Changeset 2972
- Timestamp:
- Jan 26, 2013, 7:53:56 AM (10 years ago)
- Location:
- branches/0.10-stable
- Files:
-
- 1 added
- 4 edited
Legend:
- Unmodified
- Added
- Removed
-
branches/0.10-stable/configure.ac
r2957 r2972 296 296 [Define to 1 if libbam is available])], 297 297 [YAT_MSG_ERROR([Library 'libbam' was not found])]) 298 # check if global variable bam_nt16_rev_table is available 299 YAT_BAM_NT16_REV_TABLE 298 300 AC_PATH_PROG([SAMTOOLS], [samtools], [false]) 299 301 AC_ARG_VAR([SAMTOOLS], [Tools for alignment in the SAM format]) -
branches/0.10-stable/m4/yat_check_libbam.m4
r2928 r2972 1 1 ## $Id$ 2 2 # 3 # serial 1 (yat 0.10)3 # serial 2 (yat 0.10.2) 4 4 # 5 5 # 6 # Copyright (C) 2012 Peter Johansson6 # Copyright (C) 2012, 2013 Peter Johansson 7 7 # 8 8 # This file is part of the yat library, http://dev.thep.lu.se/yat … … 78 78 LIBS=$save_LIBS 79 79 ]) # YAT_LINK_BAM_IFELSE 80 81 # YAT_BAM_NT16_REV_TABLE 82 # ==================================================================== 83 # Check if global variable bam_nt16_rev_table is available in 84 # -lbam. If found call AC_DEFINE(HAVE_BAM_NT16_REV_TABLE). 85 AC_DEFUN([YAT_BAM_NT16_REV_TABLE], 86 [ 87 AC_MSG_CHECKING([for bam_nt16_rev_table]) 88 AC_LINK_IFELSE([AC_LANG_PROGRAM( 89 [@%:@if HAVE_BAM_H 90 @%:@ include <bam.h> 91 @%:@elif HAVE_BAM_BAM_H 92 @%:@ include <bam/bam.h> 93 @%:@elif HAVE_SAMTOOLS_BAM_H 94 @%:@ include <samtools/bam.h> 95 @%:@endif 96 ],[ 97 char c = bam_nt16_rev_table@<:@7@:>@; 98 ]) 99 ],[ 100 AC_MSG_RESULT([yes]) 101 AC_DEFINE([HAVE_BAM_NT16_REV_TABLE], [1], 102 [Define to 1 if libbam contains bam_nt16_rev_table]) 103 ],[ 104 AC_MSG_RESULT([no]) 105 ]) 106 ]) # YAT_BAM_NT16_REV_TABLE -
branches/0.10-stable/test/Makefile.am
r2953 r2972 39 39 test/averager3.test \ 40 40 test/averager4.test \ 41 test/bam.test \ 41 42 test/bam_pair_analyse test/bam_iterator test/bam_region_iterator \ 42 43 test/bam_header \ -
branches/0.10-stable/yat/omic/BamRead.cc
r2969 r2972 149 149 std::string BamRead::sequence(void) const 150 150 { 151 // FIXME bam_nt16_rev_table not available in old lbam152 151 std::string result(sequence_length(), ' '); 152 #ifdef HAVE_BAM_NT16_REV_TABLE 153 153 for (size_t i=0; i<result.size(); ++i) 154 154 result[i] = bam_nt16_rev_table[sequence(i)]; 155 #else 156 std::string table = "=ACMGRSVTWYHKDBN"; 157 for (size_t i=0; i<result.size(); ++i) 158 result[i] = table[sequence(i)]; 159 #endif 155 160 return result; 156 161 }
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