void SAMOutput::SetSoftClip(T_AlignmentCandidate &alignment,
T_Sequence &read,
DNALength hardClipPrefix,
DNALength hardClipSuffix,
DNALength &softClipPrefix,
DNALength &softClipSuffix) {
DNALength qStart, qEnd;
qStart = alignment.QAlignStart();
qEnd = alignment.QAlignEnd();
assert(qStart >= hardClipPrefix);
softClipPrefix = alignment.QAlignStart() - hardClipPrefix;
assert(alignment.QAlignEnd() + hardClipSuffix <= read.length);
softClipSuffix = read.length - hardClipSuffix - alignment.QAlignEnd();
}
void SAMOutput::SetHardClip(T_AlignmentCandidate &alignment,
T_Sequence &read,
DNALength &prefixClip,
DNALength &suffixClip) {
//
// Set the hard clipping assuming the read is in the forward
// direction.
//
prefixClip = alignment.QAlignStart();
suffixClip = read.length - alignment.QAlignEnd();
if (alignment.tStrand == 1) {
//
// If the read is instead reverse, swap the clipping lengths.
//
std::swap(prefixClip, suffixClip);
}
}
void IntervalOutput::Print(T_AlignmentCandidate &alignment, std::ostream &outFile)
{
int mapQV = alignment.mapQV;
int lastBlock = alignment.blocks.size() - 1;
if (lastBlock < 0) return;
outFile << alignment.qName << " " << alignment.tName << " " << alignment.score << " "
<< alignment.pctSimilarity << " " << alignment.qStrand << " " << alignment.QAlignStart()
<< " " << alignment.QAlignEnd() << " " << alignment.qLength << " " << alignment.tStrand
<< " " << alignment.TAlignStart() << " "
<< (alignment.tAlignedSeqPos + alignment.tPos + alignment.blocks[lastBlock].tPos +
alignment.blocks[lastBlock].length)
<< " " << alignment.tLength << " " << mapQV << std::endl;
//Remove the last four fields from m4 format.
//<< " " << alignment.nCells << " " << alignment.clusterScore
//<< " " << alignment.probScore << " "
//<< alignment.numSignificantClusters
}
void SAMOutput::SetAlignedSequence(T_AlignmentCandidate &alignment, T_Sequence &read,
T_Sequence &alignedSeq,
Clipping clipping) {
//
// In both no, and hard clipping, the dna sequence that is output
// solely corresponds to the aligned sequence.
//
DNALength clippedReadLength = 0;
DNALength clippedStartPos = 0;
if (clipping == none or clipping == hard) {
DNALength qStart = alignment.QAlignStart();
DNALength qEnd = alignment.QAlignEnd();
clippedReadLength = qEnd - qStart;
clippedStartPos = qStart;
}
else if (clipping == soft) {
clippedReadLength = read.length - read.lowQualityPrefix - read.lowQualitySuffix;
clippedStartPos = read.lowQualityPrefix;
}
else if (clipping == subread) {
clippedReadLength = read.subreadEnd - read.subreadStart;
clippedStartPos = read.subreadStart;
}
else {
std::cout <<" ERROR! The clipping must be none, hard, subread, or soft when setting the aligned sequence." << std::endl;
assert(0);
}
//
// Set the aligned sequence according to the clipping boundaries.
