Changeset 2972

Timestamp:

Jan 26, 2013, 7:53:56 AM (9 years ago)

Author:

Peter

Message:

refs #745. Implement a workaround when bam_nt16_rev_table is not
available in -lbam.

Location:

branches/0.10-stable

Files:

• configure.ac (modified) (1 diff)
• m4/yat_check_libbam.m4 (modified) (2 diffs)
• test/Makefile.am (modified) (1 diff)
• test/bam.cc (added)
• yat/omic/BamRead.cc (modified) (1 diff)

branches/0.10-stable/configure.ac

@@ -296 +296 @@
                               [Define to 1 if libbam is available])],
     [YAT_MSG_ERROR([Library 'libbam' was not found])])
+  # check if global variable bam_nt16_rev_table is available
+  YAT_BAM_NT16_REV_TABLE
   AC_PATH_PROG([SAMTOOLS], [samtools], [false])
   AC_ARG_VAR([SAMTOOLS], [Tools for alignment in the SAM format])

branches/0.10-stable/m4/yat_check_libbam.m4

@@ -1 +1 @@
 ## $Id$
 #
-# serial 1 (yat 0.10)
+# serial 2 (yat 0.10.2)
 #
 #
-#   Copyright (C) 2012 Peter Johansson
+#   Copyright (C) 2012, 2013 Peter Johansson
 #
 #   This file is part of the yat library, http://dev.thep.lu.se/yat
@@ -78 +78 @@
 LIBS=$save_LIBS
 ]) # YAT_LINK_BAM_IFELSE
+
+# YAT_BAM_NT16_REV_TABLE
+# ====================================================================
+# Check if global variable bam_nt16_rev_table is available in
+# -lbam. If found call AC_DEFINE(HAVE_BAM_NT16_REV_TABLE).
+AC_DEFUN([YAT_BAM_NT16_REV_TABLE],
+[
+AC_MSG_CHECKING([for bam_nt16_rev_table])
+AC_LINK_IFELSE([AC_LANG_PROGRAM(
+                 [@%:@if HAVE_BAM_H
+                  @%:@ include <bam.h>
+                  @%:@elif HAVE_BAM_BAM_H
+                  @%:@ include <bam/bam.h>
+                  @%:@elif HAVE_SAMTOOLS_BAM_H
+                  @%:@ include <samtools/bam.h>
+                  @%:@endif
+                 ],[
+                  char c = bam_nt16_rev_table@<:@7@:>@;
+                 ])
+               ],[
+                 AC_MSG_RESULT([yes])
+                 AC_DEFINE([HAVE_BAM_NT16_REV_TABLE], [1],
+                           [Define to 1 if libbam contains bam_nt16_rev_table])
+               ],[
+                 AC_MSG_RESULT([no])
+               ])
+]) # YAT_BAM_NT16_REV_TABLE

branches/0.10-stable/test/Makefile.am

@@ -39 +39 @@
   test/averager3.test \
   test/averager4.test \
+  test/bam.test \
   test/bam_pair_analyse test/bam_iterator test/bam_region_iterator \
   test/bam_header \

branches/0.10-stable/yat/omic/BamRead.cc

@@ -149 +149 @@
   std::string BamRead::sequence(void) const
   {
-    // FIXME bam_nt16_rev_table not available in old lbam
     std::string result(sequence_length(), ' ');
+#ifdef HAVE_BAM_NT16_REV_TABLE
     for (size_t i=0; i<result.size(); ++i)
       result[i] = bam_nt16_rev_table[sequence(i)];
+#else
+    std::string table = "=ACMGRSVTWYHKDBN";
+    for (size_t i=0; i<result.size(); ++i)
+      result[i] = table[sequence(i)];
+#endif
     return result;
   }