Ignore:
Timestamp:
Sep 19, 2014, 7:41:50 AM (8 years ago)
Author:
Peter
Message:

refs #806 add test for Pileup class

File:
1 edited

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Added
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  • trunk/yat/omic/Pileup.h

    r3310 r3317  
    3333namespace omic {
    3434
     35  /**
     36     \since new in yat 0.13
     37   */
    3538  template<typename Iterator>
    3639  class Pileup
     
    5558      const yat::omic::BamRead& bam(void) const { return bam_; }
    5659
     60      /**
     61         \return cigar element at current position
     62       */
    5763      uint32_t cigar(void) const
    5864      {
     
    102108      }
    103109
     110      /**
     111         \return index of base at this position
     112       */
    104113      size_t qpos(void) const { return qpos_; }
    105114    private:
     
    118127    };
    119128
    120     // FIXME change to a filter iterator that ignores end_of_sequence entries
     129    /**
     130       \brief Const iterator that can be used to iterate over reads at
     131       current position
     132     */
    121133    typedef typename std::deque<Entry>::const_iterator const_iterator;
    122134
     
    147159
    148160    /**
     161       \brief step to next position with coverage
    149162     */
    150163    void increment(void);
     
    177190
    178191
     192  /**
     193     \relates Pileup
     194
     195     \since new in yat 0.13
     196   */
    179197  template<typename Iterator>
    180198  Pileup<Iterator> make_pileup(Iterator first, Iterator last)
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