Commit 95647b39 authored by Andreas Tille's avatar Andreas Tille

New upstream version 0.1+dfsg

parent fb57e3c9
quit
run < s_8_0100_seq.txt
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stop at SRF_Container::write
run < s_8_0100_seq.txt
file SRF_Container.cc
list SRF_Container.cc
list SRF_Container::write
stop at 153
break at 153
break 153
run < s_8_0100_seq.txt
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list SRF_Container::write
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help stop
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next
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print bytesToFirstDataBlock
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// 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.
AUTOMAKE_OPTIONS = foreign no-dependencies
SUBDIRS = src test
man_MANS =
pkginclude_HEADERS =
bin_SCRIPTS =
EXTRA_DIST =
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SRF RELEASE 0.1
===============
This is release 0.1 of the SRF package. This package corresponds to v1.3 of the SRF spec.
See srf.sf.net for more details.
INSTALLING ZTR
==============
SRF has a dependancy on ZTR. You must download and install version 1.11.0 of ZTR prior to building SRF.
http://sourceforge.net/project/showfiles.php?group_id=100316&package_id=108243&release_id=578149
Building
========
We use the GNU autoconf build mechanism.
To build:
1. ./configure
"./configure --help" will give a list of the options for GNU autoconf. For
modifying the compiler options or flags you may wish to redefine the CC or
CFLAGS variable.
Eg (in sh or bash):
CC=cc CFLAGS=-g ./configure
2. make (or gmake)
This will build the sources.
CFLAGS may also be changed a build time using (eg):
make 'CFLAGS=-g ...'
Under Microsoft Windows we recommend the use of MSYS and MINGW as a
build environment. These contain enough tools to build using the
configure script.
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dnl Process this file with autoconf to produce a configure script.
AC_INIT(srf, 1.3.0)
AM_CONFIG_HEADER(srf_config.h)
AM_INIT_AUTOMAKE
dnl Checks for programs.
AC_PROG_CC
AC_PROG_CXX
AC_PROG_INSTALL
AC_PROG_RANLIB
AC_PATH_PROG(IO_LIB_CONFIG, io_lib-config, io_lib-config)
dnl Check for libcurl and zlib
LIBCURL_CHECK_CONFIG(,,[have_curl=yes], [have_curl=no])
ZLIB_CHECK_CONFIG(,,[have_curl=yes], [have_curl=no])
dnl Socket support for Solaris (et al)
AC_SEARCH_LIBS([gethostbyname], [nsl])
AC_SEARCH_LIBS([socket], [socket], [],
[AC_CHECK_LIB([socket], [socket],
[LIBS="-lsocket -lnsl $LIBS"], [], [-lnsl])])
dnl Checks for header files.
AC_HEADER_STDC
AC_HEADER_SYS_WAIT
AC_CHECK_HEADERS(fcntl.h limits.h unistd.h)
AC_CHECK_HEADER(zlib.h)
dnl Checks for typedefs, structures, and compiler characteristics.
AC_C_BIGENDIAN
AC_CHECK_SIZEOF(short,2)
AC_CHECK_SIZEOF(int,4)
AC_CHECK_SIZEOF(long,4)
dnl AC_C_CONST
AC_C_INLINE
AC_TYPE_MODE_T
dnl AC_TYPE_OFF_T
dnl AC_TYPE_SIZE_T
dnl AC_STRUCT_TM
dnl Large file support
AC_SYS_LARGEFILE
AC_FUNC_FSEEKO
dnl Checks for library functions.
AC_SEARCH_LIBS(cos, m)
dnl AC_FUNC_MEMCMP
dnl AC_FUNC_STRFTIME
dnl AC_FUNC_VPRINTF
AC_CHECK_FUNCS(strdup)
dnl AC_CHECK_FUNCS(mktime strspn strstr strtol)
AC_OUTPUT(Makefile src/Makefile test/Makefile)
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 <plessy@debian.org> Tue, 25 Aug 2009 19:36:31 +0900
srf (0.1+dfsg-4) unstable; urgency=medium
* Add zlib1g-dev to Build-Depends
Closes: #747776
-- Andreas Tille <tille@debian.org> Mon, 12 May 2014 12:49:56 +0200
srf (0.1+dfsg-3) unstable; urgency=medium
* Fix FTBFS with clang (thanks for the patch to
Nicolas Sévelin-Radiguet <nicosr@free.fr>)
Closes: #745350
* cme fix dpkg-control
-- Andreas Tille <tille@debian.org> Sun, 20 Apr 2014 23:38:02 +0200
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 <tille@debian.org> Thu, 12 Sep 2013 14:13:46 +0200
srf (0.1+dfsg-1) unstable; urgency=low
* Initial release (Closes: #489983)
-- Charles Plessy <plessy@debian.org> Tue, 25 Aug 2009 20:31:22 +0900
Source: srf
Maintainer: Debian Med Packaging Team <debian-med-packaging@lists.alioth.debian.org>
Uploaders: Charles Plessy <plessy@debian.org>,
Andreas Tille <tille@debian.org>
Section: science
Priority: optional
Build-Depends: debhelper (>= 9),
autotools-dev,
libcurl4-gnutls-dev,
libstaden-read-dev,
zlib1g-dev
Standards-Version: 3.9.5
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.
