void
VcfWriterCandidateSV::
modifyTranslocInfo(
const SVCandidate& sv,
const bool isFirstOfPair,
InfoTag_t& infoTags) const
{
const SVBreakend& bpA( isFirstOfPair ? sv.bp1 : sv.bp2);
infoTags.push_back( str(boost::format("BND_PAIR_COUNT=%i") % bpA.getLocalPairCount()) );
infoTags.push_back( str(boost::format("PAIR_COUNT=%i") % bpA.getPairCount()) );
}
void
VcfWriterCandidateSV::
modifyInvdelInfo(
const SVCandidate& sv,
const bool isBp1First,
InfoTag_t& infoTags) const
{
const SVBreakend& bpA( isBp1First ? sv.bp1 : sv.bp2);
const SVBreakend& bpB( isBp1First ? sv.bp2 : sv.bp1);
infoTags.push_back( str(boost::format("UPSTREAM_PAIR_COUNT=%i") % bpA.getLocalPairCount()) );
infoTags.push_back( str(boost::format("DOWNSTREAM_PAIR_COUNT=%i") % bpB.getLocalPairCount()) );
infoTags.push_back( str(boost::format("PAIR_COUNT=%i") % bpA.getPairCount()) );
}
static
void
addDebugInfo(
const SVBreakend& bp1,
const SVBreakend& bp2,
const bool isFirstOfPair,
const SVCandidateAssemblyData& assemblyData,
InfoTag_t& infotags)
{
if (! isFirstOfPair) return;
// store alignment start + cigar string for each section of the jumping alignment.
// there can be several contigs per breakend, so we iterate over all of them.
// only the first breakpoint gets the alignments attached to its VCF entry
if (assemblyData.isSpanning)
{
const unsigned numAlign(assemblyData.spanningAlignments.size());
std::string cigar1;
std::string cigar2;
for (unsigned alignIndex(0); alignIndex<numAlign; ++alignIndex)
{
const SVCandidateAssemblyData::JumpAlignmentResultType align(assemblyData.spanningAlignments[alignIndex]);
infotags.push_back( str(boost::format("CTG_JALIGN_%i_POS_A=%d") %
alignIndex %
(bp1.interval.range.begin_pos()+align.align1.beginPos)) );
infotags.push_back( str(boost::format("CTG_JALIGN_%i_POS_B=%d") %
alignIndex %
(bp2.interval.range.begin_pos()+align.align2.beginPos)) );
apath_to_cigar(align.align1.apath,cigar1);
apath_to_cigar(align.align2.apath,cigar2);
infotags.push_back( str(boost::format("CTG_JALIGN_%i_CIGAR_A=%s") % alignIndex % cigar1) );
infotags.push_back( str(boost::format("CTG_JALIGN_%i_CIGAR_B=%s") % alignIndex % cigar2) );
}
}
}
void
VcfWriterRnaSV::
modifyTranslocInfo(
const SVCandidate& sv,
const bool isFirstOfPair,
const SVCandidateAssemblyData& assemblyData,
InfoTag_t& infotags) const
{
const SVScoreInfo& baseInfo(getBaseInfo());
infotags.push_back( str(boost::format("BND_DEPTH=%i") %
(isFirstOfPair ? baseInfo.bp1MaxDepth : baseInfo.bp2MaxDepth) ) );
infotags.push_back( str(boost::format("MATE_BND_DEPTH=%i") %
(isFirstOfPair ? baseInfo.bp2MaxDepth : baseInfo.bp1MaxDepth) ) );
{
///TODO better multisample handler here:
const unsigned sampleIndex(0);
const SVSampleAlleleInfo& refinfo(baseInfo.samples[sampleIndex].ref);
infotags.push_back(str(boost::format("REF_COUNT=%i") %
(isFirstOfPair ? refinfo.confidentSplitReadAndPairCountRefBp1 : refinfo.confidentSplitReadAndPairCountRefBp2)));
infotags.push_back(str(boost::format("MATE_REF_COUNT=%i") %
(isFirstOfPair ? refinfo.confidentSplitReadAndPairCountRefBp2 : refinfo.confidentSplitReadAndPairCountRefBp1)));
}
{
// if (!assemblyData.isSpanning) return;
const bool isFirst = (assemblyData.bporient.isBp1First == isFirstOfPair);
if (isFirst) infotags.push_back("RNA_FIRST");
if (assemblyData.bporient.isTranscriptStrandKnown) infotags.push_back("RNA_STRANDED");
if (!isFirstOfPair) return; // only the first breakpoint gets the additional RNA info attached to its VCF entry
