refine trimmed reads/bases counters

Author: sfchen

src/adaptertrimmer.cpp

@@ -45,7 +45,7 @@ bool AdapterTrimmer::trimByOverlapAnalysis(Read* r1, Read* r2, FilterResult* fr,
     return false;
 }
 
-bool AdapterTrimmer::trimByMultiSequences(Read* r, FilterResult* fr, vector<string>& adapterList, bool isR2, bool incTrimmedCounter) {
+bool AdapterTrimmer::trimByMultiSequences(Read* r, FilterResult* fr, vector<string>& adapterList, bool isR2) {
     int matchReq = 4;
     if(adapterList.size() > 16)
         matchReq = 5;
@@ -55,15 +55,7 @@ bool AdapterTrimmer::trimByMultiSequences(Read* r, FilterResult* fr, vector<stri
 
     string* originalSeq = r->mSeq;
     for(int i=0; i<adapterList.size(); i++) {
-        trimmed |= trimBySequence(r, NULL, adapterList[i], isR2, matchReq);
-    }
-
-    if(trimmed) {
-        string adapter = originalSeq->substr(r->length(), originalSeq->length() - r->length());
-        if(fr)
-            fr->addAdapterTrimmed(adapter, isR2, incTrimmedCounter);
-        else
-            cerr << adapter << endl;
+        trimmed |= trimBySequence(r, fr, adapterList[i], isR2, matchReq);
     }
 
     return trimmed;

src/adaptertrimmer.h

@@ -18,7 +18,7 @@ class AdapterTrimmer{
     static bool trimByOverlapAnalysis(Read* r1, Read* r2, FilterResult* fr, int diffLimit, int overlapRequire, double diffPercentLimit);
     static bool trimByOverlapAnalysis(Read* r1, Read* r2, FilterResult* fr, OverlapResult ov, int frontTrimmed1 = 0, int frontTrimmed2 = 0);
     static bool trimBySequence(Read* r1, FilterResult* fr, string& adapter, bool isR2 = false, int matchReq = 4);
-    static bool trimByMultiSequences(Read* r1, FilterResult* fr, vector<string>& adapterList, bool isR2 = false, bool incTrimmedCounter = true);
+    static bool trimByMultiSequences(Read* r1, FilterResult* fr, vector<string>& adapterList, bool isR2 = false);
     static bool test();
 
 };

src/filterresult.cpp

@@ -121,11 +121,9 @@ bool FilterResult::isLowComplexity(string& adapter) {
     return diff < adapter.length()/2;
 }
 
-void FilterResult::addAdapterTrimmed(string adapter, bool isR2, bool incTrimmedCounter ) {
+void FilterResult::addAdapterTrimmed(string adapter, bool isR2 ) {
     if(adapter.empty())
         return;
-    if(incTrimmedCounter)
-        mTrimmedAdapterRead++;
     mTrimmedAdapterBases += adapter.length();
     if(!isR2) {
         if(mAdapter1.count(adapter) >0 )
@@ -154,7 +152,6 @@ void FilterResult::addAdapterTrimmed(string adapter, bool isR2, bool incTrimmedC
 
 void FilterResult::addAdapterTrimmed(string adapter1, string adapter2) {
     // paired
-    mTrimmedAdapterRead += 2;
     mTrimmedAdapterBases += adapter1.length() + adapter2.length();
     if(!adapter1.empty()){
         if(mAdapter1.count(adapter1) >0 )
@@ -182,6 +179,10 @@ void FilterResult::addAdapterTrimmed(string adapter1, string adapter2) {
     }
 }
 
+void FilterResult::incTrimmedAdapterRead(int count) {
+    mTrimmedAdapterRead += count;
+}
+
 void FilterResult::addPolyXTrimmed(int base, int length) {
     mTrimmedPolyXReads[base] += 1;
     mTrimmedPolyXBases[base] += length;

src/filterresult.h

@@ -33,9 +33,10 @@ class FilterResult{
     static FilterResult* merge(vector<FilterResult*>& list);
     void print();
     // for single end
-    void addAdapterTrimmed(string adapter, bool isR2 = false, bool incTrimmedCounter = true);
+    void addAdapterTrimmed(string adapter, bool isR2 = false);
     // for paired end
     void addAdapterTrimmed(string adapter1, string adapter2);
+    void incTrimmedAdapterRead(int count = 1);
     void addPolyXTrimmed(int base, int length);
     long getTotalPolyXTrimmedReads();
     long getTotalPolyXTrimmedBases();

src/peprocessor.cpp

@@ -465,10 +465,16 @@ bool PairEndProcessor::processPairEnd(ReadPack* leftPack, ReadPack* rightPack, T
                         trimmed2 = AdapterTrimmer::trimBySequence(r2, config->getFilterResult(), mOptions->adapter.sequenceR2, true);
                 }
                 if(mOptions->adapter.hasFasta) {
-                    trimmed1 |= AdapterTrimmer::trimByMultiSequences(r1, config->getFilterResult(), mOptions->adapter.seqsInFasta, false, !trimmed1);
-                    trimmed2 |= AdapterTrimmer::trimByMultiSequences(r2, config->getFilterResult(), mOptions->adapter.seqsInFasta, true, !trimmed2);
+                    trimmed1 |= AdapterTrimmer::trimByMultiSequences(r1, config->getFilterResult(), mOptions->adapter.seqsInFasta, false);
+                    trimmed2 |= AdapterTrimmer::trimByMultiSequences(r2, config->getFilterResult(), mOptions->adapter.seqsInFasta, true);
                 }
 
+                if(trimmed1 )
+                    config->getFilterResult()->incTrimmedAdapterRead(1);
+                if(trimmed2 )
+                    config->getFilterResult()->incTrimmedAdapterRead(1);
+
+
                 // Check for adapter dimer: both reads shorter than threshold after adapter trimming
                 // AND adapters were detected in at least one of the reads (requires evidence)
                 if(r1 != NULL && r2 != NULL && (trimmed1 || trimmed2) &&

src/seprocessor.cpp

@@ -246,11 +246,13 @@ bool SingleEndProcessor::processSingleEnd(ReadPack* pack, ThreadConfig* config){
             bool trimmed = false;
             if(mOptions->adapter.hasSeqR1)
                 trimmed = AdapterTrimmer::trimBySequence(r1, config->getFilterResult(), mOptions->adapter.sequence, false);
-            bool incTrimmedCounter = !trimmed;
             if(mOptions->adapter.hasFasta) {
-                trimmed |= AdapterTrimmer::trimByMultiSequences(r1, config->getFilterResult(), mOptions->adapter.seqsInFasta, false, incTrimmedCounter);
+                trimmed |= AdapterTrimmer::trimByMultiSequences(r1, config->getFilterResult(), mOptions->adapter.seqsInFasta, false);
             }
 
+            if(trimmed )
+                config->getFilterResult()->incTrimmedAdapterRead(1);
+
             // Check for adapter dimer: read shorter than threshold after adapter trimming
             // AND adapter was detected (requires evidence)
             if(r1 != NULL && trimmed && r1->length() <= mOptions->adapter.dimerMaxLen) {