Commit 601f33cb authored by Andreas Tille's avatar Andreas Tille

Updated version 0.1+dfsg from 'upstream/0.1+dfsg'

with Debian dir 53ff38dee6ad1c3e475a11aabfcedc2894687a7d
parents fb57e3c9 95647b39
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file SRF_Container.cc
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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)
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#!/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=
while test $# -ne 0 ; do
pathcomp=$pathcomp$1
shift
if test ! -d "$pathcomp"; then
$mkdirprog "$pathcomp"
# mkdir can fail with a `File exist' error in case several
# install-sh are creating the directory concurrently. This
# is OK.
test -d "$pathcomp" || exit
fi
pathcomp=$pathcomp/
done
fi
if test -n "$dir_arg"; then
$doit $mkdircmd "$dst" \
&& { test -z "$chowncmd" || $doit $chowncmd "$dst"; } \
&& { test -z "$chgrpcmd" || $doit $chgrpcmd "$dst"; } \
&& { test -z "$stripcmd" || $doit $stripcmd "$dst"; } \
&& { test -z "$chmodcmd" || $doit $chmodcmd "$dst"; }
else
dstfile=`basename "$dst"`
# Make a couple of temp file names in the proper directory.
dsttmp=$dstdir/_inst.$$_
rmtmp=$dstdir/_rm.$$_
# Trap to clean up those temp files at exit.
trap 'status=$?; rm -f "$dsttmp" "$rmtmp" && exit $status' 0
trap '(exit $?); exit' 1 2 13 15
# Copy the file name to the temp name.
$doit $cpprog "$src" "$dsttmp" &&
# and set any options; do chmod last to preserve setuid bits.
#
# If any of these fail, we abort the whole thing. If we want to
# ignore errors from any of these, just make sure not to ignore
# errors from the above "$doit $cpprog $src $dsttmp" command.
#
{ test -z "$chowncmd" || $doit $chowncmd "$dsttmp"; } \
&& { test -z "$chgrpcmd" || $doit $chgrpcmd "$dsttmp"; } \
&& { test -z "$stripcmd" || $doit $stripcmd "$dsttmp"; } \
&& { test -z "$chmodcmd" || $doit $chmodcmd "$dsttmp"; } &&
# Now rename the file to the real destination.
{ $doit $mvcmd -f "$dsttmp" "$dstdir/$dstfile" 2>/dev/null \
|| {
# The rename failed, perhaps because mv can't rename something else
# to itself, or perhaps because mv is so ancient that it does not
# support -f.
# Now remove or move aside any old file at destination location.
# We try this two ways since rm can't unlink itself on some
# systems and the destination file might be busy for other
# reasons. In this case, the final cleanup might fail but the new
# file should still install successfully.
{
if test -f "$dstdir/$dstfile"; then
$doit $rmcmd -f "$dstdir/$dstfile" 2>/dev/null \
|| $doit $mvcmd -f "$dstdir/$dstfile" "$rmtmp" 2>/dev/null \
|| {
echo "$0: cannot unlink or rename $dstdir/$dstfile" >&2
(exit 1); exit
}
else
:
fi
} &&
# Now rename the file to the real destination.
$doit $mvcmd "$dsttmp" "$dstdir/$dstfile"
}
}
fi || { (exit 1); exit; }
done
# The final little trick to "correctly" pass the exit status to the exit trap.
{
(exit 0); exit
}
# Local variables:
# eval: (add-hook 'write-file-hooks 'time-stamp)
# time-stamp-start: "scriptversion="
# time-stamp-format: "%:y-%02m-%02d.%02H"
# time-stamp-end: "$"
# End:
lib_LIBRARIES = libsrf.a
libsrf_a_SOURCES = \
SRF_Container.hh \
SRF_Container.cc \
SRF_File.hh \
SRF_File.cc \
SRF_Read.hh \
SRF_Read.cc \
SRF_ReadSet.hh \
SRF_ReadSet.cc \
SRF_util.hh \
SRF_util.cc \
SRF_Ztr.hh \
SRF_Ztr.cc
INCLUDES=$(SHELL io_lib-config --cflags) -I.
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//Copyright 2007 Asim Siddiqui
//
// 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.
