Changeset 3317


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

refs #806 add test for Pileup class

Location:
trunk
Files:
1 added
3 edited

Legend:

Unmodified
Added
Removed
  • trunk/test/Makefile.am

    r3314 r3317  
    7171  test/ostream_iterator.test \
    7272  test/pca.test \
     73  test/pileup.test \
    7374  test/queue.test test/queue2.test \
    7475  test/range.test test/regression.test test/rnd.test \
     
    136137
    137138# dependencies for lazycheck
     139test/bam.log: test/data/foo.sorted.bam
     140test/bam_header.log: test/data/foo.sorted.bam
     141test/bam_header2.log: test/data/foo.sorted.bam
     142test/bam_iterator.log: test/data/foo.sorted.bam
     143test/bam_pair_analyse.log: test/data/foo.sorted.bam
     144test/bam_pair_iterator.log: test/data/foo.sorted.bam
     145test/bam_read_filter.log: test/data/foo.sorted.bam
     146test/bam_region_iterator.log: test/data/foo.sorted.bam
    138147test/cmd_test.log: test/help.test $(shell_test_deps)
    139148test/help_test.log: test/help.test $(shell_test_deps)
     149test/pileup.log: test/data/foo.sorted.bam
    140150test/static_test.log: $(srcdir)/m4/yat.m4 $(shell_test_deps)
    141151test/yat_config_test.log: build_support/yat-config \
  • trunk/yat/omic/Makefile.am

    r3175 r3317  
    5050nobase_include_HEADERS += $(srcdir)/yat/omic/GFF2.h
    5151nobase_include_HEADERS += $(srcdir)/yat/omic/GFF3.h
     52nobase_include_HEADERS += $(srcdir)/yat/omic/Pileup.h
  • 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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