added uon setting

ITBE-Lab · Sep 22, 2018 · 20f5604 · 20f5604
1 parent 9625db5
commit 20f5604
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Showing 7 changed files with 28 additions and 7 deletions.
diff --git a/inc/module/binarySeeding.h b/inc/module/binarySeeding.h
@@ -474,6 +474,7 @@ namespace libMA
             );
 
     public:
+        size_t uiUONAccMaxSize;
         /**
          * @brief Initialize a BinarySeeding Module
          * @details
@@ -485,7 +486,8 @@ namespace libMA
          */
         BinarySeeding()
                 :
-            bLrExtension(defaults::sSeedSet == "maxSpan")
+            bLrExtension(defaults::sSeedSet == "maxSpan"),
+            uiUONAccMaxSize(defaults::uiUONAccMaxSize)
         {}//constructor
 
         std::shared_ptr<Container> EXPORTED execute(std::shared_ptr<ContainerVector> vpInput);

diff --git a/inc/module/linesweep.h b/inc/module/linesweep.h
@@ -156,6 +156,8 @@ namespace libMA
 
         size_t uiSVPenalty = defaults::uiSVPenalty;
 
+        size_t uiUONAccMaxSize = defaults::uiUONAccMaxSize;
+
         LinearLineSweep() {}//default constructor
 
         //overload

diff --git a/inc/util/default_parameters.h b/inc/util/default_parameters.h
@@ -62,6 +62,7 @@ namespace libMA
         extern int64_t iMinSVDistance;
         extern size_t uiZDrop;
         extern size_t uiSVPenalty;
+        extern size_t uiUONAccMaxSize;
 
         inline void configureAccurate()
         {
@@ -87,6 +88,19 @@ namespace libMA
             //bDisableGapCostEstimationCutting = true;
         }// function
 
+        inline void configureUON()
+        {
+            sParameterSet = "uon";
+            sSeedSet = "maxSpan";
+            bDisableHeuristics = true;
+            dMaxOverlapSupplementary = 0.25;
+            fMinSecScoreRatio = 0.85;
+            uiReportN = 3;
+            uiPadding = 1000;
+            uiUONAccMaxSize = 800;
+            //bDisableGapCostEstimationCutting = true;
+        }// function
+
 #ifdef WITH_PYTHON
         void exportDefaults();
 #endif

diff --git a/src/cmdMa.cpp b/src/cmdMa.cpp
@@ -165,6 +165,8 @@ int main(int argc, char* argv[])
                     defaults::configureFast();
                 if(strcmp(argv[i+1], "pacBio") == 0)
                     defaults::configurePacBio();
+                if(strcmp(argv[i+1], "uon") == 0)
+                    defaults::configureUON();
             }// if
 
         options.add_options("Alignment options (requires -a)")

diff --git a/src/module/binarySeeding.cpp b/src/module/binarySeeding.cpp
@@ -47,7 +47,7 @@ void BinarySeeding::procesInterval(
         Interval<nucSeqIndex> xAreaCovered;
         // performs extension and records any found seeds
         // here we use bLrExtension to choose the extension scheme
-        if(bLrExtension)
+        if(bLrExtension && pQuerySeq->length() >= uiUONAccMaxSize )
             xAreaCovered = maximallySpanningExtension(
                 xAreaToCover.center(), 
                 pFM_index, 

diff --git a/src/module/linesweep.cpp b/src/module/linesweep.cpp
@@ -411,7 +411,7 @@ std::shared_ptr<Container> LinearLineSweep::execute(
             // Prof. Kutzners filter:
             // this merely checks weather we actually do have to do the harmonization at all
             //@todo uiSwitchQLen != 0 should be replaced with switch
-            if(bDoHeuristics)
+            if(bDoHeuristics || pQuery->length() < uiUONAccMaxSize) // @todo temporary
             {
                 if (pQuery->length() > uiSwitchQLen && uiSwitchQLen != 0)
                 {
@@ -587,7 +587,7 @@ std::shared_ptr<Container> LinearLineSweep::execute(
         nucSeqIndex uiCurrHarmScore = 0;
         for(const auto& rSeed : *pSeeds)
             uiCurrHarmScore += rSeed.size();
-        if(bDoHeuristics)
+        if(bDoHeuristics || pQuery->length() < uiUONAccMaxSize) // @todo temporary
         {
             if(uiCurrHarmScore < uiCurrHarmScoreMin )
             {
@@ -619,7 +619,7 @@ std::shared_ptr<Container> LinearLineSweep::execute(
                 if(b)
                     pSoCIn->vExtractOrder.back().qCoverage++;
         )// DEBUG
-        if(bDoHeuristics)
+        if(bDoHeuristics || pQuery->length() < uiUONAccMaxSize) // @todo temporary
         {
             //@todo uiSwitchQLen != 0 should be replaced with switch
             if (pQuery->length() > uiSwitchQLen && uiSwitchQLen != 0)
@@ -660,7 +660,7 @@ std::shared_ptr<Container> LinearLineSweep::execute(
 
         //FILTER
 #if FILTER_1
-        if(bDoHeuristics)
+        if(bDoHeuristics || pQuery->length() < uiUONAccMaxSize) // @todo temporary
         {
             nucSeqIndex uiAccLen = pSeeds->getScore();
             if (uiAccumulativeSeedLength > uiAccLen )
@@ -677,7 +677,7 @@ std::shared_ptr<Container> LinearLineSweep::execute(
 
     }//while
 
-    if(bDoHeuristics) 
+    if(bDoHeuristics || pQuery->length() < uiUONAccMaxSize) // @todo temporary
     {
         // @todo think about what to do here (maybe sorting is necessary)...
         for(unsigned int ui = 0; ui < uiSoCRepeatCounter && pSoCs->size() > 1; ui++)

diff --git a/src/util/default_parameters.cpp b/src/util/default_parameters.cpp
@@ -66,6 +66,7 @@ namespace libMA
         int64_t iMinSVDistance = 500;
 
         size_t uiZDrop = 200;
+        size_t uiUONAccMaxSize = 0;
 
 #ifdef WITH_PYTHON
         void exportDefaults()