//
//
//
#include <cstddef>
#include <cstdlib>
#include <cstring>
#include <SRF_util.hh>
#include <SRF_Container.hh>
#include <SRF_ReadSet.hh>
#define HEADERBLOCKTYPE "SSRF"
#define CONTAINERTYPE 'Z'
#define FORMATVERSION "1.3"
SRF_Container::SRF_Container( void )
{
formatVersion = FORMATVERSION;
headerBlockType = HEADERBLOCKTYPE;
containerType = CONTAINERTYPE;
sizeContainerHeader = 0;
}
SRF_Container::~SRF_Container( void )
{
// null
}
bool
SRF_Container::populate( std::fstream& file )
{
containerPositionInFile = file.tellg();
//read blockType, blockSize, version, containerType, baseCaller, baseCallerVersion
char tmp[4];
file.read(tmp, 4);
headerBlockType = std::string(tmp, 4);;
if ( headerBlockType.compare( HEADERBLOCKTYPE ) != 0 )
{
SRF_ReportError( "incorrect block type header" );
return FALSE;
}
sizeContainerHeader = 0;
file.read( reinterpret_cast<char *>(&sizeContainerHeader), 4 );
sizeContainerHeader = be_int4(sizeContainerHeader);
formatVersion = SRF_readString( file );
if ( formatVersion.compare( FORMATVERSION ) != 0 )
{
SRF_ReportError( "incorrect format version" );
return FALSE;
}
file.read ( &containerType, 1);
if ( containerType != CONTAINERTYPE )
{
SRF_ReportError( "unsupported container type" );
return FALSE;
}
baseCaller = SRF_readString( file );
baseCallerVersion = SRF_readString( file );
return TRUE;
}
bool
SRF_Container::setup( const std::string& baseCallerIn,
const std::string& baseCallerVersionIn )
{
baseCaller = baseCallerIn;
baseCallerVersion = baseCallerVersionIn;
return TRUE;
}
char
SRF_Container::getContainerType( void )
{
return containerType;
}
const std::string&
SRF_Container::getBaseCaller( void )
{
return baseCaller;
}
const std::string&
SRF_Container::getBaseCallerVersion( void )
{
return baseCallerVersion;
}
const std::string&
SRF_Container::getHeaderBlockType( void )
{
return headerBlockType;
}
const std::string&
SRF_Container::getFormatVersion( void )
{
return formatVersion;
}
bool
SRF_Container::filePtrToContainerStart( std::fstream& file )
{
file.seekg( containerPositionInFile );
return TRUE;
}
bool
SRF_Container::nextReadSet( std::fstream& file )
{
SRF_ReportError( "Not implemented" );
return FALSE;
}
bool
SRF_Container::previousReadSet( std::fstream& file )
{
SRF_ReportError( "Not implemented" );
return FALSE;
}
bool
SRF_Container::write( std::fstream& file )
{
sizeContainerHeader = 0;
//write blockType, blockSize, version, containerType, baseCaller, baseCallerVersion
sizeContainerHeader += headerBlockType.length();
sizeContainerHeader += 4;
char* formatVersionStr = ADOPT SRF_cStrToPascalStr( formatVersion.c_str() );
sizeContainerHeader += strlen( formatVersionStr );
sizeContainerHeader += 1;
char* baseCallerStr = ADOPT SRF_cStrToPascalStr( baseCaller.c_str() );
sizeContainerHeader += strlen( baseCallerStr );
char* baseCallerVersionStr = ADOPT SRF_cStrToPascalStr( baseCallerVersion.c_str() );
sizeContainerHeader += strlen( baseCallerVersionStr );
file << headerBlockType;
int32_t be_sizeContainerHeader = be_int4(sizeContainerHeader);
file.write(reinterpret_cast<const char*>(&be_sizeContainerHeader),4);
file << formatVersionStr;
file << containerType;
file << baseCallerStr;
file << baseCallerVersionStr;
delete [] formatVersionStr;
delete [] baseCallerStr;
delete [] baseCallerVersionStr;
}
void
SRF_Container::dump( void )
{
std::cout << "Container Block Type:" << headerBlockType <<std::endl;
std::cout << "Format Version:" << formatVersion <<std::endl;
std::cout << "Container Type:" << containerType <<std::endl;
std::cout << "Base Caller:" << baseCaller <<std::endl;
std::cout << "Base Caller Version:" << baseCallerVersion <<std::endl;
}
bool
SRF_Container::writeReadSet( std::fstream& file,
const std::string& ztrHeader,
const std::vector<ztr_t>& ztrBlobs,
const std::vector<std::string>& readIds,
const std::string& uniqueIdPrefix )
{
SRF_ReadSet newReadSet;
if ( !newReadSet.setup( uniqueIdPrefix, ztrHeader ) )
{
SRF_ReportError( "can't initialize readSet" );
return FALSE;
}
if ( !newReadSet.write( file, ztrBlobs, readIds ) )
{
SRF_ReportError( "can't write readSet" );
return FALSE;
}
return TRUE;
}
ADOPT SRF_ReadSet*
SRF_Container::firstReadSet( std::fstream& file )
{
file.seekg( ((off_t) containerPositionInFile + sizeContainerHeader) ); // TO DO fix to work with XML files
SRF_ReadSet* readSet = new SRF_ReadSet;
if ( !readSet->populate( file ) )
{
SRF_ReportError( "can't populate first read set" );