Changeset 3352

Timestamp:

Nov 22, 2014, 12:16:53 AM (8 years ago)

Author:

Peter

Message:

implement BamHeader? against htslib, except parse region which requires more love. refs #394

Location:

trunk/yat/omic

Files:

• BamHeader.cc (modified) (3 diffs)
• BamHeader.h (modified) (2 diffs)

trunk/yat/omic/BamHeader.cc

@@ -44 +44 @@
   {
     assert(header_);
+#if YAT_HAVE_HTSLIB
+    assert(0 && "FIXME: parse_region not implement against htslib");
+#else
     if (!bam_parse_region(header_, reg.c_str(), &tid, &begin, &end))
       return;
+#endif
     std::ostringstream ss;
     ss << "invalid region: '" << reg << "'";
@@ -68 +72 @@
   int32_t BamHeader::tid(const std::string& name) const
   {
+#if YAT_HAVE_HTSLIB
+    return bam_name2id(header_, name.c_str());
+#else
     if (!header_->hash) {
       // We would like to call something like bam_init_header_hash,
@@ -81 +88 @@
     }
     return bam_get_tid(header_, name.c_str());
+#endif
   }
 

trunk/yat/omic/BamHeader.h

@@ -34 +34 @@
 
   /**
-     \brief Wrapper around bam_header_t struct.
+     \brief Wrapper around bam_hdr_t struct.
 
      Class is typically created via InBamFile::header().
@@ -93 +93 @@
     int32_t n_targets(void) const;
   private:
-    bam_header_t* header_;
+#ifndef YAT_HAVE_HTSLIB
+    typedef bam_header_t bam_hdr_t;
+#endif
+    bam_hdr_t* header_;
 
     friend class InBamFile;
     friend class OutBamFile;
-    BamHeader(bam_header_t* h);
 
     // using compiler generated copy and assignment