Changeset 2943


Ignore:
Timestamp:
Jan 4, 2013, 7:38:38 AM (11 years ago)
Author:
Peter
Message:

merge release 0.10 into trunk

Location:
trunk
Files:
28 edited
1 copied

Legend:

Unmodified
Added
Removed

  • trunk

  • trunk/Makefile.am

    r2853 r2943  
    9494  esac
    9595
    96 maintainer-check-local: mc_installcheck yat-pc-check
     96maintainer-check-local: mc_installcheck yat-pc-check mc_without_samtools
    9797
    9898mc_installcheck:
    … …  
    167167
    168168include $(srcdir)/am/maintainer.am
     169
     170# run within maintainer-check
     171# try ./configure --without-samtools; make; make check
     172mc_without_samtools:
     173  @rm -rf _mc_without_samtools
     174  mkdir _mc_without_samtools
     175  cd _mc_without_samtools \
     176  && ../$(srcdir)/configure $(DISTCHECK_CONFIGURE_FLAGS) --without-samtools \
     177  && $(MAKE) $(AM_MAKEFLAGS) && $(MAKE) check $(AM_MAKEFLAGS)

  • trunk/NEWS

    r2921 r2943  
    1010yat 0.10.x series from http://dev.thep.lu.se/yat/svn/branches/0.10-stable
    1111
    12 version 0.10 (released NOT YET)
     12version 0.10 (released 4 January 2013)
     13  - samtools wrapper classes (ticket #729)
     14  - new utility functions (ticket #717)
    1315
    1416  A complete list of closed tickets can be found here [[br]]
    … …  
    290292Copyright (C) 2010, 2011 Peter Johansson
    291293Copyright (C) 2012 Jari Häkkinen, Peter Johansson
     294Copyright (C) 2013 Peter Johansson
    292295
    293296This file is part of yat library, http://dev.thep.lu.se/yat

  • trunk/README

    r2916 r2943  
    102102== Optional packages ==
    103103
     104=== Samtools ===
     105
     106Samtools available from http://samtools.sourceforge.net/ is required
     107to enable classes related to bam files. You can build yat without
     108samtools if you run configure with `--without-samtools`, in which case
     109bam related classes are not included in built library. Header files
     110<sam.h> and <bam.h> are needed as well as library libbam. If you have
     111header files available outside compiler's search path, you can help
     112the compiler with `./configure CPPFLAGS=-I<include dir>` when header
     113files are found in directory `<include dir>`. Likewise, you can run
     114`./configure LDFLAGS=-L<lib dir>` when library is found in `<lib dir>`
     115outside linker's search path. In order to run tests related to bam
     116files, the samtools binary is also needed. If not found during
     117configuration, these tests will be skipped. If you have samtools
     118available outside PATH, you can help configure to find it with
     119`./configure SAMTOOLS=/path/to/samtools`.
     120
     121=== ZLIB ===
     122
     123Zlib available from http://www.zlib.net/ is required to build samtools
     124and consequently needed to build yat too, unless you turn off samtools
     125support (please refer to samtools section above). Header file `zlib.h`
     126and library libz are required. If installed in an unconventional
     127location you can help the compiler/linker with `CPPFLAGS=-I<include
     128dir>` and `LDFLAGS=-L<lib dir>`, respectively.
     129
    104130=== ATLAS ===
    105131

  • trunk/README.developer

    r2787 r2943  
    5959way but there is still some work to do before we do exceptions in a neutral way.
    6060
     61=== Samtools ===
     62
     63Code that depends on samtools API should be excluded from the build
     64when configured --without-samtools, i.e., put files within
     65`HAVE_LIBBAM` conditionals (or alternatively put code inside `#ifdef
     66HAVE_SAMTOOL` preprocessor conditionals). In order to support multiple
     67inclusion styles we do not include <bam.h> directly, but `#include
     68<config_bam.h>` and `#include YAT_BAM_HEADER`. Similarly, for `<sam.h>`
     69include `YAT_SAM_HEADER`. For more details on this, refer to
     70`yat/omic/config_bam.h`.
     71
    6172=== Doxygen ===
    6273We generate our documentation using [http://www.doxygen.org Doxygen]

