Changeset 2960


Ignore:
Timestamp:
Jan 17, 2013, 9:19:07 AM (10 years ago)
Author:
Peter
Message:

merge patch release 0.10.1 into trunk

Location:
trunk
Files:
12 edited
1 copied

Legend:

Unmodified
Added
Removed

  • trunk

  • trunk/NEWS

    r2943 r2960  
    99
    1010yat 0.10.x series from http://dev.thep.lu.se/yat/svn/branches/0.10-stable
     11
     12version 0.10.1 (released 17 January 2013)
     13  - libyat is no longer linked against -lbam (bug #733)
     14  - yat.pc now mentions -lbam and -lz (bug #736)
     15  - include style <samtools/bam.h> now supported (bug #735)
     16  - BamHeader::target_length(1) is now implemented (bug #740)
     17
     18  A complete list of closed tickets can be found here [[br]]
     19  http://dev.thep.lu.se/yat/query?status=closed&milestone=yat+0.10.1
    1120
    1221version 0.10 (released 4 January 2013)

  • trunk/build_support/Makefile.am

    r2932 r2960  
    11## $Id$
    22
    3 # Copyright (C) 2008, 2009, 2010, 2011, 2012 Peter Johansson
     3# Copyright (C) 2008, 2009, 2010, 2011, 2012, 2013 Peter Johansson
    44#
    55# This file is part of the yat library, http://dev.thep.lu.se/yat
    … …  
    4747  -e 's|@YAT_LDFLAGS[@]|$(YAT_LDFLAGS)|g' \
    4848  -e 's|@YAT_PRIMARY_LIBS[@]|$(YAT_PRIMARY_LIBS)|g' \
     49  -e 's|@BAM_LIBS[@]|$(BAM_LIBS)|g' \
    4950  -e 's|@LIBM[@]|$(LIBM)|g' \
    5051  -e 's|@PACKAGE[@]|$(PACKAGE)|g' \

  • trunk/build_support/gen_yat_pc.sh.in

    r2853 r2960  
    22# @configure_input@
    33
    4 # Copyright (C) 2011, 2012 Peter Johansson
     4# Copyright (C) 2011, 2012, 2013 Peter Johansson
    55#
    66# This file is part of the yat library, http://dev.thep.lu.se/yat
    … …  
    8686-e 's|@BOOST_THREAD_LIB[@]|@BOOST_THREAD_LIB@|g' \
    8787-e 's|@BOOST_SYSTEM_LIB[@]|@BOOST_SYSTEM_LIB@|g' \
     88-e 's|@BAM_LIBS[@]|@BAM_LIBS@|g' \
     89-e 's|@LIBS[@]|@LIBS@|g' \
    8890< $input

  • trunk/build_support/yat-config.in

    r2842 r2960  
    22
    33# Copyright (C) 2008 Jari Häkkinen, Peter Johansson
    4 # Copyright (C) 2009, 2010, 2011, 2012 Peter Johansson
     4# Copyright (C) 2009, 2010, 2011, 2012, 2013 Peter Johansson
    55#
    66# This file is part of the yat library, http://dev.thep.lu.se/yat
    … …  
    4040YAT_LDFLAGS="@YAT_LDFLAGS@"
    4141YAT_PRIMARY_LIBS="@YAT_PRIMARY_LIBS@"
     42BAM_LIBS="@BAM_LIBS@"
    4243LIBM="@LIBM@"
    4344
    … …  
    142143    ;;
    143144    --libs)
    144     flags="$flags -lyat $YAT_PRIMARY_LIBS $YAT_CBLAS_LIB $LIBM $LIBS"
     145    flags="$flags -lyat $BAM_LIBS $YAT_PRIMARY_LIBS $YAT_CBLAS_LIB $LIBM $LIBS"
    145146    ;;
    146147    --libs-without-cblas)
    147     flags="$flags -lyat $YAT_PRIMARY_LIBS $LIBM $LIBS"
     148    flags="$flags -lyat $BAM_LIBS $YAT_PRIMARY_LIBS $LIBM $LIBS"
    148149    ;;
    149150    --ldflags)
    … …  
    159160    ;;
    160161    --link-libtool)
    161     flags="$flags $LA_FILE $YAT_CBLAS_LIB"
     162    flags="$flags $LA_FILE $BAM_LIBS $YAT_CBLAS_LIB"
    162163    ;;
    163164    --yat-la-file)

