Commit f3dafda0 authored by Haowen Zhang's avatar Haowen Zhang Committed by Li Song
Browse files

Introduced MappingGenerator. 

Some functions and definitions were moved to get the program compiled.
parent 588e405f

Makefile

+1 −1
Original line number Diff line number Diff line
@@ -2,7 +2,7 @@ CXX=g++ 
CXXFLAGS=-std=c++11 -Wall -O3 -fopenmp -msse4.1

LDFLAGS=-lm -lz



cpp_source=sequence_batch.cc index.cc candidate_processor.cc feature_barcode_matrix.cc ksw.cc mapping_writer.cc chromap.cc

cpp_source=sequence_batch.cc index.cc candidate_processor.cc alignment.cc feature_barcode_matrix.cc ksw.cc mapping_writer.cc chromap.cc

src_dir=src

objs_dir=objs

objs+=$(patsubst %.cc,$(objs_dir)/%.o,$(cpp_source))

src/alignment.cc

0 → 100644
+795 −0

File added.

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src/alignment.h

+13 −753

File changed.

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src/chromap.cc

+20 −1550

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src/chromap.h

+6 −133
Original line number Diff line number Diff line
@@ -141,6 +141,7 @@ class Chromap { 


  // For paired-end read mapping

  void MapPairedEndReads();



  uint32_t LoadPairedEndReadsWithBarcodes(SequenceBatch &read_batch1,

                                          SequenceBatch &read_batch2,

                                          SequenceBatch &barcode_batch);
@@ -151,123 +152,20 @@ class Chromap { 
                                           const SequenceBatch &barcode_batch,

                                           const SequenceBatch &read_batch1,

                                           const SequenceBatch &read_batch2);

  void GenerateBestMappingsForPairedEndReadOnOneDirection(

      Direction first_read_direction, uint32_t pair_index, int num_candidates1,

      int min_num_errors1, int num_best_mappings1, int second_min_num_errors1,

      int num_second_best_mappings1, const SequenceBatch &read_batch1,

      const std::vector<std::pair<int, uint64_t> > &mappings1,

      int num_candidates2, int min_num_errors2, int num_best_mappings2,

      int second_min_num_errors2, int num_second_best_mappings2,

      const SequenceBatch &read_batch2, const SequenceBatch &reference,

      const std::vector<std::pair<int, uint64_t> > &mappings2,

      std::vector<std::pair<uint32_t, uint32_t> > &best_mappings,

      int &min_sum_errors, int &num_best_mappings, int &second_min_sum_errors,

      int &num_second_best_mappings);

  void RecalibrateBestMappingsForPairedEndReadOnOneDirection(

      Direction first_read_direction, uint32_t pair_index, int min_sum_errors,

      int second_min_sum_errors, int min_num_errors1, int num_best_mappings1,

      int second_min_num_errors1, int num_second_best_mappings1,

      const SequenceBatch &read_batch1,

      const std::vector<std::pair<int, uint64_t> > &mappings1,

      int min_num_errors2, int num_best_mappings2, int second_min_num_errors2,

      int num_second_best_mappings2, const SequenceBatch &read_batch2,

      const SequenceBatch &reference,

      const std::vector<std::pair<int, uint64_t> > &mappings2,

      const std::vector<std::pair<uint32_t, uint32_t> > &edit_best_mappings,

      std::vector<std::pair<uint32_t, uint32_t> > *best_mappings,

      int *best_alignment_score, int *num_best_mappings,

      int *second_best_alignment_score, int *num_second_best_mappings);

  void ProcessBestMappingsForPairedEndReadOnOneDirection(

      Direction first_read_direction, Direction second_read_direction,

      uint32_t pair_index, uint8_t mapq, int num_candidates1,

      uint32_t repetitive_seed_length1, int min_num_errors1,

      int num_best_mappings1, int second_min_num_errors1,

      int num_second_best_mappings1, const SequenceBatch &read_batch1,

      const std::vector<std::pair<int, uint64_t> > &mappings1,

      const std::vector<int> &split_sites1, int num_candidates2,

      uint32_t repetitive_seed_length2, int min_num_errors2,

      int num_best_mappings2, int second_min_num_errors2,

      int num_second_best_mappings2, const SequenceBatch &read_batch2,

      const SequenceBatch &reference, const SequenceBatch &barcode_batch,

      const std::vector<int> &best_mapping_indices,

      const std::vector<std::pair<int, uint64_t> > &mappings2,

      const std::vector<int> &split_sites2,

      const std::vector<std::pair<uint32_t, uint32_t> > &best_mappings,

      int min_sum_errors, int num_best_mappings, int second_min_sum_errors,

      int num_second_best_mappings, int &best_mapping_index,

      int &num_best_mappings_reported, int force_mapq,

      std::vector<std::vector<MappingRecord> > &mappings_on_diff_ref_seqs);

  void GenerateBestMappingsForPairedEndRead(

      uint32_t pair_index, const SequenceBatch &read_batch1,

      const SequenceBatch &read_batch2, const SequenceBatch &barcode_batch,

      const SequenceBatch &reference, std::vector<int> &best_mapping_indices,

      std::mt19937 &generator, int force_mapq,

      PairedEndMappingMetadata &paired_end_mapping_metadata,

      std::vector<std::vector<MappingRecord> > &mappings_on_diff_ref_seqs);

  void EmplaceBackMappingRecord(

      uint32_t read_id, uint64_t barcode, uint32_t fragment_start_position,

      uint16_t fragment_length, uint8_t mapq, uint8_t direction,

      uint8_t is_unique, uint8_t num_dups, uint16_t positive_alignment_length,

      uint16_t negative_alignment_length,

      std::vector<MappingRecord> *mappings_on_diff_ref_seqs);