infotags.push_back(str(boost::format("RNA_FwRvReads=%i,%i") % sv.forwardTranscriptStrandReadCount % sv.reverseTranscriptStrandReadCount));
infotags.push_back(str(boost::format("RNA_Reads=%i") % sv.bp2.lowresEvidence.getTotal()));
const unsigned numContigs(assemblyData.contigs.size());
if (numContigs > 0)
{
if (numContigs != assemblyData.spanningAlignments.size())
infotags.push_back(str(boost::format("ERROR=%i,%i") % numContigs % assemblyData.spanningAlignments.size()));
const unsigned int bestAlignmentIdx(assemblyData.bestAlignmentIndex);
if (numContigs <= bestAlignmentIdx)
infotags.push_back(str(boost::format("ERROR2=%i,%i") % numContigs % bestAlignmentIdx));
infotags.push_back(str(boost::format("RNA_CONTIG=%s") % assemblyData.contigs[bestAlignmentIdx].seq));
const auto& bestAlignment(assemblyData.spanningAlignments[bestAlignmentIdx]);
infotags.push_back(str(boost::format("RNA_CONTIG_ALN=%i,%i")
% apath_matched_length(bestAlignment.align1.apath)
% apath_matched_length(bestAlignment.align2.apath)));
}
}
#ifdef DEBUG_VCF
addDebugInfo(isFirstOfPair, sv, assemblyData, infotags);
#endif
}
void
VcfWriterSV::
writeInvdel(
const SVCandidate& sv,
const SVId& svId,
const SVCandidateAssemblyData& /*adata*/,
const bool isIndel,
const EventInfo& event)
{
const bool isImprecise(sv.isImprecise());
const bool isBreakendRangeSameShift(sv.isBreakendRangeSameShift());
const bool isBp1First(sv.bp1.interval.range.begin_pos()<=sv.bp2.interval.range.begin_pos());
const SVBreakend& bpA(isBp1First ? sv.bp1 : sv.bp2);
const SVBreakend& bpB(isBp1First ? sv.bp2 : sv.bp1);
InfoTag_t infoTags;
SampleTag_t sampleTags;
// get CHROM
const std::string& chrom(_header.chrom_data[sv.bp1.interval.tid].label);
const known_pos_range2& bpArange(bpA.interval.range);
const known_pos_range2& bpBrange(bpB.interval.range);
if (! isImprecise)
{
assert(bpArange.size() == bpBrange.size());
}
// above this size all records use symbolic alleles (ie. <DEL>):
static const unsigned maxNonSymbolicRecordSize(1000);
// if the variant is a combination of simple insertion and deletions, and below
// a large-event size threshold, it is classified as a small variant. In this case
// we report the event using full REF and ALT sequences, plus a CIGAR string for
// complex in/del combinations
//
bool isSmallVariant(false);
if ((! isImprecise) && isIndel && (! sv.isUnknownSizeInsertion))
{
const unsigned deleteSize(bpBrange.begin_pos() - bpArange.begin_pos());
const unsigned insertSize(sv.insertSeq.size());
const bool isSmallDelete(deleteSize<=maxNonSymbolicRecordSize);
const bool isSmallInsert(insertSize<=maxNonSymbolicRecordSize);
isSmallVariant = (isSmallDelete && isSmallInsert);
}
// get POS and endPos
pos_t pos(bpArange.center_pos()+1);
pos_t endPos(bpBrange.center_pos());
if (! isImprecise)
{
pos = bpArange.begin_pos()+1;
if (isBreakendRangeSameShift)
{
endPos = bpBrange.begin_pos();
}
else
{
endPos = bpBrange.end_pos()-1;
}
}
else
{
/// check against the rare case arising when CIEND is a subset of CIPOS:
endPos=std::max(endPos,pos+1);
}
if (pos<1) return;
// get REF
std::string ref;
{
const pos_t beginRefPos(pos-1);
pos_t endRefPos(beginRefPos);
if (isSmallVariant) endRefPos=endPos-1;
get_standardized_region_seq(_referenceFilename, chrom, beginRefPos, endRefPos, ref);
assert(static_cast<unsigned>(1+endRefPos-beginRefPos) == ref.size());
}
// build alt:
std::string alt;
if (isSmallVariant)
{
alt = ref[0] + sv.insertSeq;
}
else
{
alt = str( boost::format("<%s>") % svId.getLabel());
}
// build INFO field
std::vector<std::string> words;
split_string(svId.getLabel(),':',words);