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 <plessy@debian.org>
© 2013 Andreas Tille <tille@debian.org>
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’.
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 <iostream>
#include <fstream>
#include <string>
+#include <cstring>
#include <vector>
#include <io_lib/ztr.h>
#include <io_lib/Read.h>
--- srf-0.1.orig/src/SRF_Ztr.cc
+++ srf-0.1/src/SRF_Ztr.cc
@@ -13,6 +13,8 @@
// limitations under the License.
//
//
+#include <cstdlib>
+#include <cstring>
#include <ios>
#include <iostream>
#include <fstream>
--- srf-0.1.orig/test/testWrite.cc
+++ srf-0.1/test/testWrite.cc
@@ -1,4 +1,5 @@
//
+#include <cstdlib>
#include <ios>
#include <iostream>
#include <fstream>
Description: fix FTBFS with clang instead of gcc
Author: Nicolas Sévelin-Radiguet <nicosr@free.fr>
Last-Update: 2014-04-20
--- a/test/testRead.cc
+++ b/test/testRead.cc
@@ -29,7 +29,7 @@
}
-main(int argc, char* argv[])
+int main(int argc, char* argv[])
{
if ( argc != 2 )
{
@@ -65,4 +65,5 @@
{
read->dump();
}
+ return 0;
}
--- a/test/testWrite.cc
+++ b/test/testWrite.cc
@@ -21,7 +21,7 @@
return oss.str();
}
-main(int argc, char **argv)
+int main(int argc, char **argv)
{
SRF_File::openType mode = SRF_File::openTypeWrite;
SRF_File file( "myFirstSSRFFile", mode );
--- a/test/testWriteFastaq.cc
+++ b/test/testWriteFastaq.cc
@@ -22,7 +22,7 @@
#include <io_lib/ztr.h>
#include <zlib.h>
-main(int argc, char* argv[])
+int main(int argc, char* argv[])
{
if ( argc != 3 )
{
@@ -115,5 +115,6 @@
}
}
newReadSet.write( file.getFile(), ztrBlobs, readIds );
+ return 0;
}
--- a/test/testWriteSFF.cc
+++ b/test/testWriteSFF.cc
@@ -31,7 +31,7 @@
return oss.str();
}
-main(int argc, char* argv[])
+int main(int argc, char* argv[])
{
if ( argc != 3 )
{
@@ -75,5 +75,6 @@
readIdCounter++;
}
newReadSet.write( file.getFile(), ztrBlobs, readIds );
+ return 0;
}
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 <plessy@debian.org>
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:
build_with_GCC-4.3.patch
io_lib_renamed.patch
clang_FTBFS_wrong-main-declaration.patch
#!/usr/bin/make -f
%:
dh $@
override_dh_compress:
dh_compress --exclude=.pdf
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
README
docs/SRF_v_1_3_2_June_19th_2008-0001.pdf
version=3
opts=dversionmangle=s/(\+dfsg)// \
http://sf.net/srf/srf-v([\d\.]*)\.tar\.gz
This diff is collapsed.
