Files in vcfppR
Rapid Manipulation of the Variant Call Format (VCF)

configure

MD5

NEWS.md README.md

NAMESPACE

DESCRIPTION

LICENSE

cleanup.win

configure.win

cleanup

R/RcppExports.R R/vcf-compare.R R/vcf-summary.R R/vcf-info.R R/vcf-popgen.R R/vcf-plot.R R/common.R R/vcfppR-package.R R/zzz.R R/vcf-tables.R

src/RcppExports.cpp

src/vcf-reader.cpp

src/vcf-popgen.cpp

src/vcf-stats.cpp

src/Makevars.win.in

src/Makevars.in

src/vcf-table.cpp

src/vcf-writer.cpp

src/htslib-1.21/vcf_sweep.c

src/htslib-1.21/errmod.c

src/htslib-1.21/htslib-s3-plugin.7

src/htslib-1.21/regidx.c

src/htslib-1.21/version.sh

src/htslib-1.21/hts_internal.h

src/htslib-1.21/sam.5

src/htslib-1.21/configure

src/htslib-1.21/thread_pool.c

src/htslib-1.21/tbx.c

src/htslib-1.21/hts_time_funcs.h

src/htslib-1.21/hfile_libcurl.c

src/htslib-1.21/config.mk.in

src/htslib-1.21/builddir_vars.mk.in

src/htslib-1.21/config.sub

src/htslib-1.21/htsfile.c

src/htslib-1.21/simd.c

src/htslib-1.21/sam.c

src/htslib-1.21/hfile_s3_write.c

src/htslib-1.21/tabix.1

src/htslib-1.21/header.h

src/htslib-1.21/textutils.c

src/htslib-1.21/hfile.c

src/htslib-1.21/tabix.c

src/htslib-1.21/bcf_sr_sort.h

src/htslib-1.21/thread_pool_internal.h

src/htslib-1.21/sam_internal.h

src/htslib-1.21/kstring.c

src/htslib-1.21/bgzip.c

src/htslib-1.21/NEWS

src/htslib-1.21/region.c

src/htslib-1.21/config.guess

src/htslib-1.21/realn.c

src/htslib-1.21/vcfutils.c

src/htslib-1.21/faidx.5

src/htslib-1.21/hfile_gcs.c

src/htslib-1.21/faidx.c

src/htslib-1.21/md5.c

src/htslib-1.21/htslib.pc.tmp

src/htslib-1.21/multipart.c

src/htslib-1.21/config.mk

src/htslib-1.21/hts.c

src/htslib-1.21/probaln.c

src/htslib-1.21/annot-tsv.c

src/htslib-1.21/plugin.c

src/htslib-1.21/README.large_positions.md

src/htslib-1.21/htscodecs_external.mk

src/htslib-1.21/htslib.map

src/htslib-1.21/README

src/htslib-1.21/htslib_vars.mk

src/htslib-1.21/htscodecs.mk

src/htslib-1.21/configure.ac

src/htslib-1.21/bgzip.1

src/htslib-1.21/hfile_s3.c

src/htslib-1.21/bcf_sr_sort.c

src/htslib-1.21/config.status

src/htslib-1.21/sam_mods.c

src/htslib-1.21/LICENSE

src/htslib-1.21/htslib-uninstalled.pc

src/htslib-1.21/hts_probe_cc.sh

src/htslib-1.21/htslib.pc.in

src/htslib-1.21/kfunc.c

src/htslib-1.21/header.c

src/htslib-1.21/vcf.5

src/htslib-1.21/config.h.in

src/htslib-1.21/bgzf.c

src/htslib-1.21/htsfile.1

src/htslib-1.21/vcf.c

src/htslib-1.21/textutils_internal.h

src/htslib-1.21/fuzz_settings.h

src/htslib-1.21/hts_expr.c

src/htslib-1.21/synced_bcf_reader.c

src/htslib-1.21/hts_os.c

src/htslib-1.21/annot-tsv.1

src/htslib-1.21/htscodecs_bundled.mk

src/htslib-1.21/htslib_static.mk

src/htslib-1.21/htslib.mk

src/htslib-1.21/Makefile

src/htslib-1.21/hfile_internal.h

src/htslib-1.21/INSTALL

src/htslib-1.21/htscodecs/NEWS.md src/htslib-1.21/htscodecs/BENCHMARKS.md src/htslib-1.21/htscodecs/LICENSE.md src/htslib-1.21/htscodecs/MAINTAINERS.md

