/usr/include/pbseq/alignment/format/CompareSequencesPrinterImpl.hpp is in libblasr-dev 0~20161219-1.
This file is owned by root:root, with mode 0o644.
The actual contents of the file can be viewed below.
1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 26 27 28 29 30 31 32 33 34 35 36 37 38 39 40 41 42 43 44 45 46 47 48 49 50 51 52 53 54 55 56 57 58 59 60 61 62 63 64 65 66 67 68 69 70 71 72 73 74 75 76 77 | #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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