  • trunk/configure.ac

    r2891 r2943  
    289289  AC_CHECK_LIB([z], [inflateEnd], [],
    290290    [YAT_MSG_ERROR([Library 'libz' was not found])])
    291   AC_CHECK_HEADER([bam.h], [],
    292     [YAT_MSG_ERROR([Header file 'bam.h' was not found])])
     291  YAT_CHECK_HEADER_BAM([],[YAT_MSG_ERROR([Header file 'bam.h' was not found])])
    293292  # try link against libbam
    294   YAT_CHECK_LIBBAM([LIBS="$BAM_LIBS $LIBS"],
     293  YAT_CHECK_LIBBAM([LIBS="$BAM_LIBS $LIBS"
     294                    AC_DEFINE([HAVE_LIBBAM], [1],
     295                              [Define to 1 if libbam is available])],
    295296    [YAT_MSG_ERROR([Library 'libbam' was not found])])
    296297  AC_PATH_PROG([SAMTOOLS], [samtools], [false])

  • trunk/m4/version.m4

    r2921 r2943  
    22#
    33# Copyright (C) 2008, 2009 Jari Häkkinen, Peter Johansson
    4 # Copyright (C) 2010, 2011, 2012 Peter Johansson
     4# Copyright (C) 2010, 2011, 2012, 2013 Peter Johansson
    55#
    66# This file is part of the yat library, http://dev.thep.lu.se/yat
    … …  
    6969# yat-0.9.1  6:1:0
    7070# yat-0.9.2  6:2:0
     71# yat-0.10   7:0:0
    7172#
    7273# *Accidently, the libtool number was not updated for yat 0.5

  • trunk/m4/yat_check_libbam.m4

    r2919 r2943  
    2121#   along with yat. If not, see <http://www.gnu.org/licenses/>.
    2222
     23# YAT_CHECK_HEADER_BAM([action-if-found], [action-if-not-found])
     24# ==============================================================
     25#
     26AC_DEFUN([YAT_CHECK_HEADER_BAM],
     27[
     28yat_bam_header=no
     29# check how to #include <bam.h>
     30AC_CHECK_HEADERS([bam/bam.h bam.h samtools/bam.h bam.h],
     31                 [yat_bam_header=yes; break])
     32AS_IF([test x$yat_bam_header = xyes], [$1], [$2])
     33]) # YAT_CHECK_HEADER_BAM
     34
    2335
    2436# YAT_CHECK_LIBBAM([action-if-found], [action-if-not-found])
    … …  
    2739AC_DEFUN([YAT_CHECK_LIBBAM],
    2840[
     41AC_REQUIRE([YAT_CHECK_HEADER_BAM])
    2942BAM_LIBS=no
    3043AC_MSG_CHECKING([for library containing bam_header_destroy])
    … …  
    3952  AC_MSG_RESULT([$BAM_LIBS])
    4053])
    41 AS_IF([test x"$BAM_LIBS" = false], [$2], [$1])
     54AS_IF([test x"$BAM_LIBS" = xno], [$2], [$1])
    4255]) # YAT_CHECK_LIBBAM
    4356
    … …  
    5164save_LIBS=$LIBS
    5265LIBS="$1 $LIBS"
    53 AC_LINK_IFELSE([AC_LANG_PROGRAM([@%:@include <bam.h>],
    54                                 [bam_header_t* hdr = bam_header_init();
     66AC_LINK_IFELSE([AC_LANG_PROGRAM([@%:@if HAVE_BAM_H
     67                                 @%:@ include <bam.h>
     68                                 @%:@elif HAVE_BAM_BAM_H
     69                                 @%:@ include <bam/bam.h>
     70                                 @%:@elif HAVE_SAMTOOLS_BAM_H
     71                                 @%:@ include <samtools/bam.h>
     72                                 @%:@endif
     73                                ],[
     74                                 bam_header_t* hdr = bam_header_init();
    5575                                 bam_header_destroy(hdr);
    5676                                ])],

