Changeset 3409 for trunk/yat/omic/BamHeader.cc

Timestamp:

Apr 17, 2015, 3:07:04 AM (8 years ago)

Author:

Peter

Message:

refs #817. Fix bug that struct was not updated in text(1) function (in libbam mode); add test to catch bug.

File:

• trunk/yat/omic/BamHeader.cc (modified) (3 diffs)

trunk/yat/omic/BamHeader.cc

@@ -25 +25 @@
 
 #include "yat/utility/Exception.h"
+
+// we need to include 'sam_header.h' when compiling against libbam
+#ifndef YAT_HAVE_HTSLIB
+  #if YAT_HAVE_SAM_H
+  #include <sam_header.h>
+  #elif YAT_HAVE_BAM_BAM_H
+  #include <bam/sam_header.h>
+  #elif YAT_HAVE_SAMTOOLS_SAM_H
+  #include <samtools/sam_header.h>
+  #else
+  #error cannot end up here
+  #endif
+#endif
 
 #include <cassert>
@@ -118 +131 @@
   }
 
+
   void BamHeader::text(const std::string& txt)
   {
@@ -130 +144 @@
     memcpy(header_->text, txt.c_str(), txt.size()+1);
 #ifndef YAT_HAVE_HTSLIB
+    // destroy dict to ensure that things are updated during parsing
+    if (header_->dict) {
+      sam_header_free(header_->dict);
+      header_->dict = 0;
+    }
     sam_header_parse(header_);
 #endif