refactor: add 10XG index file support

chungongyu · Jul 18, 2020 · 0da457d · 0da457d
1 parent 540b89f
commit 0da457d
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Showing 10 changed files with 182 additions and 58 deletions.
diff --git a/src/bigraph.cpp b/src/bigraph.cpp
@@ -26,7 +26,7 @@ std::string Edge::label() const {
  const std::string& seq = _end->seq();
  std::string label = seq.substr(unmatched.interval.start, unmatched.length());
  if (comp() == EC_REVERSE) {
- make_reverse_complement_dna(label);
+ make_dna_reverse_complement(label);
  }
  return label;
 }
@@ -60,7 +60,7 @@ void Edge::validate() const {
  std::string m1 = v1.substr(_coord.interval.start, _coord.length());
  std::string m2 = v2.substr(_twin->_coord.interval.start, _twin->_coord.length());
  if (_comp == EC_REVERSE) {
- make_reverse_complement_dna(m2);
+ make_dna_reverse_complement(m2);
  }
  if (m1 != m2) {
  LOG4CXX_ERROR(logger, "Error, matching strings are not the same length");

diff --git a/src/bigraph_search.cpp b/src/bigraph_search.cpp
@@ -100,7 +100,7 @@ bool BigraphWalk::hasLink(const Vertex* v1, const Vertex* v2, int distance, Edge
  assert(distance >= 0);
  std::string seq1 = v1->seq(), seq2 = v2->seq();
  if (comp == Edge::EC_REVERSE) {
- make_reverse_complement_dna(seq2);
+ make_dna_reverse_complement(seq2);
  }
  return (
  dir == Edge::ED_SENSE && distance < seq1.length() && boost::algorithm::starts_with(seq2, seq1.substr(distance))

diff --git a/src/correct_processor.cpp b/src/correct_processor.cpp
@@ -191,7 +191,7 @@ class KmerCorrector : public AbstractCorrector {
  size_t bestCount = 0;
  char bestBase = '$';
 
- LOG4CXX_DEBUG(logger, boost::format("baseIdx: %d kmerIdx: %d %s %s") % baseIdx % kmerIdx % kmer % make_reverse_complement_dna_copy(kmer));
+ LOG4CXX_DEBUG(logger, boost::format("baseIdx: %d kmerIdx: %d %s %s") % baseIdx % kmerIdx % kmer % make_dna_reverse_complement_copy(kmer));
 
  for (size_t i = 0; i < DNAAlphabet::size; ++i) {
  char c = DNAAlphabet::DNA[i];

diff --git a/src/kmerdistr.cpp b/src/kmerdistr.cpp
@@ -16,7 +16,7 @@ size_t KmerDistribution::sample(const FMIndex* index, size_t k, size_t n, KmerDi
 
  for (size_t j = k; j < s.length(); ++j) {
  std::string w = s.substr(j - k, k);
- std::string v = make_reverse_dna_copy(w);
+ std::string v = make_dna_reverse_copy(w);
 
  size_t count = 0;
  count += FMIndex::Interval::occurrences(w, index);

diff --git a/src/kseq.cpp b/src/kseq.cpp
@@ -14,7 +14,7 @@
 
 static log4cxx::LoggerPtr logger(log4cxx::Logger::getLogger("arcs.DNASeq"));
 
-char make_complement_dna(char c) {
+char make_dna_complement(char c) {
  static std::map<char, char> mapping = {
  {'A', 'T'},
  {'C', 'G'},
@@ -25,7 +25,7 @@ char make_complement_dna(char c) {
  return mapping[c];
 }
 
-void make_complement_dna(std::string& sequence) {
+void make_dna_complement(std::string& sequence) {
  static std::map<char, char> mapping = {
  {'A', 'T'},
  {'C', 'G'},
@@ -40,30 +40,30 @@ void make_complement_dna(std::string& sequence) {
  }
 }
 
-std::string make_complement_dna_copy(const std::string& sequence) {
+std::string make_dna_complement_copy(const std::string& sequence) {
  std::string complement = sequence;
- make_complement_dna(complement);
+ make_dna_complement(complement);
  return complement;
 }
 
-void make_reverse_dna(std::string& sequence) {
+void make_dna_reverse(std::string& sequence) {
  std::reverse(sequence.begin(), sequence.end());
 }
 
-std::string make_reverse_dna_copy(const std::string& sequence) {
+std::string make_dna_reverse_copy(const std::string& sequence) {
  std::string reverse = sequence;
- make_reverse_dna(reverse);
+ make_dna_reverse(reverse);
  return reverse;
 }
 
-void make_reverse_complement_dna(std::string& sequence) {
- make_complement_dna(sequence);
- make_reverse_dna(sequence);
+void make_dna_reverse_complement(std::string& sequence) {
+ make_dna_complement(sequence);
+ make_dna_reverse(sequence);
 }
 
