bool leftAlign(string& alternateSequence, Cigar& cigar, string& referenceSequence, bool debug = false) {
int arsOffset = 0; // pointer to insertion point in aligned reference sequence
string alignedReferenceSequence = referenceSequence;
int aabOffset = 0;
string alignmentAlignedBases = alternateSequence;
// store information about the indels
vector<VCFIndelAllele> indels;
int rp = 0; // read position, 0-based relative to read
int sp = 0; // sequence position
string softBegin;
string softEnd;
stringstream cigar_before, cigar_after;
for (vector<pair<int, string> >::const_iterator c = cigar.begin();
c != cigar.end(); ++c) {
unsigned int l = c->first;
char t = c->second.at(0);
cigar_before << l << t;
if (t == 'M') { // match or mismatch
sp += l;
rp += l;
} else if (t == 'D') { // deletion
indels.push_back(VCFIndelAllele(false, l, sp, rp, referenceSequence.substr(sp, l)));
alignmentAlignedBases.insert(rp + aabOffset, string(l, '-'));
aabOffset += l;
sp += l; // update reference sequence position
} else if (t == 'I') { // insertion
indels.push_back(VCFIndelAllele(true, l, sp, rp, alternateSequence.substr(rp, l)));
alignedReferenceSequence.insert(sp + softBegin.size() + arsOffset, string(l, '-'));
arsOffset += l;
rp += l;
} else if (t == 'S') { // soft clip, clipped sequence present in the read not matching the reference
// remove these bases from the refseq and read seq, but don't modify the alignment sequence
if (rp == 0) {
alignedReferenceSequence = string(l, '*') + alignedReferenceSequence;
softBegin = alignmentAlignedBases.substr(0, l);
} else {
alignedReferenceSequence = alignedReferenceSequence + string(l, '*');
softEnd = alignmentAlignedBases.substr(alignmentAlignedBases.size() - l, l);
}
rp += l;
} else if (t == 'H') { // hard clip on the read, clipped sequence is not present in the read
} else if (t == 'N') { // skipped region in the reference not present in read, aka splice
sp += l;
}
}
int alignedLength = sp;
VCFLEFTALIGN_DEBUG("| " << cigar_before.str() << endl
<< "| " << alignedReferenceSequence << endl
<< "| " << alignmentAlignedBases << endl);
// if no indels, return the alignment
if (indels.empty()) { return false; }
// for each indel, from left to right
// while the indel sequence repeated to the left and we're not matched up with the left-previous indel
// move the indel left
vector<VCFIndelAllele>::iterator previous = indels.begin();
for (vector<VCFIndelAllele>::iterator id = indels.begin(); id != indels.end(); ++id) {
// left shift by repeats
//
// from 1 base to the length of the indel, attempt to shift left
// if the move would cause no change in alignment optimality (no
// introduction of mismatches, and by definition no change in gap
// length), move to the new position.
// in practice this moves the indel left when we reach the size of
// the repeat unit.
//
int steppos, readsteppos;
VCFIndelAllele& indel = *id;
int i = 1;
while (i <= indel.length) {
int steppos = indel.position - i;
int readsteppos = indel.readPosition - i;
#ifdef VERBOSE_DEBUG
if (debug) {
if (steppos >= 0 && readsteppos >= 0) {
cerr << referenceSequence.substr(steppos, indel.length) << endl;
cerr << alternateSequence.substr(readsteppos, indel.length) << endl;
cerr << indel.sequence << endl;
}
}
#endif
while (steppos >= 0 && readsteppos >= 0
&& indel.sequence == referenceSequence.substr(steppos, indel.length)
&& indel.sequence == alternateSequence.substr(readsteppos, indel.length)
&& (id == indels.begin()
|| (previous->insertion && steppos >= previous->position)
|| (!previous->insertion && steppos >= previous->position + previous->length))) {
VCFLEFTALIGN_DEBUG((indel.insertion ? "insertion " : "deletion ") << indel << " shifting " << i << "bp left" << endl);
indel.position -= i;
indel.readPosition -= i;
steppos = indel.position - i;
readsteppos = indel.readPosition - i;
}
do {
++i;
} while (i <= indel.length && indel.length % i != 0);
}
// left shift indels with exchangeable flanking sequence
//
// for example:
//
// GTTACGTT GTTACGTT
// GT-----T ----> G-----TT
//
// GTGTGACGTGT GTGTGACGTGT
// GTGTG-----T ----> GTG-----TGT
//
// GTGTG-----T GTG-----TGT
// GTGTGACGTGT ----> GTGTGACGTGT
//
//
steppos = indel.position - 1;
readsteppos = indel.readPosition - 1;
while (steppos >= 0 && readsteppos >= 0
&& alternateSequence.at(readsteppos) == referenceSequence.at(steppos)
&& alternateSequence.at(readsteppos) == indel.sequence.at(indel.sequence.size() - 1)
&& (id == indels.begin()
|| (previous->insertion && indel.position - 1 >= previous->position)
|| (!previous->insertion && indel.position - 1 >= previous->position + previous->length))) {
VCFLEFTALIGN_DEBUG((indel.insertion ? "insertion " : "deletion ") << indel << " exchanging bases " << 1 << "bp left" << endl);
indel.sequence = indel.sequence.at(indel.sequence.size() - 1) + indel.sequence.substr(0, indel.sequence.size() - 1);
indel.position -= 1;
indel.readPosition -= 1;
steppos = indel.position - 1;
readsteppos = indel.readPosition - 1;
}
// tracks previous indel, so we don't run into it with the next shift
previous = id;
}
// bring together floating indels
// from left to right
// check if we could merge with the next indel
// if so, adjust so that we will merge in the next step
if (indels.size() > 1) {
previous = indels.begin();
for (vector<VCFIndelAllele>::iterator id = (indels.begin() + 1); id != indels.end(); ++id) {
VCFIndelAllele& indel = *id;
// parsimony: could we shift right and merge with the previous indel?
