void VcfAnnotateHomopolymersCommand::exec() {
auto bedStream = _streams.openForReading(homopolymerBedFile_);
auto vcfStream = _streams.openForReading(vcfFile_);
// parse 1 additional field (past chr, start stop) in bed files.
auto bedReader = TypedStreamFactory<BedParser>{1}(bedStream);
auto vcfReader = openStream<Vcf::Entry>(vcfStream);
std::ostream* outStream = _streams.get<std::ostream>(outputFile_);
std::stringstream description;
description << "short (maximum of " << maxLength_ << "bp) homopolymer indel";
Vcf::CustomType infoType(infoFieldName_, Vcf::CustomType::PER_ALLELE, 0,
Vcf::CustomType::INTEGER, description.str());
Vcf::Header newHeader = vcfReader->header();
newHeader.addInfoType(infoType);
*outStream << newHeader;
DefaultPrinter out(*outStream);
auto annotator = makeHomopolymerAnnotator(out, maxLength_,
newHeader.infoType(infoFieldName_));
bool adjacentInsertions = true;
auto intersector = makeFullIntersector(*bedReader, *vcfReader, annotator, adjacentInsertions);
intersector.execute();
}
docstring InsetInfo::toolTip(BufferView const &, int, int) const
{
return bformat(_("Information regarding %1$s '%2$s'"),
_(infoType()), from_utf8(name_));
}
void InsetInfo::write(ostream & os) const
{
os << "Info\ntype \"" << infoType()
<< "\"\narg " << Lexer::quoteString(name_);
}
docstring InsetInfo::name() const
{
return from_ascii("Info:" + infoType());
}
