Changeset 3363

Timestamp:

Nov 25, 2014, 11:42:54 AM (8 years ago)

Author:

Peter

Message:

improve docs. refs #794

Location:

trunk/yat/omic

Files:

• BamFile.h (modified) (4 diffs)
• BamHeader.h (modified) (2 diffs)
• BamReadFilter.h (modified) (1 diff)

trunk/yat/omic/BamFile.h

@@ -86 +86 @@
 
 #ifndef YAT_HAVE_HTSLIB
-    /// Old samtools 0.1.xx had a struct samfile_t, which in htslib has
-    /// changed to samFile
+    /**
+       \brief only defined when compiling against old bamlib
+
+       Old samtools 0.1.xx had a struct samfile_t, which in htslib has
+       changed to samFile
+    */
     typedef samfile_t samFile;
 #endif
@@ -122 +126 @@
        libbam, \c bam_index_t.
 
-       \see index(void)
+       \since New in yat 0.13
+
+       \see function index(void) const
      */
 #if YAT_HAVE_HTSLIB
@@ -183 +189 @@
        \brief read the next BamRead
 
+       This function is used in BamReadIterator. Typically it is more
+       convenient to read bams via a BamReadIterator than through this
+       function directly.
+
        \return true on success
      */
@@ -252 +262 @@
        \param compression a number [0,9] indicating level of
        compression. 9 gives highest compression and 0 indicates no
-       compression (suitable for piping between applications)
+       compression (suitable for piping between applications).
 
        \since yat 0.12

trunk/yat/omic/BamHeader.h

@@ -82 +82 @@
        \brief inverse of target_name(size_t)
 
-       \note If \a name does not exist, behaviour is undefined.
+       If compiled against libbam and \a name does not exist,
+       behavious is undefined. If compiled against htslib, a
+       utility::runtime_error is thrown.
 
        \since new in yat 0.11
@@ -89 +91 @@
 
     /**
-       Number of chromosomes
+       \return Number of chromosomes
      */
     int32_t n_targets(void) const;

trunk/yat/omic/BamReadFilter.h

@@ -28 +28 @@
 #include <functional>
 
+// this flag was defined in bam.h but has disappeared in htslib
 #ifndef BAM_DEF_MASK
 #define BAM_DEF_MASK (BAM_FUNMAP | BAM_FSECONDARY | BAM_FQCFAIL | BAM_FDUP)