├── .Rbuildignore ├── .gitignore ├── .gitmodules ├── .travis.yml ├── DESCRIPTION ├── LICENSE ├── Makefile ├── NAMESPACE ├── NEWS.md ├── R └── rbcf.R ├── README.md ├── TODO.md ├── doc └── rbcf_examples.pdf ├── man ├── bcf.chromosomes.Rd ├── bcf.close.Rd ├── bcf.contigs.Rd ├── bcf.dictionary.Rd ├── bcf.filters.Rd ├── bcf.formats.Rd ├── bcf.infos.Rd ├── bcf.new.writer.Rd ├── bcf.next.Rd ├── bcf.nsamples.Rd ├── bcf.open.Rd ├── bcf.query.Rd ├── bcf.sample.at.Rd ├── bcf.sample2index.Rd ├── bcf.samples.Rd ├── bcf.write.variant.Rd ├── bcf_open.Rd ├── genotype.ad.Rd ├── genotype.alleles.idx0.Rd ├── genotype.dp.Rd ├── genotype.filtered.Rd ├── genotype.float.attribute.Rd ├── genotype.gq.Rd ├── genotype.has.ad.Rd ├── genotype.has.dp.Rd ├── genotype.has.gq.Rd ├── genotype.has.pl.Rd ├── genotype.het.Rd ├── genotype.hetnonref.Rd ├── genotype.homref.Rd ├── genotype.homvar.Rd ├── genotype.int.attribute.Rd ├── genotype.nocall.Rd ├── genotype.phased.Rd ├── genotype.pl.Rd ├── genotype.ploidy.Rd ├── genotype.sample.Rd ├── genotype.string.attribute.Rd ├── htslib.version.Rd ├── rcbf.version.Rd ├── variant.alleles.Rd ├── variant.alt.alleles.Rd ├── variant.chrom.Rd ├── variant.contig.Rd ├── variant.end.Rd ├── variant.filters.Rd ├── variant.flag.attribute.Rd ├── variant.float.attribute.Rd ├── variant.format.ids.Rd ├── variant.genotype.Rd ├── variant.genotypes.Rd ├── variant.has.attribute.Rd ├── variant.has.filter.Rd ├── variant.has.id.Rd ├── variant.has.qual.Rd ├── variant.id.Rd ├── variant.info.ids.Rd ├── variant.int.attribute.Rd ├── variant.is.filtered.Rd ├── variant.is.snp.Rd ├── variant.max.ploidy.Rd ├── variant.nalleles.Rd ├── variant.nsamples.Rd ├── variant.pos.Rd ├── variant.qual.Rd ├── variant.reference.Rd ├── variant.snpeff.Rd ├── variant.start.Rd ├── variant.stop.Rd ├── variant.string.attribute.Rd ├── variant.tid.Rd ├── variant.types.Rd └── variant.vep.Rd ├── src ├── Makevars ├── rbcf.c └── rbcf_version.h └── tests ├── 0009.htslib.R ├── 0010.open.R ├── 0020.infos.R ├── 0030.formats.R ├── 0040.filters.R ├── 0050.samples.R ├── 0060.dict.R ├── 0070.contigs.R ├── 0080.scan.R ├── 0090.filter.R ├── 0100.vep.R ├── 0110.snpeff.R ├── 0120.query.R ├── 0130.vcattributes.R ├── 0140.genotypes.R ├── 0145.genotypes_vectorized.R ├── 0150.writer.R ├── data ├── 1000G.ALL.2of4intersection.20100804.genotypes.bcf ├── 1000G.ALL.2of4intersection.20100804.genotypes.bcf.csi ├── gnomad.exomes.r2.0.1.sites.bcf ├── gnomad.exomes.r2.0.1.sites.bcf.csi ├── rotavirus_rf.01.vcf ├── rotavirus_rf.02.vcf.gz ├── rotavirus_rf.02.vcf.gz.tbi ├── rotavirus_rf.03.vcf.gz ├── rotavirus_rf.03.vcf.gz.csi ├── rotavirus_rf.04.bcf ├── rotavirus_rf.04.bcf.csi ├── rotavirus_rf.ann.vcf.gz └── rotavirus_rf.ann.vcf.gz.csi └── generate.sh /.Rbuildignore: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/lindenb/rbcf/HEAD/.Rbuildignore -------------------------------------------------------------------------------- /.gitignore: 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