-std::string make_reverse_complement_dna_copy(const std::string& sequence) {
- std::string complement = make_complement_dna_copy(sequence);
- make_reverse_dna(complement);
+std::string make_dna_reverse_complement_copy(const std::string& sequence) {
+ std::string complement = make_dna_complement_copy(sequence);
+ make_dna_reverse(complement);
  return complement;
 }
 
@@ -86,7 +86,7 @@ DNASeq::DNASeq(const std::string& name, const std::string& seq, const std::strin
 }
 
 void DNASeq::make_complement() {
- make_complement_dna(seq);
+ make_dna_complement(seq);
 }
 
 void DNASeq::make_reverse() {

diff --git a/src/kseq.h b/src/kseq.h
@@ -8,13 +8,13 @@
 
 #include "quality.h"
 
-char make_complement_dna(char c);
-void make_complement_dna(std::string& dna);
-std::string make_complement_dna_copy(const std::string& dna);
-void make_reverse_dna(std::string& dna);
-std::string make_reverse_dna_copy(const std::string& dna);
-void make_reverse_complement_dna(std::string& dna);
-std::string make_reverse_complement_dna_copy(const std::string& dna);
+char make_dna_complement(char c);
+void make_dna_complement(std::string& dna);
+std::string make_dna_complement_copy(const std::string& dna);
+void make_dna_reverse(std::string& dna);
+std::string make_dna_reverse_copy(const std::string& dna);
+void make_dna_reverse_complement(std::string& dna);
+std::string make_dna_reverse_complement_copy(const std::string& dna);
 
 //
 // DNASeq represents a DNA sequence.

diff --git a/src/match.cpp b/src/match.cpp
@@ -51,7 +51,7 @@ class Match : public Runner {
  }
  DNASeq read;
  while (reader->read(read)) {
- std::cout << boost::format("%s\t%s\t%d\n") % read.name % read.seq % (FMIndex::Interval::occurrences(read.seq, &fmi) + FMIndex::Interval::occurrences(make_reverse_complement_dna_copy(read.seq), &fmi));
+ std::cout << boost::format("%s\t%s\t%d\n") % read.name % read.seq % (FMIndex::Interval::occurrences(read.seq, &fmi) + FMIndex::Interval::occurrences(make_dna_reverse_complement_copy(read.seq), &fmi));
  }
  }
  } else {

diff --git a/src/overlap_builder.cpp b/src/overlap_builder.cpp
@@ -790,7 +790,7 @@ class IrreducibleBlockListExtractor {
  assert(blocks != NULL);
  auto i = blocks->begin();
  while (i != blocks->end()) {
- char b = i->af.test(AlignFlags::QUERYCOMP_BIT) ? make_complement_dna(c) : c;
+ char b = i->af.test(AlignFlags::QUERYCOMP_BIT) ? make_dna_complement(c) : c;
  i->capped.updateR(b, i->index(_fmi, _rfmi));
 
  // remove the block from the list if its no longer valid
@@ -1092,13 +1092,13 @@ OverlapResult OverlapBuilder::overlap(const DNASeq& read, size_t minOverlap, Ove
  // Match the suffix of seq to prefixes
  finder.find(seq, kSuffixPrefixAF, &suffixfwd, &containfwd, &result);
  if (_rc) {
- finder.find(make_reverse_complement_dna_copy(seq), kPrefixPrefixAF, &prefixfwd, &containfwd, &result);
+ finder.find(make_dna_reverse_complement_copy(seq), kPrefixPrefixAF, &prefixfwd, &containfwd, &result);
  }
 
  // Match the prefix of seq to suffixes
- rfinder.find(make_reverse_dna_copy(seq), kPrefixSuffixAF, &prefixrev, &containrev, &result);
+ rfinder.find(make_dna_reverse_copy(seq), kPrefixSuffixAF, &prefixrev, &containrev, &result);
  if (_rc) {
- rfinder.find(make_complement_dna_copy(seq), kSuffixSuffixAF, &suffixrev, &containrev, &result);
+ rfinder.find(make_dna_complement_copy(seq), kSuffixSuffixAF, &suffixrev, &containrev, &result);
  }
 
  // Remove submaximal blocks for each block list including fully contained blocks
@@ -1158,7 +1158,7 @@ OverlapResult OverlapBuilder::duplicate(const DNASeq& read, OverlapBlockList* bl
  OverlapBlockFinder finder(_fmi, _rfmi, minOverlap), rfinder(_rfmi, _fmi, minOverlap);
 
  finder.find(seq, kSuffixPrefixAF, NULL, blocks, &result);
- rfinder.find(make_complement_dna_copy(seq), kSuffixSuffixAF, NULL, blocks, &result);
+ rfinder.find(make_dna_complement_copy(seq), kSuffixSuffixAF, NULL, blocks, &result);
 
  return result;
 }