Example #1
0
static
void
addDebugInfo(
    const bool isFirstOfPair,
    const SVCandidate& sv,
    const SVCandidateAssemblyData& assemblyData,
    VcfWriterSV::InfoTag_t& infotags)
{
    if (!assemblyData.isSpanning) return;

    const bool isFirst = (assemblyData.bporient.isBp1First == isFirstOfPair);
    const bool isRightOpen = (isFirstOfPair ? sv.bp1.state : sv.bp2.state) == SVBreakendState::RIGHT_OPEN;
    infotags.push_back(str(boost::format("FOOBAR_FW=%1%") % (isFirst == isRightOpen)));

    if (!isFirst) return; // only the first breakpoint gets the alignments attached to its VCF entry

    infotags.push_back(str(boost::format("FOOBAR_bp1=%i;bp2=%i") % sv.bp1.interval.tid % sv.bp2.interval.tid));

    // there can be several contigs per breakend, so we iterate over all of them.
    const unsigned numContigs(assemblyData.contigs.size());
    infotags.push_back(str(boost::format("FOOBAR_NCONTIGS=%i") % numContigs));
    if (numContigs > 0)
    {
        if (numContigs != assemblyData.spanningAlignments.size())
            infotags.push_back(str(boost::format("FOOBAR_ERROR=%i;%i") % numContigs % assemblyData.spanningAlignments.size()));
        if (numContigs <= assemblyData.bestAlignmentIndex)
            infotags.push_back(str(boost::format("FOOBAR_ERROR2=%i;%i") % numContigs % assemblyData.bestAlignmentIndex));

        infotags.push_back(str(boost::format("FOOBAR_BEST=%i") % assemblyData.bestAlignmentIndex));
        //infotags.push_back(str(boost::format("FOOBAR_EXTCONTIG=%s") % assemblyData.extendedContigs[assemblyData.bestAlignmentIndex]));
        infotags.push_back(str(boost::format("FOOBAR_CONTIGcount=%i") % assemblyData.contigs[assemblyData.bestAlignmentIndex].supportReads.size()));
    }
}
Example #2
0
static
void
addSharedInfo(
    const EventInfo& event,
    VcfWriterSV::InfoTag_t& infoTags)
{
    if (event.isEvent())
    {
        infoTags.push_back( str(boost::format("EVENT=%i") % event.label));
    }
}