Changeset 2953

Timestamp:

Jan 16, 2013, 8:39:27 AM (10 years ago)

Author:

Peter

Message:

implement BamHeader::target_length(). fixes #740

Location:

branches/0.10-stable

Files:

• test/Makefile.am (modified) (2 diffs)
• test/Suite.h (modified) (2 diffs)
• test/bam_header.cc (added)
• yat/omic/BamHeader.cc (modified) (2 diffs)

branches/0.10-stable/test/Makefile.am

@@ -7 +7 @@
 # Copyright (C) 2005 Jari Häkkinen, Peter Johansson
 # Copyright (C) 2006, 2007, 2008 Jari Häkkinen, Peter Johansson, Markus Ringnér
-# Copyright (C) 2009, 2010, 2011, 2012 Peter Johansson
+# Copyright (C) 2009, 2010, 2011, 2012, 2013 Peter Johansson
 #
 # This file is part of the yat library, http://dev.thep.lu.se/yat
@@ -40 +40 @@
   test/averager4.test \
   test/bam_pair_analyse test/bam_iterator test/bam_region_iterator \
+  test/bam_header \
   test/codon.test test/commandline.test \
   test/concept.test \

branches/0.10-stable/test/Suite.h

@@ -6 +6 @@
 /*
   Copyright (C) 2008 Jari Häkkinen, Peter Johansson
-  Copyright (C) 2009, 2010, 2011, 2012 Peter Johansson
+  Copyright (C) 2009, 2010, 2011, 2012, 2013 Peter Johansson
 
   This file is part of the yat library, http://dev.thep.lu.se/yat
@@ -28 +28 @@
 // used to tell automake that test should be skipped
 #define EXIT_SKIP 77
+
+// SKIP_BAM_TEST is defined if we should skip bam tests
+#ifndef HAVE_LIBBAM
+#define SKIP_BAM_TEST
+#endif
+#ifndef HAVE_SAMTOOLS
+#define SKIP_BAM_TEST
+#endif
 
 #include <yat/utility/VectorMutable.h>

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

@@ -1 +1 @@
 // $Id$
 //
-// Copyright (C) 2012 Peter Johansson
+// Copyright (C) 2012, 2013 Peter Johansson
 //
 // This program is free software; you can redistribute it and/or modify
@@ -32 +32 @@
 
 
+  uint32_t BamHeader::target_length(size_t tid) const
+  {
+    assert(tid < static_cast<size_t>(n_targets()));
+    return header_->target_len[tid];
+  }
+
+
   const char* BamHeader::target_name(size_t tid) const
   {