[med-svn] [SCM] jellyfish branch, master, updated. upstream/1.1.2-4-gcc8765e
Andreas Tille
tille at debian.org
Fri Mar 30 22:28:30 UTC 2012
The following commit has been merged in the master branch:
commit cc8765e7d3ffd9790334d8e2b2d0b7eb31ae2779
Author: Andreas Tille <tille at debian.org>
Date: Sat Mar 31 00:26:48 2012 +0200
Add debian/dir (is this the right way to handle this after a `git-import-orig --pristine-tar ../jellyfish_1.1.4.orig.tar.gz` moved old debian/dir out of the way????)
diff --git a/debian/changelog b/debian/changelog
new file mode 100644
index 0000000..8b62812
--- /dev/null
+++ b/debian/changelog
@@ -0,0 +1,11 @@
+jellyfish (1.1.4-1) UNRELEASED; urgency=low
+
+ * New upstream version
+
+ -- Andreas Tille <tille at debian.org> Sat, 31 Mar 2012 00:25:12 +0200
+
+jellyfish (1.1.2-1) unstable; urgency=low
+
+ * Initial release. Closes: #644925.
+
+ -- Shaun Jackman <sjackman at debian.org> Mon, 10 Oct 2011 11:49:11 -0700
diff --git a/debian/compat b/debian/compat
new file mode 100644
index 0000000..7f8f011
--- /dev/null
+++ b/debian/compat
@@ -0,0 +1 @@
+7
diff --git a/debian/control b/debian/control
new file mode 100644
index 0000000..4ae232a
--- /dev/null
+++ b/debian/control
@@ -0,0 +1,37 @@
+Source: jellyfish
+Section: science
+Priority: optional
+Maintainer: Debian Med Packaging Team <debian-med-packaging at lists.alioth.debian.org>
+DM-Upload-Allowed: yes
+Uploaders: Shaun Jackman <sjackman at debian.org>,
+ Andreas Tille <tille at debian.org>
+Build-Depends: debhelper (>= 7.0.50~)
+Standards-Version: 3.9.2
+Homepage: http://www.cbcb.umd.edu/software/jellyfish/
+Vcs-Git: git://git.debian.org/git/debian-med/jellyfish.git
+Vcs-Browser: http://git.debian.org/?p=debian-med/jellyfish.git
+
+
+Package: jellyfish
+Architecture: any-amd64
+Depends: ${shlibs:Depends}, ${misc:Depends}
+Description: count k-mers in DNA sequences
+ JELLYFISH is a tool for fast, memory-efficient counting of k-mers in
+ DNA. A k-mer is a substring of length k, and counting the occurrences
+ of all such substrings is a central step in many analyses of DNA
+ sequence. JELLYFISH can count k-mers using an order of magnitude less
+ memory and an order of magnitude faster than other k-mer counting
+ packages by using an efficient encoding of a hash table and by
+ exploiting the "compare-and-swap" CPU instruction to increase
+ parallelism.
+ .
+ JELLYFISH is a command-line program that reads FASTA and multi-FASTA
+ files containing DNA sequences. It outputs its k-mer counts in an
+ binary format, which can be translated into a human-readable text
+ format using the "jellyfish dump" command.
+ .
+ If you use JELLYFISH in your research, please cite:
+ Guillaume Marcais and Carl Kingsford, A fast, lock-free approach for
+ efficient parallel counting of occurrences of k-mers. Bioinformatics
+ (2011) 27(6): 764-770 (first published online January 7, 2011)
+ doi:10.1093/bioinformatics/btr011
diff --git a/debian/copyright b/debian/copyright
new file mode 100644
index 0000000..4e4870f
--- /dev/null
+++ b/debian/copyright
@@ -0,0 +1,42 @@
+Format: http://svn.debian.org/wsvn/dep/web/deps/dep5.mdwn?op=file&rev=174
+Upstream-Name: JELLYFISH
+Upstream-Contact: Guillaume Marçais <gmarcais at umd.edu>
+Source: http://www.cbcb.umd.edu/software/jellyfish/
+
+Files: *
+Copyright: Copyright 2011 Guillaume Marçais1, Carl Kingsford
+License: GPL-3+
+ See `/usr/share/common-licenses/GPL'.
+
+Files: randomc.h
+Copyright: Copyright 2008 Agner Fog
+License: GPL
+ See `/usr/share/common-licenses/GPL'.
+
+Files: half.h
+Copyright: Copyright 2002, Industrial Light & Magic
+License:
+ Redistribution and use in source and binary forms, with or without
+ modification, are permitted provided that the following conditions
+ are met:
+ * Redistributions of source code must retain the above copyright
+ notice, this list of conditions and the following disclaimer.
+ * Redistributions in binary form must reproduce the above
+ copyright notice, this list of conditions and the following
+ disclaimer in the documentation and/or other materials provided
+ with the distribution.
+ * Neither the name of Industrial Light & Magic nor the names of
+ its contributors may be used to endorse or promote products derived
+ from this software without specific prior written permission.
+ .
+ THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS
+ "AS IS" AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT
+ LIMITED TO, THE IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR
+ A PARTICULAR PURPOSE ARE DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT
+ OWNER OR CONTRIBUTORS BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL,
+ SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT
+ LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE,
+ DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY
+ THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT
+ (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE
+ OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE.
diff --git a/debian/docs b/debian/docs
new file mode 100644
index 0000000..64b0214
--- /dev/null
+++ b/debian/docs
@@ -0,0 +1,2 @@
+README
+doc/jellyfish.pdf
diff --git a/debian/install b/debian/install
new file mode 100644
index 0000000..e772481
--- /dev/null
+++ b/debian/install
@@ -0,0 +1 @@
+usr/bin
diff --git a/debian/manpages b/debian/manpages
new file mode 100644
index 0000000..c7a2ecf
--- /dev/null
+++ b/debian/manpages
@@ -0,0 +1 @@
+doc/jellyfish.man
diff --git a/debian/patches/cmdline b/debian/patches/cmdline
new file mode 100644
index 0000000..e658e69
--- /dev/null
+++ b/debian/patches/cmdline
@@ -0,0 +1,180 @@
+Index: jellyfish/jellyfish/cite_cmdline.cc
+===================================================================
+--- jellyfish.orig/jellyfish/cite_cmdline.cc 2011-10-10 13:15:50.000000000 -0700
++++ jellyfish/jellyfish/cite_cmdline.cc 2011-10-10 13:12:17.000000000 -0700
+@@ -337,13 +337,11 @@
+ const char *long_opt, char short_opt,
+ const char *additional_error)
+ {
+- char *stop_char = 0;
+ const char *val = value;
+ int found;
+ char **string_field;
+ FIX_UNUSED (field);
+
+- stop_char = 0;
+ found = 0;
+
+ if (!multiple_option && prev_given && (*prev_given || (check_ambiguity && *field_given)))
+@@ -420,14 +418,12 @@
+
+ int override;
+ int initialize;
+- int check_required;
+ int check_ambiguity;
+
+ package_name = argv[0];
+
+ override = params->override;
+ initialize = params->initialize;
+- check_required = params->check_required;
+ check_ambiguity = params->check_ambiguity;
+
+ if (initialize)
+Index: jellyfish/jellyfish/query_cmdline.cc
+===================================================================
+--- jellyfish.orig/jellyfish/query_cmdline.cc 2011-10-10 13:18:39.000000000 -0700
++++ jellyfish/jellyfish/query_cmdline.cc 2011-10-10 13:18:06.000000000 -0700
+@@ -354,13 +354,11 @@
+ const char *long_opt, char short_opt,
+ const char *additional_error)
+ {
+- char *stop_char = 0;
+ const char *val = value;
+ int found;
+ char **string_field;
+ FIX_UNUSED (field);
+
+- stop_char = 0;
+ found = 0;
+
+ if (!multiple_option && prev_given && (*prev_given || (check_ambiguity && *field_given)))
+@@ -437,14 +435,12 @@
+
+ int override;
+ int initialize;
+- int check_required;
+ int check_ambiguity;
+
+ package_name = argv[0];
+
+ override = params->override;
+ initialize = params->initialize;
+- check_required = params->check_required;
+ check_ambiguity = params->check_ambiguity;
+
+ if (initialize)
+Index: jellyfish/jellyfish/hash_merge_cmdline.cc
+===================================================================
+--- jellyfish.orig/jellyfish/hash_merge_cmdline.cc 2011-10-10 13:21:16.000000000 -0700
++++ jellyfish/jellyfish/hash_merge_cmdline.cc 2011-10-10 13:21:32.000000000 -0700
+@@ -472,14 +472,12 @@
+
+ int override;
+ int initialize;
+- int check_required;
+ int check_ambiguity;
+
+ package_name = argv[0];
+
+ override = params->override;
+ initialize = params->initialize;
+- check_required = params->check_required;
+ check_ambiguity = params->check_ambiguity;
+
+ if (initialize)
+Index: jellyfish/jellyfish/histo_cmdline.cc
+===================================================================
+--- jellyfish.orig/jellyfish/histo_cmdline.cc 2011-10-10 13:22:17.000000000 -0700
++++ jellyfish/jellyfish/histo_cmdline.cc 2011-10-10 13:22:22.000000000 -0700
+@@ -488,14 +488,12 @@
+
+ int override;
+ int initialize;
+- int check_required;
+ int check_ambiguity;
+
+ package_name = argv[0];
+
+ override = params->override;
+ initialize = params->initialize;
+- check_required = params->check_required;
+ check_ambiguity = params->check_ambiguity;
+
+ if (initialize)
+Index: jellyfish/jellyfish/stats_cmdline.cc