  • trunk/test/Makefile.am

    r2932 r2943  
    249249CLEANFILES += test/data/.dirstamp
    250250CLEANFILES += test/data/foo.bam
    251 CLEANFILES += test/data/foo.supported.bam
    252 CLEANFILES += test/data/foo.supported.bam.bai
     251CLEANFILES += test/data/foo.sorted.bam
     252CLEANFILES += test/data/foo.sorted.bam.bai
    253253
    254254check_DATA  = test/data/foo.sorted.bam
    … …  
    260260
    261261if HAVE_SAMTOOLS
    262 test/data/foo.bam: test/data/foo.sam test/data/.dirstamp
    263   $(SAMTOOLS) view -Sb $(srcdir)/test/data/foo.sam -o $@
     262test/data/foo.bam: test/data/foo.sam test/data/.dirstamp Makefile
     263  $(SAMTOOLS) view -Sb $(srcdir)/test/data/foo.sam > $@-t && mv $@-t $@
    264264
    265265test/data/foo.sorted.bam: test/data/foo.bam
    … …  
    269269  $(SAMTOOLS) index test/data/foo.sorted.bam
    270270else
    271 test/data/foo.sorted.bam:; : > $@
    272 test/data/foo.sorted.bam.bai:; : > $@
     271test/data/foo.sorted.bam: test/data/.dirstamp
     272  : > $@
     273
     274test/data/foo.sorted.bam.bai: test/data/.dirstamp
     275  : > $@
    273276endif

  • trunk/test/Suite.h

    r2649 r2943  
    66/*
    77  Copyright (C) 2008 Jari Häkkinen, Peter Johansson
    8   Copyright (C) 2009, 2010, 2011 Peter Johansson
     8  Copyright (C) 2009, 2010, 2011, 2012 Peter Johansson
    99
    1010  This file is part of the yat library, http://dev.thep.lu.se/yat
    … …  
    2525
    2626#define YAT_TEST_PROLOGUE "\n=== " << __func__ << " ===\n"
     27
     28// used to tell automake that test should be skipped
     29#define EXIT_SKIP 77
    2730
    2831#include <yat/utility/VectorMutable.h>

  • trunk/test/bam_iterator.cc

    r2895 r2943  
    2020#include "Suite.h"
    2121
     22#ifdef HAVE_LIBBAM
    2223#include "yat/omic/BamFile.h"
    2324#include "yat/omic/BamRead.h"
    2425#include "yat/omic/BamReadIterator.h"
    2526#include "yat/omic/BamWriteIterator.h"
     27#endif
    2628
    2729#include <algorithm>
    2830#include <cassert>
    2931#include <fstream>
    30 #include <iostream>
    3132#include <string>
    3233
    3334using namespace theplu::yat;
     35
     36void test1(test::Suite& suite);
     37
     38int main(int argc, char* argv[])
     39{
     40  test::Suite suite(argc, argv);
     41#ifndef HAVE_LIBBAM
     42  suite.out() << "no libbam\n";
     43  return EXIT_SKIP;
     44#endif
     45#ifndef HAVE_SAMTOOLS
     46  suite.out() << "no samtools\n";
     47  return EXIT_SKIP;
     48#endif
     49  test1(suite);
     50  return suite.return_value();
     51}
     52
     53#ifdef HAVE_LIBBAM
    3454using namespace omic;
    3555
    … …  
    7999};
    80100
    81 int main(int argc, char* argv[])
     101
     102void test1(test::Suite& suite)
    82103{
    83 #ifndef HAVE_SAMTOOLS
    84   return EXIT_SKIP;
    85 #endif
    86   test::Suite suite(argc, argv);
    87 
    88104  std::string file = "../../data/foo.sorted.bam";
    89105
    … …  
    99115  in.open(file);
    100116  size_t n1 = std::distance(BamReadIterator(in), BamReadIterator());
    101   std::cout << "entries in " << file << ": " << n1 << "\n";
     117  suite.out() << "entries in " << file << ": " << n1 << "\n";
    102118  in.close();
    103119
    … …  
    105121  size_t n2 = std::distance(BamReadIterator(copy), BamReadIterator());
    106122  copy.close();
    107   std::cout << "entries in " << outname << ": " << n2 << "\n";
     123  suite.out() << "entries in " << outname << ": " << n2 << "\n";
    108124  if (n1!=n2) {
    109     std::cout << "error: not same number of entries in copy\n";
    110     exit(1);
     125    suite.out() << "error: not same number of entries in copy\n";
     126    suite.add(false);
    111127  }
    112128
    … …  
    115131  if (!std::equal(BamReadIterator(in), BamReadIterator(),
    116132                  BamReadIterator(copy), BamReadEqual())) {
    117     std::cout << "error: " << file << " and " << outname << " not equal\n";
    118     exit(1);
     133    suite.out() << "error: " << file << " and " << outname << " not equal\n";
     134    suite.add(false);
    119135  }
    120136  copy.close();
    121137  in.close();
    122138  unlink(outname.c_str());
    123   std::cout << "OK\n";
    124   return 0;
    125139}
     140#endif

