Commit a1cef38d authored by Haowen Zhang's avatar Haowen Zhang
Browse files

Fix some wrong mapping positions

parent 87baa9d3

src/chromap.cc

+165 −127

File changed.

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src/chromap.h

+1 −1
Original line number Diff line number Diff line
@@ -180,7 +180,7 @@ class Chromap { 
  void BuildAugmentedTreeForPeaks(uint32_t ref_id);

  void OutputMappingsInVector(uint8_t mapq_threshold, uint32_t num_reference_sequences, const SequenceBatch &reference, const std::vector<std::vector<MappingRecord> > &mappings);

  void OutputMappings(uint32_t num_reference_sequences, const SequenceBatch &reference, const std::vector<std::vector<MappingRecord> > &mappings);

  int AdjustGapBeginning(Direction mapping_direction, const char *ref, const char *read, int *gap_beginning, int read_end, int ref_start_position, int ref_end_position, int *n_cigar, uint32_t **cigar);

  int AdjustGapBeginning(Direction mapping_direction, const char *ref, const char *read, int *read5_start_position, int read_end, int ref_start_position, int ref_end_position, int *n_cigar, uint32_t **cigar);

  void GetRefStartEndPositionForReadFromMapping(Direction mapping_direction, const std::pair<int, uint64_t> &mapping, const char *read, int read_length, int in_split_site, const SequenceBatch &reference, uint32_t *ref_start_position, uint32_t *ref_end_position, int *n_cigar, uint32_t **cigar, int *NM, std::string &MD_TAG);



  inline static double GetRealTime() {

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