#!/bin/sh
# install - install a program, script, or datafile
scriptversion=2004-07-05.00
# This originates from X11R5 (mit/util/scripts/install.sh), which was
# later released in X11R6 (xc/config/util/install.sh) with the
# following copyright and license.
#
# Copyright (C) 1994 X Consortium
#
# Permission is hereby granted, free of charge, to any person obtaining a copy
# of this software and associated documentation files (the "Software"), to
# deal in the Software without restriction, including without limitation the
# rights to use, copy, modify, merge, publish, distribute, sublicense, and/or
# sell copies of the Software, and to permit persons to whom the Software is
# furnished to do so, subject to the following conditions:
#
# The above copyright notice and this permission notice shall be included in
# all copies or substantial portions of the Software.
#
# THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR
# IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,
# FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE
# X CONSORTIUM BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER LIABILITY, WHETHER IN
# AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM, OUT OF OR IN CONNEC-
# TION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE SOFTWARE.
#
# Except as contained in this notice, the name of the X Consortium shall not
# be used in advertising or otherwise to promote the sale, use or other deal-
# ings in this Software without prior written authorization from the X Consor-
# tium.
#
#
# FSF changes to this file are in the public domain.
#
# Calling this script install-sh is preferred over install.sh, to prevent
# `make' implicit rules from creating a file called install from it
# when there is no Makefile.
#
# This script is compatible with the BSD install script, but was written
# from scratch. It can only install one file at a time, a restriction
# shared with many OS's install programs.
# set DOITPROG to echo to test this script
# Don't use :- since 4.3BSD and earlier shells don't like it.
doit="${DOITPROG-}"
# put in absolute paths if you don't have them in your path; or use env. vars.
mvprog="${MVPROG-mv}"
cpprog="${CPPROG-cp}"
chmodprog="${CHMODPROG-chmod}"
chownprog="${CHOWNPROG-chown}"
chgrpprog="${CHGRPPROG-chgrp}"
stripprog="${STRIPPROG-strip}"
rmprog="${RMPROG-rm}"
mkdirprog="${MKDIRPROG-mkdir}"
chmodcmd="$chmodprog 0755"
chowncmd=
chgrpcmd=
stripcmd=
rmcmd="$rmprog -f"
mvcmd="$mvprog"
src=
dst=
dir_arg=
dstarg=
no_target_directory=
usage="Usage: $0 [OPTION]... [-T] SRCFILE DSTFILE
or: $0 [OPTION]... SRCFILES... DIRECTORY
or: $0 [OPTION]... -t DIRECTORY SRCFILES...
or: $0 [OPTION]... -d DIRECTORIES...
In the 1st form, copy SRCFILE to DSTFILE.
In the 2nd and 3rd, copy all SRCFILES to DIRECTORY.
In the 4th, create DIRECTORIES.
Options:
-c (ignored)
-d create directories instead of installing files.
-g GROUP $chgrpprog installed files to GROUP.
-m MODE $chmodprog installed files to MODE.
-o USER $chownprog installed files to USER.
-s $stripprog installed files.
-t DIRECTORY install into DIRECTORY.
-T report an error if DSTFILE is a directory.
--help display this help and exit.
--version display version info and exit.
Environment variables override the default commands:
CHGRPPROG CHMODPROG CHOWNPROG CPPROG MKDIRPROG MVPROG RMPROG STRIPPROG
"
while test -n "$1"; do
case $1 in
-c) shift
continue;;
-d) dir_arg=true
shift
continue;;
-g) chgrpcmd="$chgrpprog $2"
shift
shift
continue;;
--help) echo "$usage"; exit 0;;
-m) chmodcmd="$chmodprog $2"
shift
shift
continue;;
-o) chowncmd="$chownprog $2"
shift
shift
continue;;
-s) stripcmd=$stripprog
shift
continue;;
-t) dstarg=$2
shift
shift
continue;;
-T) no_target_directory=true
shift
continue;;
--version) echo "$0 $scriptversion"; exit 0;;
*) # When -d is used, all remaining arguments are directories to create.
# When -t is used, the destination is already specified.
test -n "$dir_arg$dstarg" && break
# Otherwise, the last argument is the destination. Remove it from $@.
for arg
do
if test -n "$dstarg"; then
# $@ is not empty: it contains at least $arg.
set fnord "$@" "$dstarg"
shift # fnord
fi
shift # arg
dstarg=$arg
done
break;;
esac
done
if test -z "$1"; then
if test -z "$dir_arg"; then
echo "$0: no input file specified." >&2
exit 1
fi
# It's OK to call `install-sh -d' without argument.
# This can happen when creating conditional directories.
exit 0
fi
for src
do
# Protect names starting with `-'.
case $src in
-*) src=./$src ;;
esac
if test -n "$dir_arg"; then
dst=$src
src=
if test -d "$dst"; then
mkdircmd=:
chmodcmd=
else
mkdircmd=$mkdirprog
fi
else
# Waiting for this to be detected by the "$cpprog $src $dsttmp" command
# might cause directories to be created, which would be especially bad
# if $src (and thus $dsttmp) contains '*'.
if test ! -f "$src" && test ! -d "$src"; then
echo "$0: $src does not exist." >&2
exit 1
fi
if test -z "$dstarg"; then
echo "$0: no destination specified." >&2
exit 1
fi
dst=$dstarg
# Protect names starting with `-'.
case $dst in
-*) dst=./$dst ;;
esac
# If destination is a directory, append the input filename; won't work
# if double slashes aren't ignored.
if test -d "$dst"; then
if test -n "$no_target_directory"; then
echo "$0: $dstarg: Is a directory" >&2
exit 1
fi
dst=$dst/`basename "$src"`
fi
fi
# This sed command emulates the dirname command.
dstdir=`echo "$dst" | sed -e 's,[^/]*$,,;s,/$,,;s,^$,.,'`
# Make sure that the destination directory exists.
# Skip lots of stat calls in the usual case.
if test ! -d "$dstdir"; then
defaultIFS='
'
IFS="${IFS-$defaultIFS}"
oIFS=$IFS
# Some sh's can't handle IFS=/ for some reason.
IFS='%'
set - `echo "$dstdir" | sed -e 's@/@%@g' -e 's@^%@/@'`
IFS=$oIFS
pathcomp=