{
// note that there's a reasonable argument for displaying these tags only when a
// symbolic allele is used (by a strict reading of the vcf spec) -- we instead
// print these fields for all variants for uniformity within the manta vcf:
//
infoTags.push_back( str(boost::format("END=%i") % endPos));
infoTags.push_back( str(boost::format("SVTYPE=%s") % words[0]));
const pos_t refLen(endPos-pos);
pos_t svLen(refLen);
if (! sv.isUnknownSizeInsertion)
{
if (isIndel)
{
const pos_t insertLen(static_cast<pos_t>(sv.insertSeq.size()));
if ( insertLen > refLen )
{
svLen = insertLen;
}
else
{
svLen = -refLen;
}
}
infoTags.push_back( str(boost::format("SVLEN=%i") % (svLen)));
}
}
infoTags.push_back( str(boost::format("UPSTREAM_PAIR_COUNT=%i") % bpA.getLocalPairCount()) );
infoTags.push_back( str(boost::format("DOWNSTREAM_PAIR_COUNT=%i") % bpB.getLocalPairCount()) );
infoTags.push_back( str(boost::format("PAIR_COUNT=%i") % bpA.getPairCount()) );
if (isSmallVariant)
{
if (! sv.insertAlignment.empty())
{
std::string cigar;
apath_to_cigar(sv.insertAlignment,cigar);
// add the 1M to signify the leading reference base:
infoTags.push_back( str(boost::format("CIGAR=1M%s") % cigar));
}
}
if (isImprecise)
{
infoTags.push_back("IMPRECISE");
}
if (bpArange.size() > 1)
{
infoTags.push_back( str( boost::format("CIPOS=%i,%i") % ((bpArange.begin_pos()+1) - pos) % (bpArange.end_pos() - pos) ));
}
if (! isSmallVariant)
{
if (bpBrange.size() > 1)
{
infoTags.push_back( str( boost::format("CIEND=%i,%i") % (bpBrange.begin_pos() - endPos) % ((bpBrange.end_pos()-1) - endPos) ));
}
}
if (! isImprecise)
{
if (bpArange.size() > 1)
{
infoTags.push_back( str( boost::format("HOMLEN=%i") % (bpArange.size()-1) ));
std::string homref;
get_standardized_region_seq(_referenceFilename,chrom,bpArange.begin_pos()+1,bpArange.end_pos()-1,homref);
infoTags.push_back( str( boost::format("HOMSEQ=%s") % (homref) ));
}
}
if (! isSmallVariant)
{
if (! (sv.insertSeq.empty() || sv.isUnknownSizeInsertion))
{
infoTags.push_back( str( boost::format("SVINSLEN=%i") % (sv.insertSeq.size()) ));
if (isBp1First || (bpA.state != bpB.state))
{
infoTags.push_back( str( boost::format("SVINSSEQ=%s") % (sv.insertSeq) ));
}
else
{
infoTags.push_back( str( boost::format("SVINSSEQ=%s") % reverseCompCopyStr(sv.insertSeq) ));
}
}
}
if (sv.isUnknownSizeInsertion)
{
if (! sv.unknownSizeInsertionLeftSeq.empty())
{
infoTags.push_back( str( boost::format("LEFT_SVINSSEQ=%s") % (sv.unknownSizeInsertionLeftSeq) ));
}
if (! sv.unknownSizeInsertionRightSeq.empty())
{
infoTags.push_back( str( boost::format("RIGHT_SVINSSEQ=%s") % (sv.unknownSizeInsertionRightSeq) ));
}
}
if (svId.svType == EXTENDED_SV_TYPE::INVERSION)
{
if (sv.bp1.state == SVBreakendState::RIGHT_OPEN)
{
infoTags.push_back("INV3");
}
else if (sv.bp1.state == SVBreakendState::LEFT_OPEN)
{
infoTags.push_back("INV5");
}
else
{
assert(false && "Unexpected inversion configuration");
}
}
addSharedInfo(event, infoTags);
modifyInfo(event, infoTags);
modifySample(sv, sampleTags);
// write out record:
_os << chrom
<< '\t' << pos
<< '\t' << svId.localId // ID
<< '\t' << ref // REF
<< '\t' << alt // ALT
<< '\t';
writeQual();
_os << '\t';
writeFilter();
_os << '\t';
makeInfoField(infoTags,_os); // INFO
makeFormatSampleField(sampleTags, _os); // FORMAT + SAMPLE
_os << '\n';
}
void
VcfWriterSV::
writeTransloc(
const SVCandidate& sv,
const SVId& svId,
const bool isFirstBreakend,
const SVCandidateSetData& /*svData*/,
const SVCandidateAssemblyData& /*adata*/,
const EventInfo& event)
