debian/0000755000000000000000000000000012214344160007163 5ustar debian/libsrf-dev.install0000644000000000000000000000002512213115302012576 0ustar src/libsrf.a usr/lib debian/control0000644000000000000000000000317212214341143010567 0ustar Source: srf Maintainer: Debian Med Packaging Team Uploaders: Charles Plessy , Andreas Tille Section: science Priority: optional Build-Depends: debhelper (>= 9), autotools-dev, libcurl4-gnutls-dev, libstaden-read-dev Standards-Version: 3.9.4 Vcs-Browser: http://anonscm.debian.org/viewvc/debian-med/trunk/packages/srf/trunk/ Vcs-Svn: svn://anonscm.debian.org/debian-med/trunk/packages/srf/trunk/ Homepage: http://srf.sourceforge.net/ Package: srf-doc Architecture: all Section: doc Depends: ${misc:Depends} Description: specification documents for the SRF format DNA sequence data SRF (sort for Sequence Read Format) is a generic format capable of storing data generated by any DNA sequencing technology. Hence it has sufficient flexibility to store data from current and future DNA sequencing technologies at minimal cost of implementation. Benefits include a single input file format for all downstream applications and a read lookup index enabling downstream formats to reference reads without duplication of all of the read specific information. . This package contains the version 1.3.2 of the specification. Package: libsrf-dev Architecture: any Section: libdevel Depends: ${shlibs:Depends}, ${misc:Depends} Description: C++ implementation of the SRF format for DNA sequence data SRF (sort for Sequence Read Format) is a generic format capable of storing data generated by any DNA sequencing technology. This library is an implementation of SRF and provides basic input-output functions. debian/README.source0000644000000000000000000000152612213115302011337 0ustar I have added the latest version of the SRF specification to this package: - SRF_v_1_3_2_June_19th_2008-0001.pdf was downloaded from the archives of the Ssrformat mailing list (http://www.bcgsc.ca/pipermail/ssrformat/2008-September/000554.html). - SRF_v_1_3_2_June_19th_2008.doc was communicated to me by Asim Siddiqui. Since SRF_v_1_3_2_June_19th_2008.doc is the latest version, I beleive that this makes effectively free the PDF file SequenceReadFormat_v_1_3_1_Feb_27th_08.pdf, whose sources were not available in the original upstream archive. In addition, the Debian binary packages are produced after applying patches to the original sources. For more instruction about how to manage the patches, please refer to the file ‘/usr/share/doc/quilt/README.source’. -- Charles Plessy Tue, 25 Aug 2009 19:36:31 +0900 debian/rules0000755000000000000000000000012112214340623010235 0ustar #!/usr/bin/make -f %: dh $@ override_dh_compress: dh_compress --exclude=.pdf debian/watch0000644000000000000000000000013112214342511010205 0ustar version=3 opts=dversionmangle=s/(\+dfsg)// \ http://sf.net/srf/srf-v([\d\.]*)\.tar\.gz debian/copyright0000644000000000000000000000547312214343554011135 0ustar Format: http://www.debian.org/doc/packaging-manuals/copyright-format/1.0/ Upstream-Name: SRF Upstream-Contact: http://www.bcgsc.ca/mailman/listinfo/ssrformat Source: http://downloads.sourceforge.net/project/srf/srf/v0.1/srf-v0.1.tar.gz Files: * Copyright: 2007, Asim Siddiqui License: Apache-2.0 Files: src/SRF_util.cc Copyright: Genome Research Ltd (GRL). License: GRL 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 the Genome Research Limited 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 GRL ``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 GRL 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. . The upstream autor of src/SRF_util.cc confirmed in a private email that the current license the original program where it was taken from, the Staden io-lib, applies instead of the non-free statement contained in the file itself. Files: debian/* Copyright: © 2009 Charles Plessy © 2013 Andreas Tille License: Apache-2.0 License: Apache-2.0 Licensed under the Apache License, Version 2.0 (the "License"); you may not use this file