src/htslib-1.21/htscodecs/htscodecs/rle.c

src/htslib-1.21/htscodecs/htscodecs/varint2.h

src/htslib-1.21/htscodecs/htscodecs/rANS_static32x16pr_sse4.c

src/htslib-1.21/htscodecs/htscodecs/rle.h

src/htslib-1.21/htscodecs/htscodecs/permute.h

src/htslib-1.21/htscodecs/htscodecs/arith_dynamic.h

src/htslib-1.21/htscodecs/htscodecs/c_range_coder.h

src/htslib-1.21/htscodecs/htscodecs/pooled_alloc.h

src/htslib-1.21/htscodecs/htscodecs/c_simple_model.h

src/htslib-1.21/htscodecs/htscodecs/fqzcomp_qual.c

src/htslib-1.21/htscodecs/htscodecs/rANS_static.h

src/htslib-1.21/htscodecs/htscodecs/varint.h

src/htslib-1.21/htscodecs/htscodecs/rANS_word.h

src/htslib-1.21/htscodecs/htscodecs/pack.c

src/htslib-1.21/htscodecs/htscodecs/htscodecs.h

src/htslib-1.21/htscodecs/htscodecs/rANS_byte.h

src/htslib-1.21/htscodecs/htscodecs/htscodecs.c

src/htslib-1.21/htscodecs/htscodecs/rANS_static32x16pr_avx2.c

src/htslib-1.21/htscodecs/htscodecs/htscodecs_endian.h

src/htslib-1.21/htscodecs/htscodecs/arith_dynamic.c

src/htslib-1.21/htscodecs/htscodecs/fqzcomp_qual.h

src/htslib-1.21/htscodecs/htscodecs/rANS_static32x16pr.h

src/htslib-1.21/htscodecs/htscodecs/utils.h

src/htslib-1.21/htscodecs/htscodecs/rANS_static4x16.h

src/htslib-1.21/htscodecs/htscodecs/rANS_static.c

src/htslib-1.21/htscodecs/htscodecs/rANS_static32x16pr_avx512.c

src/htslib-1.21/htscodecs/htscodecs/utils.c

src/htslib-1.21/htscodecs/htscodecs/rANS_static4x16pr.c

src/htslib-1.21/htscodecs/htscodecs/pack.h

src/htslib-1.21/htscodecs/htscodecs/tokenise_name3.h

src/htslib-1.21/htscodecs/htscodecs/rANS_static32x16pr.c

src/htslib-1.21/htscodecs/htscodecs/version.h

src/htslib-1.21/htscodecs/htscodecs/rANS_static32x16pr_neon.c

src/htslib-1.21/htscodecs/htscodecs/rANS_static16_int.h

src/htslib-1.21/htscodecs/htscodecs/tokenise_name3.c

src/htslib-1.21/cram/mFILE.c

src/htslib-1.21/cram/cram_decode.h

src/htslib-1.21/cram/string_alloc.h

src/htslib-1.21/cram/cram_stats.c

src/htslib-1.21/cram/pooled_alloc.h

src/htslib-1.21/cram/cram_structs.h

src/htslib-1.21/cram/os.h

src/htslib-1.21/cram/cram_encode.h

src/htslib-1.21/cram/cram_io.h

src/htslib-1.21/cram/cram.h

src/htslib-1.21/cram/cram_stats.h

src/htslib-1.21/cram/cram_encode.c

src/htslib-1.21/cram/README

src/htslib-1.21/cram/cram_io.c

src/htslib-1.21/cram/cram_decode.c

src/htslib-1.21/cram/misc.h

src/htslib-1.21/cram/mFILE.h

src/htslib-1.21/cram/string_alloc.c

src/htslib-1.21/cram/cram_index.c

src/htslib-1.21/cram/cram_index.h

src/htslib-1.21/cram/cram_codecs.c

src/htslib-1.21/cram/cram_codecs.h

src/htslib-1.21/cram/cram_external.c

src/htslib-1.21/cram/pooled_alloc.c

src/htslib-1.21/cram/cram_samtools.h

src/htslib-1.21/cram/open_trace_file.c

src/htslib-1.21/cram/open_trace_file.h

src/htslib-1.21/os/lzma_stub.h

src/htslib-1.21/os/rand.c

src/htslib-1.21/m4/hts_hide_dynamic_syms.m4

src/htslib-1.21/m4/hts_check_compile_flags_needed.m4

src/htslib-1.21/m4/hts_prog_cc_warnings.m4

src/htslib-1.21/m4/pkg.m4

src/htslib-1.21/samples/index_fasta.c

src/htslib-1.21/samples/mod_bam.c

src/htslib-1.21/samples/read_fast_index.c

src/htslib-1.21/samples/read_fast.c

src/htslib-1.21/samples/flags_demo.c

src/htslib-1.21/samples/split2.c

src/htslib-1.21/samples/mpileup.c

src/htslib-1.21/samples/update_header.c

src/htslib-1.21/samples/rem_header.c

src/htslib-1.21/samples/add_header.c

src/htslib-1.21/samples/read_aux.c

src/htslib-1.21/samples/sample.ref.fq

src/htslib-1.21/samples/DEMO.md

src/htslib-1.21/samples/mod_aux_ba.c

src/htslib-1.21/samples/sample.bed

src/htslib-1.21/samples/sample.sam

src/htslib-1.21/samples/index_reg_read.c

