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Added Gotoh Alignment for Junction Genotyping.
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@tobiasrausch
tobiasrausch committed Aug 29, 2014
1 parent 0374dae commit cd3627a
Showing 1 changed file with 139 additions and 24 deletions.
163 changes: 139 additions & 24 deletions src/junction.h
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Original file line number Diff line number Diff line change
Expand Up @@ -36,6 +36,7 @@ Contact: Tobias Rausch ([email protected])
#include <zlib.h>
#include <stdio.h>
#include "kseq.h"
#include "fasta_reader.h"
KSEQ_INIT(gzFile, gzread)

namespace torali {
Expand Down Expand Up @@ -117,14 +118,15 @@ inline void
inline void
_getUniqueKmers(TReference const& ref, TKmerSet const& kmerSet, TUniqueKmer& uniqueKmer, unsigned int kmerLength, unsigned int alphsize) {
typedef typename TKmerSet::key_type TUSize;

char currentk[MAXKMERLENGTH];
for(unsigned int i = 0; i<MAXKMERLENGTH; ++i) currentk[i] = 0;
unsigned int kmerlen=0;
TUSize bucket = 0;
std::string::const_iterator sIt= ref.begin();
std::string::const_iterator sItEnd= ref.end();
for(unsigned int seqIndex=0;sIt!=sItEnd;++sIt,++seqIndex) {
unsigned int seqIndex=0;
for(;sIt!=sItEnd;++sIt,++seqIndex) {
if (*sIt!='N') {
if (kmerlen==kmerLength) {
if (kmerSet.find(bucket)==kmerSet.end()) uniqueKmer.insert(ref.substr(seqIndex-kmerlen, kmerlen));
Expand All @@ -142,10 +144,109 @@ inline void
if ((kmerlen == kmerLength) && (kmerSet.find(bucket)==kmerSet.end())) uniqueKmer.insert(ref.substr(ref.size()-kmerlen, kmerlen));
}

template<typename TSequence, typename TBreaks>
inline void
_getReferenceBreakpoint(TSequence const& ref, TSequence const& var, TSequence& outVar, TBreaks& bpcoord)
{
typedef std::vector<char> TAlignSeq;
typedef FastaRecord<std::string, unsigned int, Dna5GapAlphabet, TAlignSeq, void> TFastaRecord;
std::vector<TFastaRecord> alignFwd;
std::vector<TFastaRecord> alignRev;
std::vector<TFastaRecord> align;

// Convert to alignment data structure
TAlignSeq r;
for(typename TSequence::const_iterator itS = ref.begin(); itS!=ref.end(); ++itS) r.push_back(dna5_encode[(int) *itS]);
TAlignSeq v;
for(typename TSequence::const_iterator itS = var.begin(); itS!=var.end(); ++itS) v.push_back(dna5_encode[(int) *itS]);

// Decide forward or reverse alignment
DnaScore<int> scr(1, -2, -5, 0);
AlignConfig<true, false, false, true> alc;
int fwdScore=globalGotohAlignment(alignFwd, r, v, scr, alc);
reverseComplement(v);
int revScore=globalGotohAlignment(alignRev, r, v, scr, alc);
if (fwdScore > revScore) reverseComplement(v);

// Compute final alignment
globalGotohAlignment(align, r, v, scr, alc);

// Find longest internal gap
int refIndex=-1;
int varIndex=-1;
int gapStartRefIndex=0;
int gapEndRefIndex=0;
int gapStartVarIndex=0;
int gapEndVarIndex=0;
int longestGap=0;
TAlignSeq::const_iterator alRef = align[0].seq.begin();
TAlignSeq::const_iterator alVar = align[1].seq.begin();
bool inGap=false;
for (; (alRef != align[0].seq.end()) && (alVar != align[1].seq.end()); ++alRef, ++alVar) {
if (*alRef != dna5gap_encode[(int) '-']) ++refIndex;
if (*alVar != dna5gap_encode[(int) '-']) ++varIndex;
// Internal gap?
if (((*alVar == dna5gap_encode[(int) '-']) || (*alRef == dna5gap_encode[(int) '-'])) && (refIndex>0) && (varIndex>0)) {
if (!inGap) {
gapStartRefIndex=refIndex;
gapEndRefIndex=refIndex;
gapStartVarIndex=varIndex;
gapEndVarIndex=varIndex;
} else {
gapEndRefIndex=refIndex;
gapEndVarIndex=varIndex;
}
inGap=true;
} else {
if ((inGap) && ((gapEndRefIndex - gapStartRefIndex) > longestGap)) {
longestGap=gapEndRefIndex - gapStartRefIndex;
bpcoord[0]=gapStartRefIndex;
bpcoord[1]=gapEndRefIndex;
bpcoord[2]=gapStartVarIndex;
bpcoord[3]=gapEndVarIndex;
}
inGap=false;
}
}

