Changeset 3408 for trunk/yat/omic/BamHeader.h

Timestamp:

Apr 16, 2015, 2:22:24 AM (8 years ago)

Author:

Peter

Message:

Implement functions to get/set free text in BamHeader?. As setting the
header text modifies underlying data, copy and assignment are now
implemented as hard copy (rather than the implicit pointer copy as
before). It also means that the bam_hdr_t* is no longer owned by
InBamFile?, but is now owned by BamHeader? and destroyed in its
destructor.

refs #817

File:

• trunk/yat/omic/BamHeader.h (modified) (7 diffs)

trunk/yat/omic/BamHeader.h

@@ -25 +25 @@
 #include "config_bam.h"
 
+#include "yat/utility/config_public.h"
+
 #include YAT_SAM_HEADER
 
@@ -32 +34 @@
 namespace yat {
 namespace omic {
+
+#ifndef YAT_HAVE_HTSLIB
+  namespace detail {
+    bam_header_t * bam_hdr_dup(const bam_header_t* other);
+  }
+#endif
 
   /**
@@ -54 +62 @@
 
     /**
+       \brief Destructor
+     */
+    ~BamHeader(void);
+
+    /**
+       \brief Copy constructor
+     */
+    BamHeader(const BamHeader&);
+
+    /**
        Parse a region in the format: 'chr2:100,000-200,000 and return
        values in variables \a tid, \a begin and \a end. \a reg is
@@ -70 +88 @@
 
     /**
+       \brief Exchanges the content in \c *this and \a other
+
+       \since New in yat 0.13
+     */
+    void swap(BamHeader& other);
+
+    /**
        Name of chromosome with ID \a tid
      */
@@ -78 +103 @@
      */
     uint32_t target_length(size_t tid) const;
+
+    /**
+       \return text in header
+
+       \since New in yat 0.13
+     */
+    std::string text(void) const;
+
+    /**
+       \brief set text in header
+
+       This function parses \a txt and updates fields.
+
+       \since New in yat 0.13
+     */
+    void text(const std::string& txt);
 
     /**
@@ -94 +135 @@
      */
     int32_t n_targets(void) const;
+
+    /**
+       \brief assignment operator
+     */
+    BamHeader& operator=(const BamHeader& rhs);
+
   private:
 #ifndef YAT_HAVE_HTSLIB
@@ -104 +151 @@
 
     // using compiler generated copy and assignment
-    //BamHeader(const BamHeader&);
-    //BamHeader& operator=(const BamHeader& rhs);
   };
+
+  /**
+     Exchanges the content in the headers.
+
+     \since New in yat 0.13
+
+     \relates BamHeader
+   */
+  void swap(BamHeader& lhs, BamHeader& rhs);
 
 }}}