+===================================================================
+--- jellyfish.orig/jellyfish/stats_cmdline.cc 2011-10-10 13:23:21.000000000 -0700
++++ jellyfish/jellyfish/stats_cmdline.cc 2011-10-10 13:23:28.000000000 -0700
+@@ -493,14 +493,12 @@
+
+ int override;
+ int initialize;
+- int check_required;
+ int check_ambiguity;
+
+ package_name = argv[0];
+
+ override = params->override;
+ initialize = params->initialize;
+- check_required = params->check_required;
+ check_ambiguity = params->check_ambiguity;
+
+ if (initialize)
+Index: jellyfish/jellyfish/histo_fastq_main_cmdline.cc
+===================================================================
+--- jellyfish.orig/jellyfish/histo_fastq_main_cmdline.cc 2011-10-10 13:24:05.000000000 -0700
++++ jellyfish/jellyfish/histo_fastq_main_cmdline.cc 2011-10-10 13:24:13.000000000 -0700
+@@ -448,14 +448,12 @@
+
+ int override;
+ int initialize;
+- int check_required;
+ int check_ambiguity;
+
+ package_name = argv[0];
+
+ override = params->override;
+ initialize = params->initialize;
+- check_required = params->check_required;
+ check_ambiguity = params->check_ambiguity;
+
+ if (initialize)
+Index: jellyfish/jellyfish/dump_fastq_main_cmdline.cc
+===================================================================
+--- jellyfish.orig/jellyfish/dump_fastq_main_cmdline.cc 2011-10-10 13:25:26.000000000 -0700
++++ jellyfish/jellyfish/dump_fastq_main_cmdline.cc 2011-10-10 13:25:43.000000000 -0700
+@@ -469,14 +469,12 @@
+
+ int override;
+ int initialize;
+- int check_required;
+ int check_ambiguity;
+
+ package_name = argv[0];
+
+ override = params->override;
+ initialize = params->initialize;
+- check_required = params->check_required;
+ check_ambiguity = params->check_ambiguity;
+
+ if (initialize)
+Index: jellyfish/jellyfish/dump_cmdline.cc
+===================================================================
+--- jellyfish.orig/jellyfish/dump_cmdline.cc 2011-10-10 13:26:40.000000000 -0700
++++ jellyfish/jellyfish/dump_cmdline.cc 2011-10-10 13:26:46.000000000 -0700
+@@ -463,14 +463,12 @@
+
+ int override;
+ int initialize;
+- int check_required;
+ int check_ambiguity;
+
+ package_name = argv[0];
+
+ override = params->override;
+ initialize = params->initialize;
+- check_required = params->check_required;
+ check_ambiguity = params->check_ambiguity;
+
+ if (initialize)
diff --git a/debian/patches/man b/debian/patches/man
new file mode 100644
index 0000000..11dcb7d
--- /dev/null
+++ b/debian/patches/man
@@ -0,0 +1,15 @@
+--- jellyfish.orig/doc/jellyfish.man
++++ jellyfish/doc/jellyfish.man
+@@ -12,11 +12,7 @@
+ ..
+ .TH "JELLYFISH" "1" "2010/10/1" "k\-mer counter " "k\-mer counter "
+ .SH NAME
+-
+-.PP
+-Jellyfish
+-is a software to count k\-mers in DNA sequences.
+-.PP
++jellyfish - count k\-mers in DNA sequences
+ .SH SYNOPSIS
+
+ jellyfish count
diff --git a/debian/patches/ptrdiff_t b/debian/patches/ptrdiff_t
new file mode 100644
index 0000000..def13d1
--- /dev/null
+++ b/debian/patches/ptrdiff_t
@@ -0,0 +1,12 @@
+Index: jellyfish/jellyfish/seq_qual_parser.cc
+===================================================================
+--- jellyfish.orig/jellyfish/seq_qual_parser.cc 2011-10-10 13:08:53.000000000 -0700
++++ jellyfish/jellyfish/seq_qual_parser.cc 2011-10-10 13:09:07.000000000 -0700
+@@ -15,6 +15,7 @@
+ */
+
+ #include <jellyfish/seq_qual_parser.hpp>
++#include <cstddef> // for ptrdiff_t
+
+ jellyfish::seq_qual_parser *
+ jellyfish::seq_qual_parser::new_parser(const char *path) {
diff --git a/debian/patches/series b/debian/patches/series
new file mode 100644
index 0000000..0b77b7b
--- /dev/null
+++ b/debian/patches/series
@@ -0,0 +1,3 @@
+man
+ptrdiff_t
+cmdline
diff --git a/debian/rules b/debian/rules
new file mode 100755
index 0000000..31b9e46
--- /dev/null
+++ b/debian/rules
@@ -0,0 +1,12 @@
+#!/usr/bin/make -f
+
+export DH_OPTIONS
+
+%:
+ dh $@
+
+override_dh_auto_configure:
+ dh_auto_configure
+
+override_dh_auto_install:
+ dh_auto_install --destdir=debian/tmp
diff --git a/debian/source/format b/debian/source/format
new file mode 100644
index 0000000..163aaf8
--- /dev/null
+++ b/debian/source/format
@@ -0,0 +1 @@
+3.0 (quilt)
diff --git a/debian/watch b/debian/watch
new file mode 100644
index 0000000..053967b
--- /dev/null
+++ b/debian/watch
@@ -0,0 +1,2 @@
+version=3
+http://www.cbcb.umd.edu/software/jellyfish/ jellyfish-(.+)\.tar\.gz
--
count k-mers of DNA
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