// Output sequence might be reverse complemented
outVar.clear();
for(TAlignSeq::const_iterator itA = v.begin(); itA!=v.end(); ++itA) outVar.push_back(dna5_decode[(int) *itA]);

// Debug code
/*
std::cout << "FwdScore: " << fwdScore << ", RevScore: " << revScore << std::endl;
std::cout << "Alignment: " << fwd << std::endl;
std::cout << "Ref: ";
int ind=0;
for(TAlignSeq::iterator alItTmp = r.begin(); alItTmp != r.end(); ++alItTmp, ++ind) {
std::cout << dna5_decode[(int) *alItTmp];
if ((ind==bpcoord[0]) || (ind==bpcoord[1])) std::cout << " | ";
}
std::cout << std::endl;
std::cout << "Var: ";
ind=0;
for(TAlignSeq::iterator alItTmp = v.begin(); alItTmp != v.end(); ++alItTmp, ++ind) {
std::cout << dna5_decode[(int) *alItTmp];
if ((ind==bpcoord[2]) || (ind==bpcoord[3])) std::cout << " | ";
}
std::cout << std::endl;
std::cout << ">Ref" << std::endl;
for(TAlignSeq::iterator alItTmp = align[0].seq.begin(); alItTmp != align[0].seq.end(); ++alItTmp) std::cout << dna5gap_decode[(int) *alItTmp];
std::cout << std::endl;
std::cout << ">Contig" << std::endl;
for(TAlignSeq::iterator alItTmp = align[1].seq.begin(); alItTmp != align[1].seq.end(); ++alItTmp) std::cout << dna5gap_decode[(int) *alItTmp];
std::cout << std::endl;
std::cout << std::endl;
std::cout << std::endl;
*/
}


template<typename TFiles, typename TGenome, typename TSampleLibrary, typename TSVs, typename TCountMap>

template<typename TFiles, typename TGenome, typename TSampleLibrary, typename TSVs, typename TCountMap, typename TTag>
inline void
annotateJunctionReads(TFiles const& files, TGenome const& genome, uint16_t const minMapQual, TSampleLibrary& sampleLib, TSVs& svs, TCountMap& countMap)
annotateJunctionReads(TFiles const& files, TGenome const& genome, uint16_t const minMapQual, TSampleLibrary& sampleLib, TSVs& svs, TCountMap& countMap, SVType<TTag> svType)
{
typedef typename TCountMap::key_type TSampleSVPair;
typedef typename TCountMap::mapped_type TCountPair;
Expand Down Expand Up @@ -190,55 +291,69 @@ inline void
typename TSVs::const_iterator itSVEnd = svs.end();
for(;itSV!=itSVEnd;++itSV) {
if (itSV->consensus.empty()) continue;
if (itSV->chr2 == refIndex) {
int consLen = itSV->consensus.size();
// For translocations temporarily store the first reference part in the probe strings
refProbes[itSV->id]=boost::to_upper_copy(std::string(seq->seq.s + std::max(itSV->svEnd - consLen, 0), seq->seq.s + itSV->svEnd + consLen));
}
int consLen = itSV->consensus.size();

