bool VcfMaterializer::_materializeNext(seqan::Dna5String & seq,
MethylationLevels * levels,
std::vector<SmallVarInfo> & varInfos,
std::vector<std::pair<int, int> > & breakpoints,
int & rID,
int & haplotype)
{
if (levels)
SEQAN_CHECK(!empty(methFastaFileName), "Must initialize with methylation FASTA file for levels");
if (empty(vcfFileName))
{
if (currRID >= (int)(numSeqs(faiIndex) - 1))
return false;
currRID += 1;
rID = currRID;
readSequence(seq, faiIndex, currRID);
if (levels && !empty(methFastaFileName))
{
_loadLevels(currRID);
swap(*levels, currentLevels);
}
// Build identity PositionMap.
TJournalEntries journal;
reinit(journal, length(seq));
posMap.reinit(journal);
GenomicInterval gi(0, length(seq), 0, length(seq));
seqan::String<PositionMap::TInterval> intervals;
appendValue(intervals, PositionMap::TInterval(gi.svBeginPos, gi.svEndPos, gi));
createIntervalTree(posMap.svIntervalTree, intervals);
createIntervalTree(posMap.svIntervalTreeSTL, intervals);
return true;
}
// Number of sequences.
int numSeqs = length(contigNames(context(vcfFileIn)));
// Stop if there are no more haplotypes to materialize.
if (currRID >= (numSeqs - 1) && nextHaplotype == numHaplotypes)
return false;
// Load variants for next contig if necessary.
if (currRID == -1 || nextHaplotype == numHaplotypes)
{
currRID += 1;
nextHaplotype = 0;
_loadVariantsForContig(contigVariants, currRID);
readSequence(contigSeq, faiIndex, currRID);
if (levels && !empty(methFastaFileName))
_loadLevels(currRID);
}
// Materialize variants for the current haplotype.
VariantMaterializer varMat(rng, contigVariants, *methOptions);
if (levels)
varMat.run(seq, posMap, *levels, varInfos, breakpoints, contigSeq, currentLevels, nextHaplotype);
else
varMat.run(seq, posMap, varInfos, breakpoints, contigSeq, nextHaplotype);
// Write out rID and haploty
rID = currRID;
haplotype = nextHaplotype++;
return true;
}
int main(int argc, char const * argv[])
{
// Additional checks
seqan::ArgumentParser parser = buildParser();
seqan::ArgumentParser::ParseResult res = seqan::parse(parser, argc, argv);
// Check if input was successfully parsed.
if (res != seqan::ArgumentParser::PARSE_OK)
return res == seqan::ArgumentParser::PARSE_ERROR;
// Check if one or two input files (single or paired-end) were given.
int fileCount = getArgumentValueCount(parser, 0);
if (fileCount < 1) {
printShortHelp(parser);
return 1;
}
unsigned int radius = 1;
getOptionValue(radius, parser, "r");
seqan::CharString readsFileName;
getOptionValue(readsFileName, parser, "i");
// Open input file, BamFileIn can read SAM and BAM files.
seqan::BamFileIn bamFileIn(seqan::toCString(readsFileName));
seqan::CharString _filterChromosomes;
seqan::getOptionValue(_filterChromosomes, parser, "fc");
std::string filterChromosomes = seqan::toCString(_filterChromosomes);
OccurenceMap occurenceMap;
Statistics stats;
std::cout << "read bam file... ";
auto t1 = std::chrono::steady_clock::now();
seqan::BamAlignmentRecord record;
seqan::BamHeader header;
readHeader(header, bamFileIn);
const auto chromosomeFilterSet = calculateChromosomeFilter(filterChromosomes, contigNames(context(bamFileIn)));
const auto chromosomes = contigNames(context(bamFileIn));
processBamFile(bamFileIn, chromosomeFilterSet, occurenceMap, stats);
auto t2 = std::chrono::steady_clock::now();
std::cout << std::chrono::duration_cast<std::chrono::duration<float>>(t2 - t1).count() << "s" << std::endl;
std::vector<std::pair<unsigned int, unsigned int>> hits(radius * 2 + 1);
t1 = std::chrono::steady_clock::now();
std::cout << "calculating 5'-ends around peaks... ";
for (unsigned int fileIndex = 0;fileIndex < static_cast<unsigned int>(fileCount); ++fileIndex)
{
seqan::CharString fileName_;
getArgumentValue(fileName_, parser, fileIndex, 0);
const std::string fileName = seqan::toCString(fileName_);
std::ifstream infile(fileName);
std::string chromosome, dummy;
unsigned int start, end;
while (infile >> chromosome >> start >> end >> dummy)
{
int rID = -1;
for (unsigned int i = 0;i < length(chromosomes);++i)
if (chromosomes[i] == chromosome)
{
rID = i;
break;
}
if (rID == -1)
{
std::cout << "invalid chromosome name: " << chromosome << " in file " << fileName << std::endl;
return -1;
}
seqan::BamAlignmentRecord record;
record.beginPos = std::max<int>(start - radius, 0);
record.rID = rID;
record.flag = 0;
unsigned int index = 0;
if (start < radius)
index += radius - start;
while (record.beginPos <= static_cast<__int32>(start + radius))
{
BamRecordKey<NoBarcode> pos(record);
auto el = occurenceMap.find(pos);
if(el != occurenceMap.end())
hits[index].first += el->second;
pos.init(pos.getRID(), pos.get5EndPosition(), true);
el = occurenceMap.find(pos);
if (el != occurenceMap.end())
hits[index].second += el->second;
++record.beginPos;
++index;
}
}
std::string outFilename = getFilePrefix(fileName) + std::string("_5PrimeEnds.tab");
if (seqan::isSet(parser, "o"))
{
seqan::CharString outFileName_;
getOptionValue(outFileName_, parser, "o");
outFilename = seqan::toCString(outFileName_);
}
std::fstream fs;
std::cout << "writing " << outFilename << std::endl;
#ifdef _MSC_VER
fs.open(outFilename, std::fstream::out, _SH_DENYNO);
#else
fs.open(outFilename, std::fstream::out);
#endif
int i = - static_cast<int>(radius);
for (const auto& hit : hits)
fs << i++ << "\t" << hit.first << "\t" << hit.second << std::endl;
fs.close();
}
t2 = std::chrono::steady_clock::now();
std::cout << std::chrono::duration_cast<std::chrono::duration<float>>(t2 - t1).count() << "s" << std::endl;
return 0;
}
