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#ifndef _BLASR_COMPARE_SEQUENCES_PRINTER_IMPL_HPP_
#define _BLASR_COMPARE_SEQUENCES_PRINTER_IMPL_HPP_
template <typename T_Alignment, typename T_QuerySequence, typename T_TargetSequence>
void CompareSequencesOutput::Print(T_Alignment &alignment, T_QuerySequence &qseq,
T_TargetSequence &tseq, std::ostream &out, bool refForward)
{
std::string queryStr, alignStr, textStr;
CreateAlignmentStrings(alignment, qseq, tseq, textStr, alignStr, queryStr);
if (refForward == false) {
if (alignment.qStrand == 1 and alignment.tStrand == 0) {
DNALength alignedSeqToEnd = 0;
// DNALength alignedTSeqToEnd = 0;
if (alignment.blocks.size() > 0) {
// First compute the offset of the reverse of the substring that was aligned.
alignedSeqToEnd =
alignment.qLength - (alignment.qAlignedSeqPos + alignment.qAlignedSeq.length);
DNALength alignEndToSubstrEnd =
alignment.qAlignedSeq.length -
(alignment.qPos + alignment.blocks[alignment.blocks.size() - 1].qPos +
alignment.blocks[alignment.blocks.size() - 1].length);
alignment.qPos = alignEndToSubstrEnd;
}
alignment.qAlignedSeqPos = alignedSeqToEnd;
alignment.qStrand = 0;
alignment.tStrand = 1;
}
}
PrintCompareSequencesAlignmentStats(alignment, out);
// change the spaces in the align string to *s for easy parsing of alignment
VectorIndex i;
for (i = 0; i < alignStr.size(); i++) {
if (alignStr[i] == ' ') alignStr[i] = '*';
}
if (refForward == false and alignment.tStrand == 1) {
//
// Build reverse complement strings.
//
std::string queryStrRC, alignStrRC, textStrRC;
queryStrRC.resize(queryStr.size());
alignStrRC.resize(alignStr.size());
textStrRC.resize(alignStr.size());
DNALength pos;
DNALength alignStringLength = alignStr.size();
for (pos = 0; pos < alignStringLength; pos++) {
if (queryStr[pos] != '-') {
queryStrRC[alignStringLength - pos - 1] =
ReverseComplementNuc[static_cast<int>(queryStr[pos])];
} else {
queryStrRC[alignStringLength - pos - 1] = '-';
}
alignStrRC[alignStringLength - pos - 1] = alignStr[pos];
if (textStr[pos] != '-') {
textStrRC[alignStringLength - pos - 1] =
ReverseComplementNuc[static_cast<int>(textStr[pos])];
} else {
textStrRC[alignStringLength - pos - 1] = '-';
}
}
queryStr = queryStrRC;
alignStr = alignStrRC;
textStr = textStrRC;
}
// Headers of m5 format are:
// qName qSeqLength qStart qEnd qStrand
// tName tSeqLength tStart tEnd tStrand
// score numMatch numMismatch numIns numDel
// mapQV qAlignedSeq matchPattern tAlignedSeq
out << queryStr << " " << alignStr << " " << textStr << std::endl;
}
#endif
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