unsigned
SVScorer::
getBreakendMaxMappedDepth(const SVBreakend& bp)
{
/// define a new interval -/+ 50 bases around the center pos
/// of the breakpoint
static const pos_t regionSize(50);
const pos_t centerPos(bp.interval.range.center_pos());
const known_pos_range2 searchRange(std::max((centerPos-regionSize),0), (centerPos+regionSize));
std::vector<unsigned> depth(searchRange.size(),0);
bool isNormalFound(false);
const unsigned bamCount(_bamStreams.size());
for (unsigned bamIndex(0); bamIndex < bamCount; ++bamIndex)
{
if (_isAlignmentTumor[bamIndex]) continue;
bam_streamer& bamStream(*_bamStreams[bamIndex]);
// set bam stream to new search interval:
bamStream.set_new_region(bp.interval.tid, searchRange.begin_pos(), searchRange.end_pos());
while (bamStream.next())
{
const bam_record& bamRead(*(bamStream.get_record_ptr()));
// turn filtration off down to mapped only to match depth estimate method:
//if (_readScanner.isReadFiltered(bamRead)) continue;
if (bamRead.is_unmapped()) continue;
if ((bamRead.pos()-1) >= searchRange.end_pos()) break;
addReadToDepthEst(bamRead,searchRange.begin_pos(),depth);
}
isNormalFound=true;
break;
}
assert(isNormalFound);
return *(std::max_element(depth.begin(),depth.end()));
}
void
SVScorer::
getBreakendMaxMappedDepthAndMQ0(
const bool isMaxDepth,
const double cutoffDepth,
const SVBreakend& bp,
unsigned& maxDepth,
float& MQ0Frac)
{
/// define a new interval -/+ 50 bases around the center pos
/// of the breakpoint
static const pos_t regionSize(50);
maxDepth=0;
MQ0Frac=0;
unsigned totalReads(0);
unsigned totalMQ0Reads(0);
const pos_t centerPos(bp.interval.range.center_pos());
const known_pos_range2 searchRange(std::max((centerPos-regionSize),0), (centerPos+regionSize));
if (searchRange.size() == 0) return;
std::vector<unsigned> depth(searchRange.size(),0);
bool isCutoff(false);
bool isNormalFound(false);
const unsigned bamCount(_bamStreams.size());
for (unsigned bamIndex(0); bamIndex < bamCount; ++bamIndex)
{
if (_isAlignmentTumor[bamIndex]) continue;
isNormalFound=true;
bam_streamer& bamStream(*_bamStreams[bamIndex]);
// set bam stream to new search interval:
bamStream.set_new_region(bp.interval.tid, searchRange.begin_pos(), searchRange.end_pos());
while (bamStream.next())
{
const bam_record& bamRead(*(bamStream.get_record_ptr()));
// turn filtration down to mapped only to match depth estimate method:
if (bamRead.is_unmapped()) continue;
const pos_t refPos(bamRead.pos()-1);
if (refPos >= searchRange.end_pos()) break;
addReadToDepthEst(bamRead,searchRange.begin_pos(),depth);
totalReads++;
if (0 == bamRead.map_qual()) totalMQ0Reads++;
if (isMaxDepth)
{
const pos_t depthOffset(refPos-searchRange.begin_pos());
if (depthOffset>=0)
{
if (depth[depthOffset] > cutoffDepth)
{
isCutoff=true;
break;
}
}
}
}
if (isCutoff) break;
}
assert(isNormalFound);
maxDepth = *(std::max_element(depth.begin(),depth.end()));
if (totalReads>=10)
{
MQ0Frac = static_cast<float>(totalMQ0Reads)/static_cast<float>(totalReads);
}
}