Fixed a bug in the count output of seq.error when using multiple processors

diff --git a/seqerrorcommand.cpp b/seqerrorcommand.cpp
index ecd6f0ceb723290337f5856f724710eff7a751ee..99e789399e90c2b2adc429330177e7bd579e8354 100644 (file)
--- a/seqerrorcommand.cpp
+++ b/seqerrorcommand.cpp
@@ -643,7 +643,7 @@ int SeqErrorCommand::createProcesses(string filename, string qFileName, string r
                        int misMatchSize;
                        in >> misMatchSize; m->gobble(in);
                        if (misMatchSize > misMatchCounts.size()) {     misMatchCounts.resize(misMatchSize, 0); }
-                       for (int j = 0; j < misMatchCounts.size(); j++) {
+                       for (int j = 0; j < misMatchSize; j++) {
                                in >> tempNum; misMatchCounts[j] += tempNum;
                        }
                        m->gobble(in);

diff --git a/sequence.cpp b/sequence.cpp
index 224ecb10cb1529db7d6bdb10c268be047dae5834..4c631a23451d4d9723aec3a29bed423737b243ba 100644 (file)
--- a/sequence.cpp
+++ b/sequence.cpp
@@ -772,6 +772,8 @@ void Sequence::trim(int length){
        if(numBases > length){
                unaligned = unaligned.substr(0,length);
                numBases = length;
+        aligned = "";
+        isAligned = 0;
        }
        
 }

diff --git a/trimseqscommand.cpp b/trimseqscommand.cpp
index 935b9a9297e08d1f50e89d4b9a059cf9cbe8e54a..ec136dbe7eb02df1a659111766c5bff8bfc22222 100644 (file)
--- a/trimseqscommand.cpp
+++ b/trimseqscommand.cpp
@@ -1854,7 +1854,13 @@ bool TrimSeqsCommand::keepFirstTrim(Sequence& sequence, QualityScores& qscores){
                if(qscores.getName() != ""){
                        qscores.trimQScores(-1, keepFirst);
                }
+
+//        sequence.printSequence(cout);cout << endl;
+        
                sequence.trim(keepFirst);
+        
+//        sequence.printSequence(cout);cout << endl << endl;;
+
                return success;
        }
        catch(exception& e) {