 +1,5 @@
 #!/bin/sh -e
 # Adapted from build time test
-set -x
 
 pkg=minimac4
 
@@ -11,19 +10,20 @@ fi
 cd $AUTOPKGTEST_TMP
 cp -a /usr/share/doc/${pkg}/examples/* $AUTOPKGTEST_TMP
 
-d=m4_simple_test_output
+testit() {
+d=$1
 mkdir -p $d
 
 sampledata=ref_panel.vcf
 tarpanel=tar_panel.vcf
-ref_vcf=$d/$(basename $sampledata).gz
-ref_msav=$d/$(basename $sampledata .vcf).msav
-tar_vcf=$d/$(basename $tarpanel).gz
+ref_vcf=$d/$(basename $2).gz
+ref_msav=$d/$(basename $2 .vcf).msav
+tar_vcf=$d/$(basename $3).gz
 imputed_vcf=$d/imputed.vcf.gz
 
-bcftools view $sampledata -Oz -o $ref_vcf
+bcftools view $2 -Oz -o $ref_vcf
 bcftools index $ref_vcf
-bcftools view $tarpanel -Oz -o $tar_vcf
+bcftools view $3 -Oz -o $tar_vcf
 bcftools index $tar_vcf
 minimac4 --compress-reference $ref_vcf > $ref_msav
 minimac4 $ref_msav $tar_vcf -f GT -O vcf.gz > $imputed_vcf
@@ -31,3 +31,7 @@ minimac4 $ref_msav $tar_vcf -f GT -O vcf.gz > $imputed_vcf
 gzip -cd $imputed_vcf | grep -v "^#" | cut -f9- > $d/imputed_gt_matrix.tsv
 gzip -cd $ref_vcf | grep -v "^#" | cut -f9- > $d/ref_gt_matrix.tsv
 diff $d/ref_gt_matrix.tsv $d/imputed_gt_matrix.tsv
+}
+
+testit m4_simple_test_output ref_panel.vcf tar_panel.vcf
+testit m4_haploid_and_diploid_test_output ref_panel_with_haploid_sample.vcf tar_panel_with_haploid_sample.vcf



View it on GitLab: https://salsa.debian.org/med-team/minimac4/-/compare/73be6ef522ebe2901f294f8a5453ddad94d4273b...1074eebd02787fde2e8fd93c49ce7c6ebff3b725

-- 
View it on GitLab: https://salsa.debian.org/med-team/minimac4/-/compare/73be6ef522ebe2901f294f8a5453ddad94d4273b...1074eebd02787fde2e8fd93c49ce7c6ebff3b725
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