Changeset 3431


Ignore:
Timestamp:
Oct 26, 2015, 8:09:34 AM (6 years ago)
Author:
Peter
Message:

revert r3426 and some cosmetic changes (refs #794)

Location:
branches/0.13-stable
Files:
6 edited

Legend:

Unmodified
Added
Removed
  • branches/0.13-stable/NEWS

    r3430 r3431  
    1010  - AveragerWeighted::n(void) now return 0, when object is empty (ticket #802)
    1111  - added support for htslib (see ticket #794)
    12       - YAT_HAVE_LIBBAM is defined if linking against libbam (not against libhts)
    13       - YAT_BAM_HEADER is only defined when building against libbam
     12      - `YAT_HAVE_LIBBAM` is defined if linking against either libbam
     13        or libhts. Use #if defined YAT_HAVE_LIBBAM && !defined
     14        (YAT_HAVE_HTSLIB) to check that building against libbam.
     15      - `YAT_BAM_HEADER` is only defined when building against libbam
    1416  - Container2DIterator is now tagged with
    1517    boost::random_access_traversal_tag (see ticket #803, r3393)
  • branches/0.13-stable/configure.ac

    r3426 r3431  
    385385      AC_MSG_CHECKING([samtools API])
    386386      AC_MSG_RESULT([yes])
    387       AC_DEFINE([YAT_HAVE_LIBBAM], [1],
    388                 [Define to 1 if yat is built against libbam])
    389 
    390387      LIBS="$BAM_LIBS $LIBS"
    391388      # check if function bam_calend works. Result of this test can be
     
    401398  ])
    402399  AC_SUBST([HAVE_HTSLIB], [$have_hts])
     400
     401  AC_DEFINE([YAT_HAVE_LIBBAM], [1],
     402            [Define to 1 if yat is built with bam support])
    403403
    404404  YAT_CHECK_LA_LIBS([
  • branches/0.13-stable/test/Suite.cc

    r3417 r3431  
    4646    if (require_bam) {
    4747#ifndef YAT_HAVE_LIBBAM
    48       out() << "no libbam\n";
     48      out() << "no bam support\n";
    4949      exit (EXIT_SKIP);
    5050#endif
  • branches/0.13-stable/test/Suite.h

    r3322 r3431  
    2424*/
    2525
     26// ensure that config.h always is included first
     27#ifndef YAT_VERSION
     28#error header 'config.h' not included
     29#endif
     30
     31#include <yat/utility/config_public.h>
     32
    2633#define YAT_TEST_PROLOGUE "\n=== " << __func__ << " ===\n"
    2734
     
    3037
    3138// 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
     39#if !defined (YAT_HAVE_LIBBAM) || !defined (HAVE_SAMTOOLS_EXECUTABLE)
    3640#define SKIP_BAM_TEST
    3741#endif
  • branches/0.13-stable/test/pileup.cc

    r3417 r3431  
    2323
    2424#include "Suite.h"
     25
     26#include <yat/utility/config_public.h>
    2527
    2628#ifdef YAT_HAVE_LIBBAM
     
    5052
    5153
    52 #ifdef YAT_HAVE_LIBBAM
    5354char seq_nt16(size_t x)
    5455{
     
    6364}
    6465
     66#ifdef YAT_HAVE_LIBBAM
    6567void test1(test::Suite& suite, const std::string& fn)
    6668{
  • branches/0.13-stable/yat/utility/config_public.h.in

    r3426 r3431  
    4444#undef YAT_HAVE_HTS_H
    4545
    46 /// Define to 1 if yat is built against libbam
     46/// Define to 1 if yat is built with bam support
    4747#undef YAT_HAVE_LIBBAM
    4848
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