Changeset 3410 for trunk/yat/omic/BamHeader.h

Timestamp:

Apr 22, 2015, 1:05:43 AM (8 years ago)

Author:

Peter

Message:

add two new functions read_group and program_group to access data in BamHeader?. closes #817

File:

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

trunk/yat/omic/BamHeader.h

@@ -29 +29 @@
 #include YAT_SAM_HEADER
 
+#include <map>
 #include <string>
 
@@ -88 +89 @@
 
     /**
+       \brief Access value in \c \@PG lines.
+
+       A program group line in the header typically looks like
+
+       \code @PG  ID:bwa  PN:bwa  VN:0.6.1-r104 \endcode
+
+       and for this line \c program_group("bwa", "VN") returns
+       \c "0.6.1-r104"
+
+       \return value for \a key for line with ID \a id.
+
+       \since New in yat 0.13
+    */
+    const std::string& program_group(const std::string& id,
+                                     const std::string& key) const;
+
+    /**
+       \brief Access value in \c \@RG lines.
+
+       A read group line in the header typically looks like
+
+       \code @RG  ID:foo  PL:ILLUMINA SM:Tumour \endcode
+
+       and for this line \c read_group("foo", "SM") returns \c "Tumour"
+
+       \return value for \a key for line with ID \a id.
+
+       \since New in yat 0.13
+    */
+    //
+    const std::string& read_group(const std::string& id,
+                                  const std::string& key) const;
+
+    /**
        \brief Exchanges the content in \c *this and \a other
 
@@ -146 +181 @@
 #endif
     bam_hdr_t* header_;
+    typedef std::map<std::string, std::string> strMap;
+    typedef std::map<std::string, strMap> strMap2;
+    mutable strMap2 read_group_;
+    mutable strMap2 program_group_;
 
     friend class InBamFile;
     friend class OutBamFile;
+
+    const std::string& group(strMap2& map, const std::string& type,
+                             const std::string& id,
+                             const std::string& key) const;
 
     // using compiler generated copy and assignment