  • trunk/test/bam_pair_analyse.cc

    r2902 r2943  
    2020#include "Suite.h"
    2121
     22using namespace theplu::yat;
     23
     24#if HAVE_LIBBAM
    2225#include "yat/omic/algorithm.h"
    2326#include "yat/omic/BamRead.h"
    2427#include "yat/omic/BamReadIterator.h"
     28#endif
    2529
    26 using namespace theplu::yat;
     30void test1(test::Suite& suite);
     31
     32int main(int argc, char* argv[])
     33{
     34  test::Suite suite(argc, argv);
     35#ifndef HAVE_LIBBAM
     36  suite.out() << "no libbam\n";
     37  return EXIT_SKIP;
     38#endif
     39#ifndef HAVE_SAMTOOLS
     40  suite.out() << "no samtools available\n";
     41  return EXIT_SKIP;
     42#endif
     43
     44#ifdef HAVE_LIBBAM
     45  test1(suite);
     46#endif
     47  return suite.return_value();
     48}
     49
     50
     51#ifdef HAVE_LIBBAM
    2752using namespace omic;
    2853
    … …  
    3964};
    4065
    41 
    42 int main(int argc, char* argv[])
     66void test1(test::Suite& suite)
    4367{
    44 #ifndef HAVE_SAMTOOLS
    45   return EXIT_SKIP;
    46 #endif
    47   test::Suite suite(argc, argv);
    48 
    4968  std::string file = "../../data/foo.sorted.bam";
    5069
    … …  
    5473  Counter counter;
    5574  bam_pair_analyse(iter, end, counter);
    56 
    5775  suite.out() << counter.n_ << "\n";
    58 
    5976  suite.add(counter.n_==395);
    60 
    6177  is.close();
    62   return suite.return_value();
    6378}
     79#endif

