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#include <alignment/format/SAMPrinter.hpp>
#include <algorithm> //reverse
using namespace SAMOutput;
void SAMOutput::BuildFlag(T_AlignmentCandidate &alignment, AlignmentContext &context,
uint16_t &flag)
{
/*
* Much of the flags are commented out for now since they do not
* generate PICARD compliant SAM. This needs to be worked out.
*/
//
// Without supporting strobe, assume 1 segment per template.
flag = 0;
/*
if (context.nSubreads > 1) {
flag |= MULTI_SEGMENTS;
}*/
// if (context.AllSubreadsAligned() and context.nSubreads > 1) {
// flag |= ALL_SEGMENTS_ALIGNED;
// }
if (alignment.tStrand == 1) {
flag |= SEQ_REVERSED;
}
/*
if (context.hasNextSubreadPos == false and context.nSubreads > 1) {
flag |= NEXT_SEGMENT_UNMAPPED;
}
if (context.nextSubreadDir == 1) {
flag |= SEQ_NEXT_REVERSED;
}
if (context.IsFirst() and context.nSubreads > 1) {
flag |= FIRST_SEGMENT;
}
*/
else if (context.nSubreads > 1) {
/*
* Remember, if you're not first, you're last.
*/
// flag |= LAST_SEGMENT;
}
if (context.isPrimary == false) {
flag |= SECONDARY_ALIGNMENT;
}
}
void SAMOutput::CreateDNAString(DNASequence &seq, DNASequence &clippedSeq,
//
// Trimming is used for both hard non-clipping
// so it is called trim instead of clip.
//
DNALength trimFront, DNALength trimEnd)
{
assert(seq.length >= trimEnd and seq.length - trimEnd >= trimFront);
clippedSeq.seq = &seq.seq[trimFront];
clippedSeq.length = seq.length - trimEnd - trimFront;
}
void SAMOutput::AddGaps(T_AlignmentCandidate &alignment, int gapIndex, std::vector<int> &opSize,
std::vector<char> &opChar)
{
for (size_t g = 0; g < alignment.gaps[gapIndex].size(); g++) {
if (alignment.gaps[gapIndex][g].seq == blasr::Gap::Query) {
opSize.push_back(alignment.gaps[gapIndex][g].length);
opChar.push_back('D');
} else if (alignment.gaps[gapIndex][g].seq == blasr::Gap::Target) {
opSize.push_back(alignment.gaps[gapIndex][g].length);
opChar.push_back('I');
}
}
}
void SAMOutput::AddMatchBlockCigarOps(DNASequence &qSeq, DNASequence &tSeq, blasr::Block &b,
DNALength &qSeqPos, DNALength &tSeqPos,
std::vector<int> &opSize, std::vector<char> &opChar)
{
DNALength qPos = qSeqPos + b.qPos, tPos = tSeqPos + b.tPos;
bool started = false, prevSeqMatch = false;
for (DNALength i = 0; i < b.length; i++) {
bool curSeqMatch = (qSeq[qPos + i] == tSeq[tPos + i]);
if (started) {
if (curSeqMatch == prevSeqMatch)
opSize[opSize.size() - 1]++;
else {
opSize.push_back(1);
opChar.push_back(curSeqMatch ? '=' : 'X');
}
} else {
started = true;
opSize.push_back(1);
opChar.push_back(curSeqMatch ? '=' : 'X');
}
prevSeqMatch = curSeqMatch;
}
}
void SAMOutput::MergeAdjacentIndels(std::vector<int> &opSize, std::vector<char> &opChar,
const char mismatchChar)
{
assert(opSize.size() == opChar.size() and not opSize.empty());
size_t i, j;
for (i = 0, j = 1; i < opSize.size() and j < opSize.size(); j++) {
const int ni = opSize[i], nj = opSize[j];
const char ci = opChar[i], cj = opChar[j];
if (ci == cj) {
opSize[i] = ni + nj; // merge i and j to i
} else {
if ((ci == 'I' and cj == 'D') or (ci == 'D' and cj == 'I')) {
opSize[i] = std::min(ni, nj);
opChar[i] = mismatchChar; // merge 'I' and 'D' to Mismatch
if (i != 0 and i != opSize.size() and opChar[i] == opChar[i - 1]) {
assert(i >= 1);
opSize[i - 1] += opSize[i]; // merge with i - 1?
