Rename two funcs to supplement candidates.

haowenz · Nov 13, 2022 · 157e5b1 · 157e5b1
1 parent e5377e7
commit 157e5b1
Show file tree

Hide file tree

Showing 5 changed files with 32 additions and 31 deletions.
diff --git a/src/candidate_processor.cc b/src/candidate_processor.cc
@@ -162,18 +162,18 @@ int CandidateProcessor::SupplementCandidates(
       int negative_rescue_result = 0;
       if (mate_positive_candidates->size() > 0) {
         positive_rescue_result =
-            GenerateCandidatesFromRepetitiveReadWithMateInfo(
-                error_threshold, index, *minimizers, *repetitive_seed_length,
-                *negative_hits, *augment_negative_candidates,
-                *mate_positive_candidates, kNegative, search_range);
+            GenerateCandidatesFromRepetitiveReadWithMateInfoOnOneStrand(
+                kNegative, search_range, error_threshold, index, *minimizers,
+                *mate_positive_candidates, *repetitive_seed_length,
+                *negative_hits, *augment_negative_candidates);
       }
 
       if (mate_negative_candidates->size() > 0) {
         negative_rescue_result =
-            GenerateCandidatesFromRepetitiveReadWithMateInfo(
-                error_threshold, index, *minimizers, *repetitive_seed_length,
-                *positive_hits, *augment_positive_candidates,
-                *mate_negative_candidates, kPositive, search_range);
+            GenerateCandidatesFromRepetitiveReadWithMateInfoOnOneStrand(
+                kPositive, search_range, error_threshold, index, *minimizers,
+                *mate_negative_candidates, *repetitive_seed_length,
+                *positive_hits, *augment_positive_candidates);
       }
 
       // If one of the strand did not supplement due to too many best candidate,
@@ -262,16 +262,18 @@ void CandidateProcessor::ReduceCandidatesForPairedEndRead(
       filtered_negative_candidates1, filtered_positive_candidates2);
 }
 
-int CandidateProcessor::GenerateCandidatesFromRepetitiveReadWithMateInfo(
-    int error_threshold, const Index &index,
-    const std::vector<Minimizer> &minimizers, uint32_t &repetitive_seed_length,
-    std::vector<uint64_t> &hits, std::vector<Candidate> &candidates,
-    const std::vector<Candidate> &mate_candidates, const Strand strand,
-    uint32_t search_range) const {
-  int max_seed_count = index.CollectSeedHitsFromRepetitiveReadWithMateInfo(
-      error_threshold, minimizers, repetitive_seed_length, hits,
-      mate_candidates, strand, search_range,
-      min_num_seeds_required_for_mapping_, max_seed_frequencies_[0]);
+int CandidateProcessor::
+    GenerateCandidatesFromRepetitiveReadWithMateInfoOnOneStrand(
+        const Strand strand, uint32_t search_range, int error_threshold,
+        const Index &index, const std::vector<Minimizer> &minimizers,
+        const std::vector<Candidate> &mate_candidates,
+        uint32_t &repetitive_seed_length, std::vector<uint64_t> &hits,
+        std::vector<Candidate> &candidates) const {
+  int max_seed_count =
+      index.GenerateCandidatePositionsFromRepetitiveReadWithMateInfo(
+          error_threshold, minimizers, repetitive_seed_length, hits,
+          mate_candidates, strand, search_range,
+          min_num_seeds_required_for_mapping_, max_seed_frequencies_[0]);
 
   GenerateCandidatesOnOneStrand(error_threshold, /*num_seeds_required=*/1,
                                 minimizers.size(), hits, candidates);

diff --git a/src/candidate_processor.h b/src/candidate_processor.h
@@ -46,13 +46,12 @@ class CandidateProcessor {
                                      std::vector<uint64_t> &hits,
                                      std::vector<Candidate> &candidates) const;
 
-  int GenerateCandidatesFromRepetitiveReadWithMateInfo(
-      int error_threshold, const Index &index,
-      const std::vector<Minimizer> &minimizers,
+  int GenerateCandidatesFromRepetitiveReadWithMateInfoOnOneStrand(
+      const Strand strand, uint32_t search_range, int error_threshold,
+      const Index &index, const std::vector<Minimizer> &minimizers,
+      const std::vector<Candidate> &mate_candidates,
       uint32_t &repetitive_seed_length, std::vector<uint64_t> &hits,
-      std::vector<Candidate> &candidates,
-      const std::vector<Candidate> &mate_candidates, const Strand strand,
-      uint32_t search_range) const;
+      std::vector<Candidate> &candidates) const;
 
   void MergeCandidates(int error_threshold, std::vector<Candidate> &c1,
                        std::vector<Candidate> &c2,

diff --git a/src/chromap.h b/src/chromap.h
@@ -29,7 +29,7 @@
 #include "temp_mapping.h"
 #include "utils.h"
 
-#define CHROMAP_VERSION "0.2.3-r435"
+#define CHROMAP_VERSION "0.2.3-r436"
 
 namespace chromap {
 

diff --git a/src/index.cc b/src/index.cc
@@ -459,7 +459,7 @@ int Index::GenerateCandidatePositions(
   return repetitive_seed_count;
 }
 
-int Index::CollectSeedHitsFromRepetitiveReadWithMateInfo(
+int Index::GenerateCandidatePositionsFromRepetitiveReadWithMateInfo(
     int error_threshold, const std::vector<Minimizer> &minimizers,
     uint32_t &repetitive_seed_length, std::vector<uint64_t> &hits,
     const std::vector<Candidate> &mate_candidates, const Strand strand,

diff --git a/src/index.h b/src/index.h
@@ -72,11 +72,11 @@ class Index {
       const CandidatePositionGeneratingConfig &generating_config,
       MappingMetadata &mapping_metadata) const;
 
-  // Input a search range, for each best mate candidate, serach for minimizer
-  // hits. Return the minimizer count of the best candidate if it finishes
-  // normally. Or return a negative value if it stops early due to too many
-  // candidates with low minimizer count.
-  int CollectSeedHitsFromRepetitiveReadWithMateInfo(
+  // Input a search range, for each best mate candidate, serach for candidate
+  // positions for the read. Return the minimizer count of the best candidate if
+  // it finishes normally. Or return a negative value if it stops early due to
+  // too many candidates with low minimizer count.
+  int GenerateCandidatePositionsFromRepetitiveReadWithMateInfo(
       int error_threshold, const std::vector<Minimizer> &minimizers,
       uint32_t &repetitive_seed_length, std::vector<uint64_t> &hits,
       const std::vector<Candidate> &mate_candidates, const Strand strand,