  • trunk/build_support/yat.pc.in

    r2853 r2960  
    22
    33# Copyright (C) 2008 Jari Häkkinen, Peter Johansson
    4 # Copyright (C) 2009, 2010, 2012 Peter Johansson
     4# Copyright (C) 2009, 2010, 2012, 2013 Peter Johansson
    55#
    66# This file is part of the yat library, http://dev.thep.lu.se/yat
    … …  
    2929Version: @VERSION@
    3030Requires: gsl >= @gsl_version@
    31 Libs: -L${libdir} -lyat @YAT_LDFLAGS@ @LDFLAGS@
    32 Libs.private: @BOOST_THREAD_LIB@ @BOOST_SYSTEM_LIB@
     31Libs: -L${libdir} -lyat @BAM_LIBS@ @YAT_LDFLAGS@ @LDFLAGS@ @LIBS@
     32Libs.private: -lz @BOOST_THREAD_LIB@ @BOOST_SYSTEM_LIB@
    3333Cflags: @YAT_CPPFLAGS@ @YAT_CXXFLAGS@ @CPPFLAGS@ @CXXFLAGS@ -I${includedir}

  • trunk/configure.ac

    r2948 r2960  
    428428          [YAT_PRIMARY_LIBS="$YAT_PRIMARY_LIBS $lib"])
    429429done
     430# workaround for ticket #736
     431for lib in $BAM_LIBS; do
     432  APR_REMOVEFROM([YAT_PRIMARY_LIBS], [$lib])
     433done
     434AC_SUBST(BAM_LIBS)
    430435AC_SUBST(YAT_PRIMARY_LIBS)
    431436AC_SUBST(YAT_LIBS)

  • trunk/m4/version.m4

    r2943 r2960  
    7070# yat-0.9.2  6:2:0
    7171# yat-0.10   7:0:0
     72# yat-0.10.1 7:1:0
    7273#
    7374# *Accidently, the libtool number was not updated for yat 0.5

  • trunk/test/Makefile.am

    r2951 r2960  
    3838  test/averager4.test \
    3939  test/bam_pair_analyse test/bam_iterator test/bam_region_iterator \
     40  test/bam_header \
    4041  test/codon.test test/commandline.test \
    4142  test/concept.test \

  • trunk/test/Suite.h

    r2943 r2960  
    66/*
    77  Copyright (C) 2008 Jari Häkkinen, Peter Johansson
    8   Copyright (C) 2009, 2010, 2011, 2012 Peter Johansson
     8  Copyright (C) 2009, 2010, 2011, 2012, 2013 Peter Johansson
    99
    1010  This file is part of the yat library, http://dev.thep.lu.se/yat
    … …  
    2828// used to tell automake that test should be skipped
    2929#define EXIT_SKIP 77
     30
     31// SKIP_BAM_TEST is defined if we should skip bam tests
     32#ifndef HAVE_LIBBAM
     33#define SKIP_BAM_TEST
     34#endif
     35#ifndef HAVE_SAMTOOLS
     36#define SKIP_BAM_TEST
     37#endif
    3038
    3139#include <yat/utility/VectorMutable.h>

  • trunk/yat/omic/BamHeader.cc

    r2883 r2960  
    11// $Id$
    22//
    3 // Copyright (C) 2012 Peter Johansson
     3// Copyright (C) 2012, 2013 Peter Johansson
    44//
    55// This program is free software; you can redistribute it and/or modify
    … …  
    3232
    3333
     34  uint32_t BamHeader::target_length(size_t tid) const
     35  {
     36    assert(tid < static_cast<size_t>(n_targets()));
     37    return header_->target_len[tid];
     38  }
     39
     40
    3441  const char* BamHeader::target_name(size_t tid) const
    3542  {

  • trunk/yat/utility/config_public.h.in

    r2943 r2960  
    66/*
    77  Copyright (C) 2008 Jari Häkkinen, Peter Johansson
    8   Copyright (C) 2009, 2011, 2012 Peter Johansson
     8  Copyright (C) 2009, 2011, 2012, 2013 Peter Johansson
    99
    1010  This file is part of the yat library, http://dev.thep.lu.se/yat
    … …  
    3434#undef HAVE_BAM_H
    3535
    36 /// Define if samtools executable is available
    37 #undef HAVE_SAMTOOLS
     36/// Define to 1 if you have the <samtools/bam.h> header file.
     37#undef HAVE_SAMTOOLS_BAM_H
    3838
    3939/// Define if compiler supports deprecated attribute, as in g++ 4.0
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