Changeset 3317 for trunk/yat/omic/Pileup.h

Timestamp:

Sep 19, 2014, 7:41:50 AM (9 years ago)

Author:

Peter

Message:

refs #806 add test for Pileup class

File:

• trunk/yat/omic/Pileup.h (modified) (6 diffs)

trunk/yat/omic/Pileup.h

@@ -33 +33 @@
 namespace omic {
 
+  /**
+     \since new in yat 0.13
+   */
   template<typename Iterator>
   class Pileup
@@ -55 +58 @@
       const yat::omic::BamRead& bam(void) const { return bam_; }
 
+      /**
+         \return cigar element at current position
+       */
       uint32_t cigar(void) const
       {
@@ -102 +108 @@
       }
 
+      /**
+         \return index of base at this position
+       */
       size_t qpos(void) const { return qpos_; }
     private:
@@ -118 +127 @@
     };
 
-    // FIXME change to a filter iterator that ignores end_of_sequence entries
+    /**
+       \brief Const iterator that can be used to iterate over reads at
+       current position
+     */
     typedef typename std::deque<Entry>::const_iterator const_iterator;
 
@@ -147 +159 @@
 
     /**
+       \brief step to next position with coverage
      */
     void increment(void);
@@ -177 +190 @@
 
 
+  /**
+     \relates Pileup
+
+     \since new in yat 0.13
+   */
   template<typename Iterator>
   Pileup<Iterator> make_pileup(Iterator first, Iterator last)