  • trunk/test/bam_region_iterator.cc

    r2895 r2943  
    2020#include "Suite.h"
    2121
     22#ifdef HAVE_LIBBAM
    2223#include "yat/omic/BamReadIterator.h"
    2324#include "yat/omic/BamWriteIterator.h"
     25#include "yat/omic/config_bam.h"
     26#endif
    2427
    25 #include <bam.h>
     28#ifdef YAT_BAM_HEADER
     29#include YAT_BAM_HEADER
     30#endif
    2631
    2732#include <algorithm>
    … …  
    3237
    3338using namespace theplu::yat;
    34 using namespace theplu::yat::omic;
     39
     40void test1(test::Suite& suite);
     41int main(int argc, char* argv[])
     42{
     43  test::Suite suite(argc, argv);
     44#ifndef HAVE_LIBBAM
     45  suite.out() << "no libbam\n";
     46  return EXIT_SKIP;
     47#endif
     48#ifndef HAVE_SAMTOOLS
     49  suite.out() << "no samtools\n";
     50  return EXIT_SKIP;
     51#endif
     52
     53  try {
     54    test1(suite);
     55  }
     56  catch (std::runtime_error& e) {
     57    suite.err() << "what: " << e.what() << "\n";
     58    suite.add(false);
     59  }
     60
     61  return suite.return_value();
     62}
    3563
    3664void test1(test::Suite& suite)
    3765{
     66#ifdef HAVE_LIBBAM
     67  using namespace omic;
    3868  std::string file = "../../data/foo.sorted.bam";
    3969
    … …  
    6393  suite.err() << "count: " << count << "\nexpected: 185\n";
    6494  suite.add(false);
     95#endif
    6596}
    66 
    67 
    68 int main(int argc, char* argv[])
    69 {
    70 #ifndef HAVE_SAMTOOLS
    71   return EXIT_SKIP;
    72 #endif
    73   test::Suite suite(argc, argv);
    74 
    75   try {
    76     test1(suite);
    77   }
    78   catch (std::runtime_error& e) {
    79     suite.err() << "what: " << e.what() << "\n";
    80     suite.add(false);
    81   }
    82 
    83   return suite.return_value();
    84 }

  • trunk/test/common_defs.sh.in

    r2927 r2943  
    22# $Id$
    33
    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
    … …  
    115115@MKDIR_P@ --verbose $test_dir
    116116
     117# Taken from Automake 1.11 tests/defs.sh.in
     118
     119# Unset some MAKE... variables that may cause 'make' to act like a
     120# recursively invoked sub-make.  Any 'make' invocation in a test is
     121# conceptually an independent invocation, not part of the main
     122# 'yat' build.
     123unset MFLAGS
     124unset MAKEFLAGS
     125unset MAKELEVEL
     126unset DESTDIR
     127unset V
     128unset TESTS
     129unset TEST_LOGS
     130unset RECHECK_LOGS
     131unset VERBOSE
     132
    117133cd $test_dir
    118134

  • trunk/test/rng-mt.cc

    r2881 r2943  
    22
    33/*
    4   Copyright (C) 2012 Peter Johansson
     4  Copyright (C) 2012, 2013 Peter Johansson
    55
    66  This file is part of the yat library, http://dev.thep.lu.se/yat
    … …  
    2929
    3030#include <algorithm>
     31#include <cstdlib>
    3132#include <iostream>
    3233#include <iterator>
     34#include <stdexcept>
    3335#include <vector>
    3436
    … …  
    4446  void operator()(void)
    4547  {
    46     for (std::vector<int>::iterator i=begin_; i!=end_; ++i)
    47       *i = rnd_(100);
     48    try {
     49      for (std::vector<int>::iterator i=begin_; i!=end_; ++i)
     50        *i = rnd_(100);
     51    }
     52    catch (std::exception& e) {
     53      std::cerr << e.what() << "\n";
     54      exit(EXIT_FAILURE);
     55    }
    4856  }
    4957
    … …  
    8795  suite.out() << "\ny: ";
    8896  std::copy(y.begin(), y.end(), std::ostream_iterator<int>(suite.out(), " "));
    89   suite.out() << "\n";
     97  suite.out() << std::endl;
    9098
    9199  if (x==y) {
    … …  
    93101    suite.err() << "x and y are equal\n";
    94102  }
     103}
    95104
     105
     106std::vector<int> rnd_vec(void)
     107{
     108  std::vector<int> x(10);
     109  Visitor visitor1(x);
     110  boost::thread_group threads;
     111  threads.create_thread(visitor1);
     112  threads.join_all();
     113  return x;
    96114}
    97115
    … …  
    102120  // test that we get same number with same seed
    103121  RNG::instance()->seed(0);
    104   std::vector<int> x(10);
    105   Visitor visitor1(x);
    106   boost::thread_group threads;
    107   threads.create_thread(visitor1);
    108   threads.join_all();
    109   std::vector<int> y(x);
     122  std::vector<int> y = rnd_vec();
     123  suite.out() << "y: ";
     124  std::copy(y.begin(), y.end(), std::ostream_iterator<int>(suite.out(), " "));
     125  suite.out() << std::endl;
     126
    110127  RNG::instance()->seed(0);
    111   threads.create_thread(visitor1);
    112   threads.join_all();
     128  std::vector<int> x = rnd_vec();
    113129  suite.out() << "x: ";
    114130  std::copy(x.begin(), x.end(), std::ostream_iterator<int>(suite.out(), " "));
    115   suite.out() << "\ny: ";
    116   std::copy(y.begin(), y.end(), std::ostream_iterator<int>(suite.out(), " "));
    117   suite.out() << "\n";
     131  suite.out() << std::endl;
    118132  if (x!=y) {
    119133    suite.add(false);
    … …  
    135149  Visitor visitor(x);
    136150  visitor();
    137 
    138   std::vector<int> y(x);
    139   Visitor visitor1(y);
    140   boost::thread_group threads;
    141   threads.create_thread(visitor1);
    142   threads.join_all();
    143 
    144151  suite.out() << "x: ";
    145152  std::copy(x.begin(), x.end(), std::ostream_iterator<int>(suite.out(), " "));
    146   suite.out() << "\ny: ";
     153  suite.out() << std::endl;
     154
     155  std::vector<int> y = rnd_vec();
     156  suite.out() << "y: ";
    147157  std::copy(y.begin(), y.end(), std::ostream_iterator<int>(suite.out(), " "));
    148   suite.out() << "\n";
     158  suite.out() << std::endl;
    149159
    150160  if (x==y) {

