Commit d8ec11ec authored by Li's avatar Li
Browse files

Finalize the split alignment without end fixing

parent a99e6272

src/chromap.cc

+645 −481

File changed.

Preview size limit exceeded, changes collapsed.

src/chromap.h

+3 −2
Original line number Diff line number Diff line
@@ -145,11 +145,12 @@ class Chromap { 
  // Supportive functions

  void ConstructIndex();

  int BandedAlignPatternToText(const char *pattern, const char *text, const int read_length, int *mapping_end_location);

  int BandedAlignPatternToTextWithDropOff(const char *pattern, const char *text, const int read_length, int *mapping_end_location);

  int BandedAlignPatternToTextWithDropOffFrom3End(const char *pattern, const char *text, const int read_length, int *mapping_end_position);

  int BandedAlignPatternToTextWithDropOff(const char *pattern, const char *text, const int read_length, int *mapping_end_location, int *read_mapping_length);

  int BandedAlignPatternToTextWithDropOffFrom3End(const char *pattern, const char *text, const int read_length, int *mapping_end_position, int *read_mapping_length);

  void BandedAlign4PatternsToText(const char **patterns, const char *text, int read_length, int32_t *mapping_edit_distances, int32_t *mapping_end_positions);

  void BandedAlign8PatternsToText(const char **patterns, const char *text, int read_length, int16_t *mapping_edit_distances, int16_t *mapping_end_positions);

  void BandedTraceback(int min_num_errors, const char *pattern, const char *text, const int read_length, int *mapping_start_position);

  void BandedTracebackToEnd(int min_num_errors, const char *pattern, const char *text, const int read_length, int *mapping_end_position);

  void MergeCandidates(std::vector<Candidate> &c1, std::vector<Candidate> &c2, std::vector<Candidate> &buffer);

  void SupplementCandidates(const Index &index, uint32_t repetitive_seed_length1, uint32_t repetitive_seed_length2, std::vector<std::pair<uint64_t, uint64_t> > &minimizers1, std::vector<std::pair<uint64_t, uint64_t> > &minimizers2, std::vector<uint64_t> &positive_hits1, std::vector<uint64_t> &positive_hits2, std::vector<Candidate> &positive_candidates1, std::vector<Candidate> &positive_candidates2, std::vector<Candidate> &positive_candidates1_buffer, std::vector<Candidate> &positive_candidates2_buffer, std::vector<uint64_t> &negative_hits1, std::vector<uint64_t> &negative_hits2, std::vector<Candidate> &negative_candidates1, std::vector<Candidate> &negative_candidates2, std::vector<Candidate> &negative_candidates1_buffer, std::vector<Candidate> &negative_candidates2_buffer);

  void PostProcessingInLowMemory(uint32_t num_mappings_in_mem, uint32_t num_reference_sequences, const SequenceBatch &reference);

src/output_tools.h

+46 −46

File changed.

Contains only whitespace changes.

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