debian/changelog

+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@gmail.com>  Mon, 12 Mar 2018 05:31:00 -0700
+
 jellyfish (2.2.8-1) unstable; urgency=medium
 
   * New upstream version

debian/copyright

-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@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

+From 6dfc57b516249454dc0a708ceb4833623cbf0ffd Mon Sep 17 00:00:00 2001
+From: Guillaume Marcais <gmarcais@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

+From 0adb7ea223a6718bad4e82fc9813ae7708b59ee2 Mon Sep 17 00:00:00 2001
+From: Guillaume Marcais <gmarcais@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

@@ -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

-Author: Michael R. Crusoe <michael.crusoe@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