i--;
}
if (ni != nj) {
i++; // the remaining 'I' or 'D'
opSize[i] = std::abs(ni - nj);
opChar[i] = (ni > nj) ? ci : cj;
}
} else {
i++; // move forward.
opSize[i] = nj;
opChar[i] = cj;
}
}
}
assert(i < opSize.size());
opSize.erase(opSize.begin() + i + 1, opSize.end());
opChar.erase(opChar.begin() + i + 1, opChar.end());
}
void SAMOutput::CreateNoClippingCigarOps(T_AlignmentCandidate &alignment, std::vector<int> &opSize,
std::vector<char> &opChar, bool cigarUseSeqMatch,
const bool allowAdjacentIndels)
{
//
// Create the cigar string for the aligned region of a read,
// excluding the clipping.
//
int b;
// Each block creates a match NM (N=block.length)
int nBlocks = alignment.blocks.size();
int nGaps = alignment.gaps.size();
opSize.clear();
opChar.clear();
//
// Add gaps at the beginning of the alignment.
//
if (nGaps > 0) {
AddGaps(alignment, 0, opSize, opChar);
}
for (b = 0; b < nBlocks; b++) {
//
// Determine the gap before printing the match, since it is
// possible that the qurey and target are gapped at the same
// time, which merges into a mismatch.
//
int qGap = 0, tGap = 0;
int matchLength = alignment.blocks[b].length;
if (nGaps == 0) {
if (b + 1 < nBlocks) {
qGap = alignment.blocks[b + 1].qPos - alignment.blocks[b].qPos -
alignment.blocks[b].length;
tGap = alignment.blocks[b + 1].tPos - alignment.blocks[b].tPos -
alignment.blocks[b].length;
int commonGap;
commonGap = std::abs(qGap - tGap);
qGap -= commonGap;
tGap -= commonGap;
matchLength += commonGap;
if (cigarUseSeqMatch) {
AddMatchBlockCigarOps(alignment.qAlignedSeq, alignment.tAlignedSeq,
alignment.blocks[b], alignment.qPos, alignment.tPos,
opSize, opChar);
} else {
opSize.push_back(matchLength);
opChar.push_back('M');
}
assert((qGap > 0 and tGap == 0) or (qGap == 0 and tGap > 0));
if (qGap > 0) {
opSize.push_back(qGap);
opChar.push_back('I');
}
if (tGap > 0) {
opSize.push_back(tGap);
opChar.push_back('D');
}
}
} else {
if (cigarUseSeqMatch) {
AddMatchBlockCigarOps(alignment.qAlignedSeq, alignment.tAlignedSeq,
alignment.blocks[b], alignment.qPos, alignment.tPos, opSize,
opChar);
} else {
opSize.push_back(matchLength);
opChar.push_back('M');
}
int gapIndex = b + 1;
AddGaps(alignment, gapIndex, opSize, opChar);
}
}
if (alignment.tStrand == 1) {
std::reverse(opSize.begin(), opSize.end());
std::reverse(opChar.begin(), opChar.end());
}
if (not allowAdjacentIndels) {
MergeAdjacentIndels(opSize, opChar, (cigarUseSeqMatch ? 'X' : 'M'));
}
}
void SAMOutput::CigarOpsToString(std::vector<int> &opSize, std::vector<char> &opChar,
std::string &cigarString)
{
std::stringstream sstrm;
int i, nElem;
for (i = 0, nElem = opSize.size(); i < nElem; i++) {
sstrm << opSize[i] << opChar[i];
}
cigarString = sstrm.str();
}
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