Merge pull request #3 from J35P312/master

Pull request 6 july

src/FindTranslocations.cpp

@@ -53,8 +53,6 @@ int main(int argc, char *argv[]) {
  //MAIN VARIABLE
  string alignmentFile = ""; // alignment file name
  bool outtie = true; // library orientation
- uint32_t windowSize = 1000; // Window size
- uint32_t windowStep = 100; // Window step
  uint32_t minimumSupportingPairs = 10;
  int min_insert = 100; // min insert size
  int max_insert = 1000000; // max insert size
@@ -93,8 +91,6 @@ int main(int argc, char *argv[]) {
  ("orientation", po::value<string>(), "expected reads orientations, possible values \"innie\" (-> <-) or \"outtie\" (<- ->). Default outtie") 
  ("minimum-supporting-pairs", po::value<unsigned int>(), "Minimum number of supporting pairs in order to call a variation event (default 10)")
  ("minimum-mapping-quality", po::value<int>(), "Minimum mapping quality to consider an alignment (default 20)")
- ("window-size", po::value<unsigned int>(), "Size of the sliding window (default 1000)")
- ("window-step", po::value<unsigned int>(), "size of the step in overlapping window (must be lower than window-size) (default 100)")
  ("coverage", po::value<float>(), "do not compute coverage from bam file, use the one specified here (must be used in combination with --insert --insert-std)")
  ("insert", po::value<float>(), "do not compute insert size from bam file, use the one specified here (must be used in combination with --coverage --insert-std)")
  ("insert-std", po::value<float>(), "do not compute insert size standard deviation from bam file, use the one specified here (must be used in combination with --insert --coverage)");
@@ -288,18 +284,6 @@ int main(int argc, char *argv[]) {
  if (vm.count("minimum-mapping-quality")) {
  minimum_mapping_quality = vm["minimum-mapping-quality"].as<int>();
  }
-
- if (vm.count("window-size")) {
- windowSize = vm["window-size"].as<unsigned int>();
- }
-
- if (vm.count("window-step")) {
- windowStep = vm["window-step"].as<unsigned int>();
- if (windowStep > windowSize) {
- DEFAULT_CHANNEL << "window-step cannot be larger than window-size\n";
- return 2;
- }
- }
 
  if (vm.count("minimum-supporting-pairs")) {
  minimumSupportingPairs = vm["minimum-supporting-pairs"].as<unsigned int>();
@@ -328,8 +312,7 @@ int main(int argc, char *argv[]) {
 
  StructuralVariations *FindTranslocations;
  FindTranslocations = new StructuralVariations();
- FindTranslocations -> findTranslocationsOnTheFly(alignmentFile, min_insert, max_insert, outtie, minimum_mapping_quality,
- windowSize, windowStep, minimumSupportingPairs, coverage, meanInsert, insertStd, outputFileHeader, indexFile);
+ FindTranslocations -> findTranslocationsOnTheFly(alignmentFile, min_insert, max_insert, outtie, minimum_mapping_quality, minimumSupportingPairs, coverage, meanInsert, insertStd, outputFileHeader, indexFile,contigsNumber);
 
 
  //if the find copy number variation module is chosen

src/common.h

@@ -8,6 +8,7 @@
 #include <algorithm> // std::sort
 #include <vector> // std::vector
 #include <cstring>
+#include <queue>
 
 
 #include <climits>

src/data_structures/ProgramModules.h

@@ -28,7 +28,7 @@ class StructuralVariations{
  StructuralVariations();
  //main function
  void findTranslocationsOnTheFly(string bamFileName, int32_t min_insert, int32_t max_insert, bool outtie, uint16_t minimum_mapping_quality,
- uint32_t windowSize , uint32_t windowStep, uint32_t minimumSupportingPairs, float meanCoverage, float meanInsertSize, float StdInsertSize, string outputFileHeader, string indexFile);
+ uint32_t minimumSupportingPairs, float meanCoverage, float meanInsertSize, float StdInsertSize, string outputFileHeader, string indexFile, int contigsNumber);
 };
 
 #endif /* PROGRAMMODULES_H_ */