except in compliance with the License. You may obtain a copy of the License at . http://www.apache.org/licenses/LICENSE-2.0 . Unless required by applicable law or agreed to in writing, software distributed under the License is distributed on an "AS IS" BASIS, WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. See the License for the specific language governing permissions and limitations under the License. . On Debian systems, the complete text of the Apache license version 2 is distributed in the file ’/usr/share/common-licenses/Apache-2.0’. debian/source/0000755000000000000000000000000012214301062010455 5ustar debian/source/format0000644000000000000000000000001412214301062011663 0ustar 3.0 (quilt) debian/srf-doc.doc-base0000644000000000000000000000064412213115302012114 0ustar Document: srf Title: SRF specification version 1.3.2 Author: This format has been developed as an open collaborative effort between many groups and individuals (see inside). Abstract: This document describes a machine and technology independent format for storing DNA sequence data and associated quality values. Section: Science/Biology Format: PDF Files: /usr/share/doc/srf-doc/SRF_v_1_3_2_June_19th_2008-0001.pdf debian/changelog0000644000000000000000000000114212214344160011033 0ustar srf (0.1+dfsg-2) unstable; urgency=low * Update to recent packaging standards and rebuild * debian/source/format: 3.0 (quilt) * debian/control: - cme fix dpkg-control - Add myself to uploaders - debhelper 9 - anonscm in VCS fields - drop cdbs+quilt from Build-Depends * debian/rules: short dh * debian/watch: mangle version * debian/copyright: DEP5 -- Andreas Tille Thu, 12 Sep 2013 14:13:46 +0200 srf (0.1+dfsg-1) unstable; urgency=low * Initial release (Closes: #489983) -- Charles Plessy Tue, 25 Aug 2009 20:31:22 +0900 debian/patches/0000755000000000000000000000000012213115302010603 5ustar debian/patches/build_with_GCC-4.3.patch0000644000000000000000000000137212213115302014737 0ustar Description: Adds missing headers to build with the GCC 4.3. Origin: vendor : Debian Forwarded: https://sourceforge.net/support/tracker.php?aid=2013397 --- srf-0.1.orig/src/SRF_util.hh +++ srf-0.1/src/SRF_util.hh @@ -32,6 +32,7 @@ #include #include #include +#include #include #include #include --- srf-0.1.orig/src/SRF_Ztr.cc +++ srf-0.1/src/SRF_Ztr.cc @@ -13,6 +13,8 @@ // limitations under the License. // // +#include +#include #include #include #include --- srf-0.1.orig/test/testWrite.cc +++ srf-0.1/test/testWrite.cc @@ -1,4 +1,5 @@ // +#include #include #include #include debian/patches/io_lib_renamed.patch0000644000000000000000000000215312213115302014555 0ustar Description: Corrections after the io-lib has been renamed. This patch replaces ’-lread’ by ’-lstaden-read’ in the makefile of the test directory. Other parts of SRF do not need correction as they use io_lib-config. Author: Charles Plessy Forwarded: https://sourceforge.net/support/tracker.php?aid=2838340 --- a/test/Makefile.am +++ b/test/Makefile.am @@ -15,5 +15,5 @@ testWriteSFF_LDADD = $(top_builddir)/src/libsrf.a @LDFLAGS@ $(LDLIB) INCLUDES= -I${top_srcdir} $(SHELL io_lib-config --cflags) -I../src AM_LDFLAGS=$(SHELL io_lib-config --libs) -LDLIB=-lstdc++ -lz -lcurl -lread +LDLIB=-lstdc++ -lz -lcurl -lstaden-read diff --git a/test/Makefile.in b/test/Makefile.in index 9d17fd3..ff188b3 100644 --- a/test/Makefile.in +++ b/test/Makefile.in @@ -181,7 +181,7 @@ testWriteSFF_SOURCES = testWriteSFF.cc testWriteSFF_LDADD = $(top_builddir)/src/libsrf.a @LDFLAGS@ $(LDLIB) INCLUDES = -I${top_srcdir} $(SHELL io_lib-config --cflags) -I../src AM_LDFLAGS = $(SHELL io_lib-config --libs) -LDLIB = -lstdc++ -lz -lcurl -lread +LDLIB = -lstdc++ -lz -lcurl -lstaden-read all: all-am .SUFFIXES: debian/patches/series0000644000000000000000000000005612213115302012021 0ustar build_with_GCC-4.3.patch io_lib_renamed.patch debian/compat0000644000000000000000000000000212214337776010400 0ustar 9 debian/srf-doc.docs0000644000000000000000000000006012213115302011357 0ustar README docs/SRF_v_1_3_2_June_19th_2008-0001.pdf