[med-svn] [bioperl-run] 01/03: Add patch fixing failing tests for Bowtie

[Alex Mestiashvili]

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malex-guest pushed a commit to branch master
in repository bioperl-run.

commit d4f51967f115c13d0b3741f4e9ee0c1a001f2681
Author: Alexandre Mestiashvili <alex at biotec.tu-dresden.de>
Date:   Thu Dec 7 18:16:54 2017 +0100

    Add patch fixing failing tests for Bowtie
---
 debian/patches/adjust_bowtie_tests.patch | 22 ++++++++++++++++++++++
 debian/patches/series                    |  1 +
 2 files changed, 23 insertions(+)

diff --git a/debian/patches/adjust_bowtie_tests.patch b/debian/patches/adjust_bowtie_tests.patch
new file mode 100644
index 0000000..68928f5
--- /dev/null
+++ b/debian/patches/adjust_bowtie_tests.patch
@@ -0,0 +1,22 @@
+Description: adjust expected test output, bowtie-1.2.1+ returns 2000 processed
+reads instead of 1000
+From: Alex Mestiashvili <mailatgoogl at gmail.com>
+--- bioperl-run.orig/t/Bowtie.t
++++ bioperl-run/t/Bowtie.t
+@@ -185,14 +185,14 @@
+     ok $bowtiefac->_run( -ind => $refseq,
+                          -seq => $rda1,  -seq2 => $rda2 ), "read paired fasta sequence";
+     
+-    like($bowtiefac->stderr, qr/reads processed: 1000/, "bowtie success");
++    like($bowtiefac->stderr, qr/reads processed: 2000/, "bowtie success");
+ 
+     $bowtiefac->reset_parameters( -fasta => 0 );
+     $bowtiefac->set_parameters( -fastq => 1 );
+     ok $bowtiefac->_run( -ind => $refseq,
+                          -seq => $rdq1,  -seq2 => $rdq2 ), "read paired fastq sequence";
+     
+-    like($bowtiefac->stderr, qr/reads processed: 1000/, "bowtie success");
++    like($bowtiefac->stderr, qr/reads processed: 2000/, "bowtie success");
+     
+ 
+     # test single
diff --git a/debian/patches/series b/debian/patches/series
index 35f663e..22a230c 100644
--- a/debian/patches/series
+++ b/debian/patches/series
@@ -1,3 +1,4 @@
+adjust_bowtie_tests.patch
 skip_tests_for_wise.patch
 skip_tests_for_phylip.patch
 skip_tests_for_phyml.patch

-- 
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