void SimpleAligner::align(dagcon::Alignment& aln) {
// This alignment type defined in blasr code base
blasr::Alignment initialAln, refinedAln;
FASTQSequence query;
query.seq = (Nucleotide*)aln.qstr.c_str();
query.length = aln.qstr.length();
DNASequence target;
target.seq = (Nucleotide*)aln.tstr.c_str();
target.length = aln.tstr.length();
SDPAlign(query, target, distScoreFn_, tupleMetrics_.tupleSize,
config_.sdpIndel, config_.sdpIndel, config_.indelRate*2,
initialAln, Local);
GuidedAlign(query, target, initialAln, distScoreFn_,
config_.bandSize, refinedAln);
std::string queryStr, alignStr, targetStr;
//StickPrintAlignment(initialAln, query, target, std::cout);
//StickPrintAlignment(refinedAln, query, target, std::cout);
CreateAlignmentStrings(refinedAln, query.seq, target.seq,
targetStr, alignStr, queryStr, query.length, target.length);
// alignment coordinates may change, update alignment object
aln.start += refinedAln.GenomicTBegin();
aln.end = aln.start + refinedAln.GenomicTEnd();
if (aln.strand == '-') {
aln.start = aln.tlen - aln.end;
aln.qstr = revComp(queryStr);
aln.tstr = revComp(targetStr);
} else {
aln.qstr = queryStr;
aln.tstr = targetStr;
}
aln.start++;
}
void SimpleAligner::align(dagcon::Alignment& aln) {
// This alignment type defined in blasr code base
blasr::Alignment initialAln, refinedAln;
FASTQSequence query;
query.seq = (Nucleotide*)aln.qstr.c_str();
query.length = aln.qstr.length();
query.AllocateRichQualityValues(query.length);
query.qual.Allocate(query.length);
DNASequence target;
target.seq = (Nucleotide*)aln.tstr.c_str();
target.length = aln.tstr.length();
SDPAlign(query, target, distScoreFn_, tupleMetrics_.tupleSize,
config_.sdpIndel, config_.sdpIndel, config_.indelRate*2,
initialAln, Local);
GuidedAlign(query, target, initialAln, distScoreFn_,
config_.bandSize, refinedAln);
//StickPrintAlignment(initialAln, query, target, std::cout);
//StickPrintAlignment(refinedAln, query, target, std::cout);
std::string queryStr, alignStr, targetStr;
CreateAlignmentStrings(refinedAln, query.seq, target.seq,
targetStr, alignStr, queryStr, query.length, target.length);
if (aln.strand == '-') {
aln.start = aln.len - (aln.end + refinedAln.tPos);
aln.qstr = revComp(queryStr);
aln.tstr = revComp(targetStr);
} else {
aln.start += refinedAln.tPos;
aln.qstr = queryStr;
aln.tstr = targetStr;
}
aln.start++;
}
void Print(T_Alignment &alignment, T_Sequence &query, T_Sequence &text, std::ostream &out,
int qPrintStart = 0, int tPrintStart = 0, int maxPrintLength = 50)
{
(void)(qPrintStart);
(void)(tPrintStart);
(void)(maxPrintLength);
/*
* Sample alignment:
*
<hit name="x15_y33_1220208-0008_m081205_152444_Uni_p2_b15" unalignedLength="1301" start="1051" end="1016" strand="-" targetStart="1" targetEnd="44" targetStrand="+">
<zScore value="-6.091"/>
<nInsert value="1" percent="2.86" />
<nDelete value="9" percent="25.71" />
<nMismatch value="1" percent="2.86" />
<nCorrect value="24" percent="68.57" />
<alignment><query>
AG--CGTTCC-TATGG-TG-GGGTCGTTA-ACT---GTCGCCAG
</query><target>
AGCCCG-TCCTTATGGTTGAGGGTTGTTACACTTCGGTCGCCAG
</target></alignment>
</hit>
*/
char strand[2] = {'+', '-'};
std::string tAlignStr, alignStr, qAlignStr;
CreateAlignmentStrings(alignment, query.seq, text.seq, tAlignStr, alignStr, qAlignStr);
int alignLength = tAlignStr.size();
if (alignLength == 0) {
alignLength = 1; // Make sure there are no divide by zero.
alignment.nIns = 0;
alignment.nDel = 0;
alignment.nMismatch = 0;
alignment.nMatch = 0;
}
out << BeginDataEntry(
std::string("hit"),
CreateKeywordValuePair(std::string("name"), alignment.qName) +
CreateKeywordValuePair(std::string("unalignedLength"), alignment.qLength) +
CreateKeywordValuePair(std::string("start"), alignment.qPos) +
CreateKeywordValuePair(std::string("end"),
alignment.qPos + alignment.qAlignLength) +
CreateKeywordValuePair(std::string("strand"), strand[alignment.qStrand]) +
CreateKeywordValuePair(std::string("targetStart"), alignment.tPos) +
CreateKeywordValuePair(std::string("targetEnd"),
alignment.tPos + alignment.tAlignLength) +
CreateKeywordValuePair(std::string("targetStrand"), strand[alignment.tStrand]))
<< std::endl;
out << CreateDataEntry(std::string("zScore"),
CreateKeywordValuePair(std::string("value"), alignment.zScore))
<< std::endl;
out << CreateDataEntry(std::string("nInsert"),
CreateKeywordValuePair(std::string("value"), alignment.nIns) + " " +
CreateKeywordValuePair(std::string("percent"),
alignment.nIns * 0.5 / alignLength))
<< std::endl;
out << CreateDataEntry(std::string("nDelete"),
CreateKeywordValuePair(std::string("value"), alignment.nDel) + " " +
CreateKeywordValuePair(std::string("percent"),
alignment.nDel * 0.5 / alignLength))
<< std::endl;
out << CreateDataEntry(std::string("nMismatch"),
CreateKeywordValuePair(std::string("value"), alignment.nMismatch) + " " +
CreateKeywordValuePair(std::string("percent"),
alignment.nMismatch * 0.5 / alignLength))
<< std::endl;
out << CreateDataEntry(std::string("nCorrect"),
CreateKeywordValuePair(std::string("value"), alignment.nMatch) + " " +
CreateKeywordValuePair(std::string("percent"),
alignment.nMatch * 0.5 / alignLength))
<< std::endl;
out << CreateStartEntry(std::string("alignment"), std::string(""))
<< CreateStartEntry(std::string("query"), std::string("")) << std::endl;
out << qAlignStr << std::endl;
out << CreateEndEntry(std::string("query")) << std::endl;
out << CreateStartEntry(std::string("target"), std::string("")) << std::endl;
out << tAlignStr << std::endl;
out << CreateEndEntry(std::string("target")) << std::endl;
out << CreateEndEntry(std::string("alignment")) << std::endl;
out << CreateEndEntry(std::string("hit")) << std::endl;
}
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;
}