// if so, do it
int prev_end_ref = previous->insertion ? previous->position : previous->position + previous->length;
int prev_end_read = !previous->insertion ? previous->readPosition : previous->readPosition + previous->length;
if (previous->insertion == indel.insertion
&& ((previous->insertion
&& (previous->position < indel.position
&& previous->readPosition + previous->readPosition < indel.readPosition))
||
(!previous->insertion
&& (previous->position + previous->length < indel.position)
&& (previous->readPosition < indel.readPosition)
))) {
if (previous->homopolymer()) {
string seq = referenceSequence.substr(prev_end_ref, indel.position - prev_end_ref);
string readseq = alternateSequence.substr(prev_end_read, indel.position - prev_end_ref);
VCFLEFTALIGN_DEBUG("seq: " << seq << endl << "readseq: " << readseq << endl);
if (previous->sequence.at(0) == seq.at(0)
&& FBhomopolymer(seq)
&& FBhomopolymer(readseq)) {
VCFLEFTALIGN_DEBUG("moving " << *previous << " right to "
<< (indel.insertion ? indel.position : indel.position - previous->length) << endl);
previous->position = indel.insertion ? indel.position : indel.position - previous->length;
}
}
else {
int pos = previous->position;
while (pos < (int) referenceSequence.length() &&
((previous->insertion && pos + previous->length <= indel.position)
||
(!previous->insertion && pos + previous->length < indel.position))
&& previous->sequence
== referenceSequence.substr(pos + previous->length, previous->length)) {
pos += previous->length;
}
if (pos < previous->position &&
((previous->insertion && pos + previous->length == indel.position)
||
(!previous->insertion && pos == indel.position - previous->length))
) {
VCFLEFTALIGN_DEBUG("right-merging tandem repeat: moving " << *previous << " right to " << pos << endl);
previous->position = pos;
}
}
}
previous = id;
}
}
// for each indel
// if ( we're matched up to the previous insertion (or deletion)
// and it's also an insertion or deletion )
// merge the indels
//
// and simultaneously reconstruct the cigar
Cigar newCigar;
if (!softBegin.empty()) {
newCigar.push_back(make_pair(softBegin.size(), "S"));
}
vector<VCFIndelAllele>::iterator id = indels.begin();
VCFIndelAllele last = *id++;
if (last.position > 0) {
newCigar.push_back(make_pair(last.position, "M"));
newCigar.push_back(make_pair(last.length, (last.insertion ? "I" : "D")));
} else {
newCigar.push_back(make_pair(last.length, (last.insertion ? "I" : "D")));
}
int lastend = last.insertion ? last.position : (last.position + last.length);
VCFLEFTALIGN_DEBUG(last << ",");
for (; id != indels.end(); ++id) {
VCFIndelAllele& indel = *id;
VCFLEFTALIGN_DEBUG(indel << ",");
if (indel.position < lastend) {
cerr << "impossibility?: indel realigned left of another indel" << endl
<< referenceSequence << endl << alternateSequence << endl;
exit(1);
} else if (indel.position == lastend && indel.insertion == last.insertion) {
pair<int, string>& op = newCigar.back();
op.first += indel.length;
} else if (indel.position >= lastend) { // also catches differential indels, but with the same position
newCigar.push_back(make_pair(indel.position - lastend, "M"));
newCigar.push_back(make_pair(indel.length, (indel.insertion ? "I" : "D")));
}
last = *id;
lastend = last.insertion ? last.position : (last.position + last.length);
}
if (lastend < alignedLength) {
newCigar.push_back(make_pair(alignedLength - lastend, "M"));
}
if (!softEnd.empty()) {
newCigar.push_back(make_pair(softEnd.size(), "S"));
}
VCFLEFTALIGN_DEBUG(endl);
cigar = newCigar;
for (vector<pair<int, string> >::const_iterator c = cigar.begin();
c != cigar.end(); ++c) {
unsigned int l = c->first;
char t = c->second.at(0);
cigar_after << l << t;
}
//cerr << cigar_before.str() << " changes to " << cigar_after.str() << endl;
VCFLEFTALIGN_DEBUG(cigar_after.str() << endl);
// check if we're realigned
if (cigar_after.str() == cigar_before.str()) {
return false;
} else {
return true;
}
}
std::string Cigar::toString(const Cigar &cigarBuffer, unsigned offset, unsigned length)
{
ISAAC_ASSERT_MSG(cigarBuffer.size() >= offset + length, "Requested end is outside of cigarBuffer");
return toString(cigarBuffer.begin() + offset, cigarBuffer.begin() + offset + length);
}