// See documentation in header file.
void searchMEIBreakpoints(MEI_data& currentState, std::vector<bam_info>& bam_sources, const Chromosome* chromosome,
UserDefinedSettings* userSettings) {
LOG_DEBUG(*logStream << time_log() << "Start searching for breakpoints..." << std::endl);
std::vector<std::vector<simple_read*> > clusters;
cluster_reads(currentState.discordant_reads, currentState.current_insert_size, clusters, userSettings);
// Find breakpoints per cluster.
int bp_count = 0;
for (size_t i = 0; i < clusters.size(); i++) {
// print cluster debug info
std::vector<simple_read*> cluster = clusters.at(i);
if (cluster.size() < ((size_t) userSettings->MIN_DD_CLUSTER_SIZE)) {
// Fluke cluster, skip it. (If there are very few reads in the cluster,
// we likely won't find enough split reads supporting an insertion)
continue;
}
// Find breakpoint for this cluster
char cluster_strand = cluster.at(0)->strand;
int cluster_tid = cluster.at(0)->tid;
std::vector<MEI_breakpoint> MEI_bps;
std::vector<MEI_breakpoint>::iterator MEI_iter;
get_breakpoints(cluster, bam_sources, currentState.current_insert_size, cluster_tid, cluster_strand, chromosome,
currentState.sample_names, MEI_bps, userSettings);
if (MEI_bps.size() > 1) {
// More than one breakpoints found for current cluster. Select only the one with the
// most split reads supporting it.
size_t best_support = 0;
MEI_breakpoint best_bp;
for (MEI_iter = MEI_bps.begin(); MEI_iter != MEI_bps.end(); ++MEI_iter) {
if (MEI_iter->associated_split_reads.size() > best_support) {
best_bp = *MEI_iter;
best_support = MEI_iter->associated_split_reads.size();
}
}
MEI_bps.clear();
MEI_bps.push_back(best_bp);
} else if (MEI_bps.size() == 0) {
// No breakpoint found with split read support. Estimate breakpoint from cluster reads.
get_breakpoint_estimation(cluster, currentState.current_insert_size, cluster_tid, cluster_strand, MEI_bps);
}
// Check breakpoint validity.
for (MEI_iter = MEI_bps.begin(); MEI_iter != MEI_bps.end(); ++MEI_iter) {
currentState.MEI_breakpoints.push_back(*MEI_iter);
bp_count += 1;
LOG_INFO(*logStream << "Found potential DD breakpoint: " << (*MEI_iter).breakpoint_tid << ", " <<
(*MEI_iter).breakpoint_pos << ", " << (*MEI_iter).cluster_strand << ", " <<
(*MEI_iter).associated_reads.size() << ", " <<
(*MEI_iter).associated_split_reads.size() << std::endl);
}
}
LOG_DEBUG(*logStream << time_log() << "Found " << bp_count << " breakpoints for " << clusters.size() <<
" clusters." << std::endl);
}
/* create a stream of breakpoint values from a breakpoint file
initialize stream counter and increment value */
BRKSTREAM* bps_newstream(FILE* fp, unsigned long srate, unsigned long* size)
{
BRKSTREAM* stream;
BREAKPOINT* points;
unsigned long npoints;
if (srate==0)
{
printf("Error creating stream - sample rate cannot be zero.\n");
return NULL;
}
stream = (BRKSTREAM*)malloc(sizeof(BRKSTREAM));
if (stream==NULL)
return NULL;
/* load breakpoint file and setup stream info */
points = get_breakpoints(fp,&npoints);
if (points == NULL)
{
free(stream);
return NULL;
}
if (npoints<2)
{
printf("breakpoint file is too small - "
"at least two points required\n");
free(stream);
return(NULL);
}
/* init the stream object */
stream->points = points;
stream->npoints = npoints;
/* counters */
stream->curpos = 0.0;
stream->ileft = 0;
stream->iright = 1;
stream->incr = 1.0/srate;
/* first span */
stream->leftpoint = stream->points[stream->ileft];
stream->rightpoint = stream->points[stream->iright];
stream->width = stream->rightpoint.time - stream->leftpoint.time;
stream->height = stream->rightpoint.value - stream->leftpoint.value;
stream->more_points = 1;
if (size)
*size = stream->npoints;
return stream;
}
