Beispiel #1
0
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;
    }

}
Beispiel #2
0
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);
}