static
void
runESL(const ESLOptions& opt)
{
TimeTracker timer;
timer.resume();
{
// early test that we have permission to write to output file
OutStream outs(opt.outputFilename);
}
typedef std::shared_ptr<bam_streamer> stream_ptr;
std::vector<stream_ptr> bamStreams;
// setup all data for main alignment loop:
for (const std::string& afile : opt.alignFileOpt.alignmentFilename)
{
stream_ptr tmp(new bam_streamer(afile.c_str(),
(opt.region.empty()
? NULL
: opt.region.c_str())));
bamStreams.push_back(tmp);
}
const unsigned bamCount(bamStreams.size());
assert(0 != bamCount);
// check bam header compatibility:
if (bamCount > 1)
{
/// TODO: provide a better error exception for failed bam header check:
const bam_header_t* compareHeader(bamStreams[0]->get_header());
for (unsigned bamIndex(1); bamIndex<bamCount; ++bamIndex)
{
const bam_header_t* indexHeader(bamStreams[bamIndex]->get_header());
if (! check_header_compatibility(compareHeader,indexHeader))
{
log_os << "ERROR: incompatible bam headers between files:\n"
<< "\t" << opt.alignFileOpt.alignmentFilename[0] << "\n"
<< "\t" << opt.alignFileOpt.alignmentFilename[bamIndex] << "\n";
exit(EXIT_FAILURE);
}
}
}
// assume headers compatible after this point....
const bam_header_t& header(*(bamStreams[0]->get_header()));
const bam_header_info bamHeader(header);
int32_t tid(0), beginPos(0), endPos(0);
parse_bam_region(bamHeader,opt.region,tid,beginPos,endPos);
const GenomeInterval scanRegion(tid,beginPos,endPos);
#ifdef DEBUG_ESL
static const std::string log_tag("EstimateSVLoci");
log_os << log_tag << " scanRegion= " << scanRegion << "\n";
#endif
// grab the reference for segment we're estimating plus a buffer around the segment edges:
static const unsigned refEdgeBufferSize(500);
reference_contig_segment refSegment;
getIntervalReferenceSegment(opt.referenceFilename, bamHeader, refEdgeBufferSize, scanRegion, refSegment);
SVLocusSetFinder locusFinder(opt, scanRegion, bamHeader, refSegment);
input_stream_data sdata;
for (unsigned bamIndex(0); bamIndex<bamCount; ++bamIndex)
{
sdata.register_reads(*bamStreams[bamIndex],bamIndex);
}
// loop through alignments:
input_stream_handler sinput(sdata);
while (sinput.next())
{
const input_record_info current(sinput.get_current());
if (current.itype != INPUT_TYPE::READ)
{
log_os << "ERROR: invalid input condition.\n";
exit(EXIT_FAILURE);
}
const bam_streamer& readStream(*bamStreams[current.sample_no]);
const bam_record& read(*(readStream.get_record_ptr()));
locusFinder.update(read, current.sample_no);
}
// finished updating:
locusFinder.flush();
timer.stop();
const CpuTimes totalTimes(timer.getTimes());
#ifdef DEBUG_ESL
log_os << log_tag << " found " << locusFinder.getLocusSet().size() << " loci. \n";
log_os << log_tag << " totalTime: ";
totalTimes.reportHr(log_os);
log_os << "\n";
#endif
locusFinder.setBuildTime(totalTimes);
locusFinder.getLocusSet().save(opt.outputFilename.c_str());
}
static
void
runESL(const ESLOptions& opt)
{
{
// early test that we have permission to write to output file
OutStream outs(opt.outputFilename);
}
typedef boost::shared_ptr<bam_streamer> stream_ptr;
std::vector<stream_ptr> bam_streams;
// setup all data for main alignment loop:
BOOST_FOREACH(const std::string& afile, opt.alignmentFilename)
{
stream_ptr tmp(new bam_streamer(afile.c_str(),opt.region.c_str()));
bam_streams.push_back(tmp);
}
// TODO check header compatibility between all open bam streams
const unsigned n_inputs(bam_streams.size());
// assume headers compatible after this point....
assert(0 != n_inputs);
const bam_header_t& header(*(bam_streams[0]->get_header()));
const bam_header_info bamHeader(header);
int32_t tid(0), beginPos(0), endPos(0);
parse_bam_region(bamHeader,opt.region,tid,beginPos,endPos);
const GenomeInterval scanRegion(tid,beginPos,endPos);
SVLocusSetFinder locusFinder(opt,scanRegion);
locusFinder.setBamHeader(header);
input_stream_data sdata;
for (unsigned i(0); i<n_inputs; ++i)
{
sdata.register_reads(*bam_streams[i],i);
}
// loop through alignments:
input_stream_handler sinput(sdata);
while (sinput.next())
{
const input_record_info current(sinput.get_current());
if (current.itype != INPUT_TYPE::READ)
{
log_os << "ERROR: invalid input condition.\n";
exit(EXIT_FAILURE);
}
const bam_streamer& read_stream(*bam_streams[current.sample_no]);
const bam_record& read(*(read_stream.get_record_ptr()));
locusFinder.update(read,current.sample_no);
}
// finished updating:
locusFinder.flush();
locusFinder.getLocusSet().save(opt.outputFilename.c_str());
}