{
const bool isImprecise(sv.isImprecise());
const bool isBreakendRangeSameShift(sv.isBreakendRangeSameShift());
const SVBreakend& bpA( isFirstBreakend ? sv.bp1 : sv.bp2);
const SVBreakend& bpB( isFirstBreakend ? sv.bp2 : sv.bp1);
InfoTag_t infotags;
SampleTag_t sampletags;
// get CHROM
const std::string& chrom(_header.chrom_data[bpA.interval.tid].label);
const std::string& mateChrom(_header.chrom_data[bpB.interval.tid].label);
const known_pos_range2& bpArange(bpA.interval.range);
const known_pos_range2& bpBrange(bpB.interval.range);
if (! isImprecise)
{
assert(bpArange.size() == bpBrange.size());
}
// get POS
pos_t pos(bpArange.center_pos()+1);
pos_t matePos(bpBrange.center_pos()+1);
if (! isImprecise)
{
pos = bpArange.begin_pos()+1;
if (isBreakendRangeSameShift)
{
matePos = bpBrange.begin_pos()+1;
}
else
{
matePos = bpBrange.end_pos();
}
}
// get ID
const std::string& localId(isFirstBreakend ? svId.localId : svId.mateId);
const std::string& mateId(isFirstBreakend ? svId.mateId : svId.localId);
// get REF
std::string ref;
get_standardized_region_seq(_referenceFilename,chrom,pos-1,pos-1,ref);
assert(1 == ref.size());
const bool isReverseInsertSeq(! (isFirstBreakend || (bpA.state != bpB.state)));
std::string tmpString;
const std::string* insertSeqPtr(&sv.insertSeq);
if (isReverseInsertSeq)
{
tmpString = reverseCompCopyStr(sv.insertSeq);
insertSeqPtr = &tmpString;
}
const std::string& insertSeq(*insertSeqPtr);
// build alt:
boost::format altFormat("%4%%3%%1%:%2%%3%%5%");
{
std::string altPrefix;
std::string altSuffix;
if (bpA.state == SVBreakendState::RIGHT_OPEN)
{
altPrefix = ref + insertSeq;
}
else if (bpA.state == SVBreakendState::LEFT_OPEN)
{
altSuffix = insertSeq + ref;
}
else
{
assert(false && "Unexpected bpA.state");
}
char altSep('?');
if (bpB.state == SVBreakendState::RIGHT_OPEN)
{
altSep=']';
}
else if (bpB.state == SVBreakendState::LEFT_OPEN)
{
altSep='[';
}
else
{
assert(false && "Unexpected bpB.state");
}
altFormat % mateChrom % matePos % altSep % altPrefix % altSuffix;
}
// build INFO field
infotags.push_back("SVTYPE=BND");
infotags.push_back("MATEID="+mateId);
infotags.push_back( str(boost::format("BND_PAIR_COUNT=%i") % bpA.getLocalPairCount()) );
infotags.push_back( str(boost::format("PAIR_COUNT=%i") % bpA.getPairCount()) );
if (isImprecise)
{
infotags.push_back("IMPRECISE");
}
if (bpArange.size() > 1)
{
infotags.push_back( str( boost::format("CIPOS=%i,%i") % ((bpArange.begin_pos()+1) - pos) % (bpArange.end_pos() - pos) ));
}
if (! isImprecise)
{
if (bpArange.size() > 1)
{
infotags.push_back( str( boost::format("HOMLEN=%i") % (bpArange.size()-1) ));
std::string homref;
get_standardized_region_seq(_referenceFilename,chrom,bpArange.begin_pos()+1,bpArange.end_pos()-1,homref);
infotags.push_back( str( boost::format("HOMSEQ=%s") % (homref) ));
}
}
if (! insertSeq.empty())
{
infotags.push_back( str( boost::format("SVINSLEN=%i") % (insertSeq.size()) ));
infotags.push_back( str( boost::format("SVINSSEQ=%s") % (insertSeq) ));
}
addSharedInfo(event, infotags);
modifyInfo(event, infotags);
modifyTranslocInfo(isFirstBreakend, infotags);
modifySample(sv, sampletags);
#ifdef DEBUG_VCF
addDebugInfo(bpA, bpB, isFirstBreakend, adata, infotags);
#endif
// write out record:
_os << chrom
<< '\t' << pos
<< '\t' << localId // ID
<< '\t' << ref // REF
<< '\t' << str( altFormat ) // ALT
<< '\t';
writeQual();
_os << '\t';
writeFilter();
_os << '\t';
makeInfoField(infotags,_os); // INFO
makeFormatSampleField(sampletags, _os); // FORMAT + SAMPLE
_os << '\n';
}
