Changeset 3335 for trunk/yat/omic/Pileup.h

Timestamp:

Oct 23, 2014, 4:33:47 PM (7 years ago)

Author:

Peter

Message:

closes #806

File:

• trunk/yat/omic/Pileup.h (modified) (4 diffs)

trunk/yat/omic/Pileup.h

@@ -28 +28 @@
 #include "yat/utility/yat_assert.h"
 
+#include <boost/iterator/iterator_traits.hpp>
+#include <boost/concept/assert.hpp>
 #include <boost/shared_ptr.hpp>
 
@@ -38 +40 @@
 
   /**
+     Pileup takes a range of BamReads and pile them up on the current
+     position. User can investigate the pile of reads at current
+     (locus) position via begin() and end(), which provide access to
+     reads at current position. The position can be incremented and in
+     that way the user can investigate each position of the genome.
+
      \since new in yat 0.13
+
+     Type Requirments:
+     - \c Iterator is a \input_iterator
+     - \c value_type is convertible to BamRead
    */
   template<typename Iterator>
@@ -178 +190 @@
        each Entry that has an insertion. Otherwise increment to next
        position and update each Entry accordingly.
+
+       If the position is not covered by any read, the Pileup
+       fastforward to next covered locus.
      */
     void increment(void);
@@ -225 +240 @@
     : bam_(first), bam_end_(last), pos_(0), tid_(0), skip_ref_(0)
   {
+    BOOST_CONCEPT_ASSERT((boost::InputIterator<Iterator>));
+    using boost::Convertible;
+    typedef typename boost::iterator_value<Iterator>::type value_type;
+    BOOST_CONCEPT_ASSERT((Convertible<value_type, BamRead>));
     increment();
   }