  • trunk/test/utility.cc

    r2908 r2943  
    44  Copyright (C) 2006 Jari Häkkinen, Markus Ringnér
    55  Copyright (C) 2007, 2008 Jari Häkkinen, Peter Johansson
    6   Copyright (C) 2009, 2010, 2011, 2012 Peter Johansson
     6  Copyright (C) 2009, 2010, 2011 Peter Johansson
     7  Copyright (C) 2012 Jari Häkkinen, Peter Johansson
    78
    89  This file is part of the yat library, http://dev.thep.lu.se/yat
    … …  
    3637#include <boost/concept_archetype.hpp>
    3738
     39#include <cassert>
    3840#include <cerrno>
    3941#include <fstream>

  • trunk/test/version.cc

    r2919 r2943  
    4949  suite.out() << "    patch:   " << patch_version() << "\n";
    5050
     51  suite.add(YAT_VERSION == version());
     52
    5153  suite.out() << "Boost API version: " << BOOST_LIB_VERSION << "\n";
    5254  suite.out() << "GSL API version: " << GSL_VERSION << "\n";

  • trunk/yat/omic/BamFile.cc

    r2897 r2943  
    2020#include "BamFile.h"
    2121#include "BamHeader.h"
     22#include "config_bam.h"
    2223
    2324#include "yat/utility/Exception.h"
    2425
    25 #include <bam.h>
     26#include YAT_BAM_HEADER
    2627
    2728#include <stdexcept>

  • trunk/yat/omic/BamFile.h

    r2897 r2943  
    2121#include "BamHeader.h"
    2222#include "BamRead.h"
     23#include "config_bam.h"
    2324
    2425#include "yat/utility/Exception.h"
    2526
    26 #include <sam.h>
     27#include YAT_SAM_HEADER
    2728
    2829#include <boost/utility.hpp>

  • trunk/yat/omic/BamHeader.h

    r2884 r2943  
    1919// along with this program. If not, see <http://www.gnu.org/licenses/>.
    2020
    21 #include <bam.h>
     21#include "config_bam.h"
     22
     23#include YAT_BAM_HEADER
    2224
    2325namespace theplu {

