702ce22305
sequences. It stands for Sequence Search and Alignment by Hashing Algorithm. It achieves its fast search speed by converting sequence information into a `hash table' data structure, which can then be searched very rapidly for matches. WWW: http://www.sanger.ac.uk/Software/analysis/SSAHA/ PR: ports/124525 Submitted by: Fernan Aguero <fernan@iib.unsam.edu.ar> Approved by: gabor (mentor, implicit)
32 lines
1.3 KiB
C++
32 lines
1.3 KiB
C++
--- ./SequenceReader/SequenceReaderFasta.cpp.orig 2004-03-01 13:51:29.000000000 -0300
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+++ ./SequenceReader/SequenceReaderFasta.cpp 2008-06-12 15:39:31.000000000 -0300
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@@ -135,9 +135,9 @@
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seqStopChar_( rhs.seqStopChar_ ),
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pInputFileStream_( new ifstream( rhs.fileName_.c_str() ) ),
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fileName_( rhs.fileName_.c_str() ),
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- seqPositions_( rhs.seqPositions_ ),
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// lastSourceSeqNum_(0),
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- pEncoder_( rhs.pEncoder_->clone() )
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+ pEncoder_( rhs.pEncoder_->clone() ),
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+ seqPositions_( rhs.seqPositions_ )
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{
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monitoringStream_ << "copy constructing SequenceReaderFile" << this
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<< endl;
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@@ -603,7 +603,7 @@
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throw SSAHAException
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("Requested seq start exceeds requested seq end in SequenceReaderFile::extractSource");
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} // ~if
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- else if (seqEnd>lastSourceSeq_.size() )
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+ else if (seqEnd>(SequenceOffset)lastSourceSeq_.size() )
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{
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throw SSAHAException
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("Requested last byte exceeds end of seq in SequenceReaderFile::extractSource");
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@@ -628,7 +628,7 @@
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computeNumSequencesInFile(); // ensure have scanned to end of file
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fileFile << fileName_ << endl;
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SeqIndexInfo* pIndex = new SeqIndexInfo[seqPositions_.size()];
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- for (int i(0) ; i < seqPositions_.size() ; i++)
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+ for (unsigned int i(0) ; i < seqPositions_.size() ; i++)
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{
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pIndex[i].fileNum=fileNumber;
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pIndex[i].seqPos=seqPositions_[i];
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