// Create a pseudo structural variant record
StructuralVariantRecord svRec;
svRec.chr = itSV->chr;
svRec.chr2 = itSV->chr2;
svRec.svStartBeg = std::max(itSV->svStart - consLen, 0);
svRec.svStart = itSV->svStart;
svRec.svStartEnd = std::min(itSV->svStart + consLen, references[itSV->chr].RefLength);
svRec.svEndBeg = std::max(itSV->svEnd - consLen, 0);
svRec.svEnd = itSV->svEnd;
svRec.svEndEnd = std::min(itSV->svEnd + consLen, references[itSV->chr2].RefLength);
if ((itSV->chr != itSV->chr2) && (itSV->chr2 == refIndex)) {
refProbes[itSV->id] = _getSVRef(seq->seq.s, svRec, refIndex, svType);
}
if (itSV->chr == refIndex) {
int consLen = itSV->consensus.size();
std::string sourceRight=refProbes[itSV->id];
// Get the reference string
if (itSV->chr != itSV->chr2) svRec.consensus=refProbes[itSV->id];
refProbes[itSV->id]="";
std::string sourceLeft=boost::to_upper_copy(std::string(seq->seq.s + std::max(itSV->svStart - consLen, 0), seq->seq.s + itSV->svStart + consLen));
std::string cons=boost::to_upper_copy(itSV->consensus);
std::string svRefStr = _getSVRef(seq->seq.s, svRec, refIndex, svType);
std::string consensus;
std::vector<int> bpcoord(4);
std::fill(bpcoord.begin(), bpcoord.end(), 0);
_getReferenceBreakpoint(svRefStr, itSV->consensus, consensus, bpcoord);
// Has a breakpoint been found
if ((bpcoord[2]==0) || (bpcoord[3]==0)) continue;
// Find tagging kmers
for (unsigned int kmerLength=11; kmerLength<MAXKMERLENGTH; kmerLength+=2) {
unsigned int minReqHammingDist = (unsigned int) ((std::log(kmerLength) * std::log(kmerLength)) / std::log(4));
typedef std::set<boost::multiprecision::uint128_t> TKmerSet;
TKmerSet refKmerSet;
std::string refLeft=sourceLeft;
std::string refRight=sourceRight;
_getKmers(refLeft, refKmerSet, kmerLength, 4);
_getKmers(refRight, refKmerSet, kmerLength, 4);
_getKmers(svRefStr, refKmerSet, kmerLength, 4);
typedef boost::unordered_set<std::string> TUniqueKmers;
TUniqueKmers uniqueKmers;
_getUniqueKmers(cons, refKmerSet, uniqueKmers, kmerLength, 4);
std::string consPiece=consensus.substr(std::max(bpcoord[2] - (int) kmerLength, 0), 2 * kmerLength);
_getUniqueKmers(consPiece, refKmerSet, uniqueKmers, kmerLength, 4);
unsigned int maxHammingDistance=0;
std::string maxHammingKmer="";
if (uniqueKmers.size()) {
TUniqueKmers::iterator itK = uniqueKmers.begin();
for(;itK!=uniqueKmers.end();++itK) {
unsigned int hammingDist = std::min(_getMinHammingDistance(refLeft, *itK, minReqHammingDist), _getMinHammingDistance(refRight, *itK, minReqHammingDist));
unsigned int hammingDist = _getMinHammingDistance(svRefStr, *itK, minReqHammingDist);
if ((hammingDist>minReqHammingDist) && (hammingDist>maxHammingDistance)) {
maxHammingDistance=hammingDist;
maxHammingKmer=*itK;
}
}
}
if (maxHammingDistance) {
// Found suitable kmer
// Found suitable kmer, find reference tagging kmer
TKmerSet consKmerSet;
_getKmers(cons, consKmerSet, kmerLength, 4);
_getKmers(consensus, consKmerSet, kmerLength, 4);
TUniqueKmers uniqueRefKmers;
refLeft=refLeft.substr(std::max((int) refLeft.size()/2 - (int) kmerLength, 0), 2 * kmerLength);
refRight=refRight.substr(std::max((int) refRight.size()/2 - (int) kmerLength, 0), 2 * kmerLength);
std::string refLeft=svRefStr.substr(std::max(bpcoord[0] - (int) kmerLength, 0), 2 * kmerLength);
std::string refRight=svRefStr.substr(std::max(bpcoord[1] - (int) kmerLength, 0), 2 * kmerLength);
_getUniqueKmers(refLeft, consKmerSet, uniqueRefKmers, kmerLength, 4);
_getUniqueKmers(refRight, consKmerSet, uniqueRefKmers, kmerLength, 4);
unsigned int maxRefHammingDistance=0;
std::string maxRefHammingKmer="";
if (uniqueRefKmers.size()) {
TUniqueKmers::iterator itK = uniqueRefKmers.begin();
for(;itK!=uniqueRefKmers.end();++itK) {
unsigned int hammingDist = _getMinHammingDistance(cons, *itK, minReqHammingDist);
unsigned int hammingDist = _getMinHammingDistance(consensus, *itK, minReqHammingDist);
if ((hammingDist>minReqHammingDist) && (hammingDist>maxRefHammingDistance)) {
maxRefHammingDistance=hammingDist;
maxRefHammingKmer=*itK;
Expand Down

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