  • trunk/yat/omic/BamRead.cc

    r2886 r2943  
    1919
    2020#include "BamRead.h"
    21 
    22 #include <bam.h>
     21#include "config_bam.h"
     22
     23#include YAT_BAM_HEADER
    2324
    2425#include <algorithm>

  • trunk/yat/omic/BamRead.h

    r2911 r2943  
    1919// along with this program. If not, see <http://www.gnu.org/licenses/>.
    2020
    21 #include <sam.h>
    22 #include <bam.h>
     21#include "config_bam.h"
     22
     23#include YAT_BAM_HEADER
     24#include YAT_SAM_HEADER
    2325
    2426#include <functional>

  • trunk/yat/omic/BamReadIterator.h

    r2896 r2943  
    2121#include "BamFile.h"
    2222#include "BamRead.h"
     23#include "config_bam.h"
    2324
    24 #include <sam.h>
     25#include YAT_SAM_HEADER
    2526
    2627#include <boost/iterator/iterator_facade.hpp>

  • trunk/yat/omic/BamWriteIterator.cc

    r2883 r2943  
    1919
    2020#include "BamFile.h"
     21#include "config_bam.h"
    2122
    22 #include <sam.h>
     23#include YAT_SAM_HEADER
    2324
    2425#include <cassert>

  • trunk/yat/omic/Makefile.am

    r2932 r2943  
    3939nobase_include_HEADERS += $(srcdir)/yat/omic/BamReadIterator.h
    4040nobase_include_HEADERS += $(srcdir)/yat/omic/BamWriteIterator.h
     41nobase_include_HEADERS += $(srcdir)/yat/omic/config_bam.h
    4142endif
    4243nobase_include_HEADERS += $(srcdir)/yat/omic/Codon.h

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

    r2673 r2943  
    66/*
    77  Copyright (C) 2008 Jari Häkkinen, Peter Johansson
    8   Copyright (C) 2009, 2011 Peter Johansson
     8  Copyright (C) 2009, 2011, 2012 Peter Johansson
    99
    1010  This file is part of the yat library, http://dev.thep.lu.se/yat
    … …  
    2828///
    2929
     30/// Define to 1 if you have the <bam/bam.h> header file.
     31#undef HAVE_BAM_BAM_H
     32
     33/// Define to 1 if you have the <bam.h> header file.
     34#undef HAVE_BAM_H
     35
     36/// Define if samtools executable is available
     37#undef HAVE_SAMTOOLS
     38
    3039/// Define if compiler supports deprecated attribute, as in g++ 4.0
    3140#undef YAT_HAVE_GCC_DEPRECATED

  • trunk/yat/utility/utility.cc

    r2919 r2943  
    44  Copyright (C) 2005, 2006 Jari Häkkinen, Markus Ringnér
    55  Copyright (C) 2007, 2008 Jari Häkkinen, Peter Johansson
    6   Copyright (C) 2010, 2012 Peter Johansson
     6  Copyright (C) 2010 Peter Johansson
     7  Copyright (C) 2012 Jari Häkkinen, Peter Johansson
    78
    89  This file is part of the yat library, http://dev.thep.lu.se/yat
    … …  
    3031#include "stl_utility.h"
    3132
     33#include <cassert>
    3234#include <fnmatch.h>
    3335#include <fstream>

  • trunk/yat/utility/utility.h

    r2908 r2943  
    88  Copyright (C) 2006 Jari Häkkinen
    99  Copyright (C) 2007, 2008 Jari Häkkinen, Peter Johansson
    10   Copyright (C) 2009, 2010, 2011, 2012 Peter Johansson
     10  Copyright (C) 2009, 2010, 2011, 2012, 2013 Peter Johansson
    1111
    1212  This file is part of the yat library, http://dev.thep.lu.se/yat
    … …  
    335335     \see http://linux.die.net/man/3/mkdir
    336336
    337      \throw if creation failed
     337     \throw runtime_error if creation failed
    338338   */
    339339  void mkdir(const std::string& dir, mode_t mode=0777);
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