[med-svn] [Git][med-team/jellyfish][master] 2 commits: Add the missing small_mers.sh file, courtesy upstream.
Michael R. Crusoe
gitlab at salsa.debian.org
Mon Mar 12 13:20:58 UTC 2018
Michael R. Crusoe pushed to branch master at Debian Med / jellyfish
Commits:
8cac4aa0 by Michael R. Crusoe at 2018-03-12T05:22:40-07:00
Add the missing small_mers.sh file, courtesy upstream.
- - - - -
3952220c by Michael R. Crusoe at 2018-03-12T05:31:14-07:00
add fix from upstream for arm/ppc
- - - - -
6 changed files:
- debian/changelog
- debian/copyright
- + debian/patches/6dfc57b516249454dc0a708ceb4833623cbf0ffd.patch
- + debian/patches/add_small_mers.sh.patch
- debian/patches/series
- − debian/patches/skip_small_mers.sh
Changes:
=====================================
debian/changelog
=====================================
--- a/debian/changelog
+++ b/debian/changelog
@@ -1,3 +1,10 @@
+jellyfish (2.2.8-2) unstable; urgency=medium
+
+ * Add the missing small_mers.sh file, courtesy upstream.
+ * Fix arm/powerpc build, patch courtesy upstream (Closes: #890137)
+
+ -- Michael R. Crusoe <michael.crusoe at gmail.com> Mon, 12 Mar 2018 05:31:00 -0700
+
jellyfish (2.2.8-1) unstable; urgency=medium
* New upstream version
=====================================
debian/copyright
=====================================
--- a/debian/copyright
+++ b/debian/copyright
@@ -1,4 +1,4 @@
-Format: http://www.debian.org/doc/packaging-manuals/copyright-format/1.0/
+Format: https://www.debian.org/doc/packaging-manuals/copyright-format/1.0/
Upstream-Name: JELLYFISH
Upstream-Contact: Guillaume Marçais <gmarcais at umd.edu>
Source: http://www.cbcb.umd.edu/software/jellyfish/
@@ -7,7 +7,6 @@ Files: *
Copyright: Copyright 2011-2014 Guillaume Marçais1, Carl Kingsford
License: GPL-3+
-
Files: jellyfish/randomc.h
Copyright: Copyright 2008 Agner Fog
License: GPL
=====================================
debian/patches/6dfc57b516249454dc0a708ceb4833623cbf0ffd.patch
=====================================
--- /dev/null
+++ b/debian/patches/6dfc57b516249454dc0a708ceb4833623cbf0ffd.patch
@@ -0,0 +1,22 @@
+From 6dfc57b516249454dc0a708ceb4833623cbf0ffd Mon Sep 17 00:00:00 2001
+From: Guillaume Marcais <gmarcais at cs.cmu.edu>
+Date: Wed, 14 Feb 2018 07:29:54 -0500
+Subject: [PATCH] Fix testing on arm64.
+
+---
+ jellyfish/fastq2sam.cc | 2 +-
+ 1 file changed, 1 insertion(+), 1 deletion(-)
+
+diff --git a/jellyfish/fastq2sam.cc b/jellyfish/fastq2sam.cc
+index e152ccf..b0b6b0d 100644
+--- a/jellyfish/fastq2sam.cc
++++ b/jellyfish/fastq2sam.cc
+@@ -25,7 +25,7 @@ int main(int argc, char* argv[]) {
+ // os << "@PG\tID:fastq2sam\tPN:fastq2sam\n";
+
+ std::string name, seq, quals;
+- char c = is.get();
++ int c = is.get();
+ while(c == '@') {
+ std::getline(is, name);
+ std::getline(is, seq);
=====================================
debian/patches/add_small_mers.sh.patch
=====================================
--- /dev/null
+++ b/debian/patches/add_small_mers.sh.patch
@@ -0,0 +1,27 @@
+From 0adb7ea223a6718bad4e82fc9813ae7708b59ee2 Mon Sep 17 00:00:00 2001
+From: Guillaume Marcais <gmarcais at cs.cmu.edu>
+Date: Mon, 12 Feb 2018 14:32:29 -0500
+Subject: [PATCH] Added missing tests/small_mers.sh file.
+
+---
+ tests/small_mers.sh | 11 +++++++++++
+ 1 file changed, 11 insertions(+)
+ create mode 100644 tests/small_mers.sh
+
+diff --git a/tests/small_mers.sh b/tests/small_mers.sh
+new file mode 100644
+index 0000000..5eb7db0
+--- /dev/null
++++ b/tests/small_mers.sh
+@@ -0,0 +1,11 @@
++#! /bin/sh
++
++cd tests
++. ./compat.sh
++
++sort -k2,2 > ${pref}.md5sum <<EOF
++
++EOF
++
++$JF count -t $nCPUs -o ${pref}_m10_10M.jf -s 1M -m 7 -C seq10m.fa
++$JF histo ${pref}_m10_10M.jf > ${pref}_m10_10M.histo
=====================================
debian/patches/series
=====================================
--- a/debian/patches/series
+++ b/debian/patches/series
@@ -6,4 +6,5 @@ spelling
gcc-7.patch
reproducible.patch
portability.patch
-skip_small_mers.sh
+add_small_mers.sh.patch
+6dfc57b516249454dc0a708ceb4833623cbf0ffd.patch
=====================================
debian/patches/skip_small_mers.sh deleted
=====================================
--- a/debian/patches/skip_small_mers.sh
+++ /dev/null
@@ -1,22 +0,0 @@
-Author: Michael R. Crusoe <michael.crusoe at gmail.com>
-Description: Skip missing test file from upstream
---- jellyfish.orig/Makefile.am
-+++ jellyfish/Makefile.am
-@@ -146,8 +146,7 @@
- TESTS = tests/generate_sequence.sh tests/parallel_hashing.sh \
- tests/merge.sh tests/bloom_filter.sh tests/big.sh \
- tests/subset_hashing.sh tests/multi_file.sh \
-- tests/bloom_counter.sh tests/large_key.sh tests/sam.sh \
-- tests/small_mers.sh
-+ tests/bloom_counter.sh tests/large_key.sh tests/sam.sh
-
- EXTRA_DIST += $(TESTS)
- clean-local: clean-local-check
-@@ -165,7 +164,6 @@
- tests/large_key.log: tests/generate_sequence.log
- tests/quality_filter.log: tests/generate_sequence.log
- tests/sam.log: tests/generate_sequence.log
--tests/small_mers.log: tests/generate_sequence.log
-
- # SWIG tests
- TESTS += tests/swig_python.sh tests/swig_ruby.sh tests/swig_perl.sh
View it on GitLab: https://salsa.debian.org/med-team/jellyfish/compare/c2cdb414c927d03d225db69bacd80490554c75fb...3952220cbaca160a19165bc19ea655ab5f66a6bc
---
View it on GitLab: https://salsa.debian.org/med-team/jellyfish/compare/c2cdb414c927d03d225db69bacd80490554c75fb...3952220cbaca160a19165bc19ea655ab5f66a6bc
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