Merge pull request #6 from jfostier/libraryRefactor

Library refactor. Merging as remaining performance issues are likely related to stage 5.

src/brownie.cpp

@@ -53,7 +53,7 @@ void Brownie::printInFile()
 void Brownie::parameterEstimationInStage4(DBGraph &graph){
         cout <<endl<< " ================ Parameter Estimation ===============" << endl;
         double  estimatedKmerCoverage=0,estimatedMKmerCoverageSTD=0, cutOffvalue=0, readLength=0;
-        readLength=libraries.getReadLength();
+        readLength=libraries.getAvgReadLength();
         if (readLength<=settings.getK() ||readLength>500)
                 readLength=150;
 

src/bubble.cpp

@@ -23,6 +23,8 @@
 #include "settings.h"
 #include "library.h"
 
+#include <queue>
+
 using namespace std;
 class PathInfo {
 public:

src/coverage.cpp

@@ -658,7 +658,7 @@ double DBGraph::getInitialEstimateForCoverage ( const ReadLibrary& input,
         DBGraph::graph = this;
         sort ( sortedNodes.begin(), sortedNodes.end(), sortByLength );
 
-        size_t RL = input.getReadLength();
+        size_t RL = input.getAvgReadLength();
         size_t k = Kmer::getK();
 
         // for the biggest nodes compute the coverage
@@ -680,7 +680,7 @@ double DBGraph::estimateReadStartCoverage ( const ReadLibrary &input,
 {
         size_t nom = 0, denom = 0;
         size_t k = Kmer::getK();
-        size_t RL = input.getReadLength();
+        size_t RL = input.getAvgReadLength();
 
         for ( NodeID id = 1; id <= numNodes; id++ ) {
                 DSNode& node = getDSNode ( id );

src/global.h

@@ -68,6 +68,10 @@ typedef uint32_t KmerLSB;       // set to uint16_t and all hell will break loose
 
 #define SCAFFOLD_SNAP_LINK 5
 
+// The number of recordBlocks simulataneously held in memory. Higher values
+// result in more parallel chunks at the cost of increased memory use.
+#define NUM_RECORD_BLOCKS 2
+
 // ============================================================================
 // TYPEDEFS
 // ============================================================================