//
if (alignment.tStrand == 0) {
alignedSeq.ReferenceSubstring(read, clippedStartPos, clippedReadLength);
}
else {
T_Sequence subSeq;
subSeq.ReferenceSubstring(read, clippedStartPos, clippedReadLength);
subSeq.MakeRC(alignedSeq);
assert(alignedSeq.deleteOnExit);
}
}
void SAMOutput::PrintAlignment(T_AlignmentCandidate &alignment,
T_Sequence &read,
std::ostream &samFile,
AlignmentContext &context,
SupplementalQVList & qvList,
Clipping clipping,
bool cigarUseSeqMatch) {
std::string cigarString;
uint16_t flag;
T_Sequence alignedSequence;
DNALength prefixSoftClip = 0, suffixSoftClip = 0;
DNALength prefixHardClip = 0, suffixHardClip = 0;
CreateCIGARString(alignment, read, cigarString, clipping, prefixSoftClip, suffixSoftClip, prefixHardClip, suffixHardClip, cigarUseSeqMatch);
SetAlignedSequence(alignment, read, alignedSequence, clipping);
BuildFlag(alignment, context, flag);
samFile << alignment.qName << "\t"
<< flag << "\t"
<< alignment.tName << "\t"; // RNAME
if (alignment.tStrand == 0) {
samFile << alignment.TAlignStart() + 1 << "\t";
// POS, add 1 to get 1 based coordinate system
}
else {
samFile << alignment.tLength - (alignment.TAlignStart() + alignment.TEnd()) + 1 << "\t"; // includes - 1 for rev-comp, +1 for one-based
}
samFile << (int) alignment.mapQV << "\t"// MAPQ
<< cigarString << "\t"; // CIGAR
//
// Determine RNEXT
std::string rNext;
rNext = "*";
/*
if (context.hasNextSubreadPos == false) {
rNext = "*";
}
else {
if (context.rNext == alignment.tName) {
rNext = "=";
}
else {
rNext = context.rNext;
}
}
*/
samFile << rNext << "\t"; // RNEXT
DNALength nextSubreadPos = 0;
/*
if (context.hasNextSubreadPos) {
nextSubreadPos = context.nextSubreadPos + 1;
}*/
samFile << nextSubreadPos << "\t"; // RNEXT, add 1 for 1 based
// indexing
//DNALength tLen = alignment.GenomicTEnd() - alignment.GenomicTBegin();
//SAM v1.5, tLen is set as 0 for single-segment template
samFile << 0 << "\t"; // TLEN
// Print the sequence on one line, and suppress printing the
// newline (by setting the line length to alignedSequence.length
(static_cast<DNASequence*>(&alignedSequence))->PrintSeq(samFile, 0); // SEQ
samFile << "\t";
if (alignedSequence.qual.data != NULL && qvList.useqv == 0) {
alignedSequence.PrintAsciiQual(samFile, 0); // QUAL
}
else {
samFile <<"*";
}
samFile << "\t";
//
// Add optional fields
//
samFile << "RG:Z:" << context.readGroupId << "\t";
samFile << "AS:i:" << alignment.score << "\t";
//
// "RG" read group Id
// "AS" alignment score
// "XS" read alignment start position without counting previous soft clips (1 based)
// "XE" read alignment end position without counting previous soft clips (1 based)
// "XL" aligned read length
// "XQ" query sequence length
// "XT" # of continues reads, always 1 for blasr
// "NM" edit distance
// "FI" read alignment start position (1 based)
//
DNALength qAlignStart = alignment.QAlignStart();
DNALength qAlignEnd = alignment.QAlignEnd();
if (clipping == none) {
samFile << "XS:i:" << qAlignStart + 1 << "\t";
samFile << "XE:i:" << qAlignEnd + 1 << "\t";
}
else if (clipping == hard or clipping == soft or clipping == subread) {
DNALength xs = prefixHardClip;
DNALength xe = read.length - suffixHardClip;
if (alignment.tStrand == 1) {
xs = suffixHardClip;
xe = read.length - prefixHardClip;
}
samFile << "XS:i:" << xs + 1 << "\t"; // add 1 for 1-based indexing in sam
assert(read.length - suffixHardClip == prefixHardClip + alignedSequence.length);
samFile << "XE:i:" << xe + 1 << "\t";
}
samFile << "YS:i:" << read.subreadStart << "\t";
samFile << "YE:i:" << read.subreadEnd << "\t";
samFile << "ZM:i:" << read.zmwData.holeNumber << "\t";
samFile << "XL:i:" << alignment.qAlignedSeq.length << "\t";
samFile << "XT:i:1\t"; // reads are allways continuous reads, not
// referenced based circular consensus when
// output by blasr.
samFile << "NM:i:" << context.editDist << "\t";
samFile << "FI:i:" << alignment.qAlignedSeqPos + 1;
// Add query sequence length
samFile << "\t" << "XQ:i:" << alignment.qLength;
//
// Write out optional quality values. If qvlist does not
// have any qv's signaled to print, this is a no-op.
//
// First transform characters that are too large to printable ones.
qvList.FormatQVOptionalFields(alignedSequence);
qvList.PrintQVOptionalFields(alignedSequence, samFile);
samFile << std::endl;
}