  void EmplaceBackMappingRecord(

      uint32_t read_id, const char *read1_name, const char *read2_name,

      uint16_t read1_length, uint16_t read2_length, uint64_t barcode,

      uint32_t fragment_start_position, uint16_t fragment_length, uint8_t mapq1,

      uint8_t mapq2, uint8_t direction, uint8_t is_unique, uint8_t num_dups,

      uint16_t positive_alignment_length, uint16_t negative_alignment_length,

      std::vector<MappingRecord> *mappings_on_diff_ref_seqs);

  void EmplaceBackMappingRecord(

      uint32_t read_id, const char *read_name, uint64_t cell_barcode, int rid1,

      int rid2, uint32_t pos1, uint32_t pos2, int direction1, int direction2,

      uint8_t mapq, uint8_t is_unique, uint8_t num_dups,

      std::vector<MappingRecord> *mappings_on_diff_ref_seqs);



  void ApplyTn5ShiftOnPairedEndMapping(

      uint32_t num_reference_sequences,

      std::vector<std::vector<MappingRecord> > &mappings);



  // For single-end read mapping

  void MapSingleEndReads();

  void GenerateBestMappingsForSingleEndRead(

      const SequenceBatch &read_batch, uint32_t read_index,

      const SequenceBatch &reference, const SequenceBatch &barcode_batch,

      MappingMetadata &mapping_metadata,

      std::vector<std::vector<MappingRecord> > &mappings_on_diff_ref_seqs);

  void ProcessBestMappingsForSingleEndRead(

      Direction mapping_direction, uint8_t mapq, int num_candidates,

      uint32_t repetitive_seed_length, int min_num_errors,

      int num_best_mappings, int second_min_num_errors,

      int num_second_best_mappings, const SequenceBatch &read_batch,

      uint32_t read_index, const SequenceBatch &reference,

      const SequenceBatch &barcode_batch,

      const std::vector<int> &best_mapping_indices,

      const std::vector<std::pair<int, uint64_t> > &mappings,

      const std::vector<int> &split_sites, int &best_mapping_index,

      int &num_best_mappings_reported,

      std::vector<std::vector<MappingRecord> > &mappings_on_diff_ref_seqs);

  void EmplaceBackMappingRecord(

      uint32_t read_id, uint64_t barcode, uint32_t fragment_start_position,

      uint16_t fragment_length, uint8_t mapq, uint8_t direction,

      uint8_t is_unique, uint8_t num_dups,

      std::vector<MappingRecord> *mappings_on_diff_ref_seqs);

  void EmplaceBackMappingRecord(

      uint32_t read_id, const char *read_name, uint16_t read_length,

      uint64_t barcode, uint32_t fragment_start_position,

      uint16_t fragment_length, uint8_t mapq, uint8_t direction,

      uint8_t is_unique, uint8_t num_dups,

      std::vector<MappingRecord> *mappings_on_diff_ref_seqs);

  void EmplaceBackMappingRecord(

      uint32_t read_id, const char *read_name, uint64_t cell_barcode,

      uint8_t num_dups, int64_t position, int rid, int flag, uint8_t direction,

      uint8_t is_unique, uint8_t mapq, uint32_t NM, int n_cigar,

      uint32_t *cigar, std::string &MD_tag, const char *read,

      const char *read_qual,

      std::vector<MappingRecord> *mappings_on_diff_ref_seqs);



  uint32_t LoadSingleEndReadsWithBarcodes(SequenceBatch *read_batch,

                                          SequenceBatch *barcode_batch);



  void ApplyTn5ShiftOnSingleEndMapping(

      uint32_t num_reference_sequences,

      std::vector<std::vector<MappingRecord> > *mappings);

  uint32_t LoadSingleEndReadsWithBarcodes(SequenceBatch *read_batch,

                                          SequenceBatch *barcode_batch);



  // Supportive functions

  void ConstructIndex();
@@ -315,24 +213,6 @@ class Chromap { 
      const std::vector<std::vector<MappingRecord> > &uni_mappings,

      const std::vector<std::vector<MappingRecord> > &multi_mappings);



  uint8_t GetMAPQForSingleEndRead(

      int error_threshold, int num_candidates, uint32_t repetitive_seed_length,

      uint16_t alignment_length, int min_num_errors, int num_best_mappings,

      int second_min_num_errors, int num_second_best_mappings,

      int max_num_error_difference, int read_length);



  uint8_t GetMAPQForPairedEndRead(

      int num_positive_candidates, int num_negative_candidates,

      uint32_t repetitive_seed_length1, uint32_t repetitive_seed_length2,

      uint16_t positive_alignment_length, uint16_t negative_alignment_length,

      int min_sum_errors, int num_best_mappings, int second_min_sum_errors,

      int num_second_best_mappings, int num_errors1, int num_errors2,

      int min_num_errors1, int min_num_errors2, int num_best_mappings1,

      int num_best_mappings2, int second_min_num_errors1,

      int second_min_num_errors2, int num_second_best_mappings1,

      int num_second_best_mappings2, int read1_length, int read2_length,

      int force_mapq, uint8_t &mapq1, uint8_t &mapq2);



  void LoadBarcodeWhitelist();



  void ComputeBarcodeAbundance(uint64_t max_num_sample_barcodes);
@@ -356,13 +236,6 @@ class Chromap { 
                      const SequenceBatch &reference,

                      const std::vector<std::vector<MappingRecord> > &mappings);



  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);



  void GenerateCustomizedRidRank(const std::string rid_order_path,

                                 const SequenceBatch &reference,

                                 std::vector<int> &rid_rank);

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