src/htslib-1.21/samples/sample.ref.fa

src/htslib-1.21/samples/index_multireg_read.c

src/htslib-1.21/samples/qtask_unordered.c

src/htslib-1.21/samples/qtask_ordered.c

src/htslib-1.21/samples/dump_aux.c

src/htslib-1.21/samples/index_write.c

src/htslib-1.21/samples/split_thread1.c

src/htslib-1.21/samples/pileup_mod.c

src/htslib-1.21/samples/read_refname.c

src/htslib-1.21/samples/flags_htsopt_field.c

src/htslib-1.21/samples/split_thread2.c

src/htslib-1.21/samples/pileup.c

src/htslib-1.21/samples/read_bam.c

src/htslib-1.21/samples/split.c

src/htslib-1.21/samples/read_header.c

src/htslib-1.21/samples/write_fast.c

src/htslib-1.21/samples/cram.c

src/htslib-1.21/samples/modstate.c

src/htslib-1.21/samples/mod_aux.c

src/htslib-1.21/samples/Makefile

src/htslib-1.21/htslib/hfile.h

src/htslib-1.21/htslib/faidx.h

src/htslib-1.21/htslib/synced_bcf_reader.h

src/htslib-1.21/htslib/kstring.h

src/htslib-1.21/htslib/thread_pool.h

src/htslib-1.21/htslib/kfunc.h

src/htslib-1.21/htslib/hts_os.h

src/htslib-1.21/htslib/hts_expr.h

src/htslib-1.21/htslib/hts_defs.h

src/htslib-1.21/htslib/khash_str2int.h

src/htslib-1.21/htslib/cram.h

src/htslib-1.21/htslib/ksort.h

src/htslib-1.21/htslib/kroundup.h

src/htslib-1.21/htslib/hts_endian.h

src/htslib-1.21/htslib/knetfile.h

src/htslib-1.21/htslib/hts.h

src/htslib-1.21/htslib/bgzf.h

src/htslib-1.21/htslib/tbx.h

src/htslib-1.21/htslib/vcf.h

src/htslib-1.21/htslib/sam.h

src/htslib-1.21/htslib/khash.h

src/htslib-1.21/htslib/vcfutils.h

src/htslib-1.21/htslib/regidx.h

src/htslib-1.21/htslib/klist.h

src/htslib-1.21/htslib/hts_log.h

src/htslib-1.21/htslib/vcf_sweep.h

src/htslib-1.21/htslib/kseq.h

src/htslib-1.21/htslib/kbitset.h

inst/COPYRIGHTS

inst/CITATION

inst/include/vcfpp.h

inst/include/htslib/hfile.h

inst/include/htslib/faidx.h

inst/include/htslib/synced_bcf_reader.h

inst/include/htslib/kstring.h

inst/include/htslib/thread_pool.h

inst/include/htslib/kfunc.h

inst/include/htslib/hts_os.h

inst/include/htslib/hts_expr.h

inst/include/htslib/hts_defs.h

inst/include/htslib/khash_str2int.h

inst/include/htslib/cram.h

inst/include/htslib/ksort.h

inst/include/htslib/kroundup.h

inst/include/htslib/hts_endian.h

inst/include/htslib/knetfile.h

inst/include/htslib/hts.h

inst/include/htslib/bgzf.h

inst/include/htslib/tbx.h

inst/include/htslib/vcf.h

inst/include/htslib/sam.h

inst/include/htslib/khash.h

inst/include/htslib/vcfutils.h

inst/include/htslib/regidx.h

inst/include/htslib/klist.h

inst/include/htslib/hts_log.h

inst/include/htslib/vcf_sweep.h

inst/include/htslib/kseq.h

inst/include/htslib/kbitset.h

inst/doc/concordance-of-two-vcf-files.Rmd

inst/doc/concordance-of-two-vcf-files.html

inst/doc/concordance-of-two-vcf-files.R

inst/extdata/test.bcf

inst/extdata/sv.vcf.gz

inst/extdata/sv.vcf.gz.csi

inst/extdata/imputed.gt.vcf.gz

inst/extdata/raw.gt.vcf.gz

inst/extdata/test.bcf.csi

inst/extdata/obj_vcfcomp.rds

inst/extdata/raw.gt.vcf.gz.csi

build/vignette.rds

tests/testthat.R tests/testthat/test-popgen.R tests/testthat/test-vcf-writer.R tests/testthat/test-vcf-summary.R tests/testthat/test-vcf-info.R tests/testthat/test-vcf-table.R tests/testthat/test-modify-vcf.R tests/testthat/test-vcf-reader.R tests/testthat/test-vcf-comp.R vignettes/concordance-of-two-vcf-files.Rmd man/vcfreader.Rd man/vcfplot.Rd man/vcfwriter.Rd man/vcfppR-package.Rd man/vcfcomp.Rd man/vcfpopgen.Rd man/vcftable.Rd man/vcfsummary.Rd man/vcfinfo.Rd

man/figures/README-pse-1.png

man/figures/README-dp-1.png

man/figures/README-summary_sm-1.png

man/figures/README-r2-1.png

man/figures/README-summary_sv-1.png

vcfppR documentation built on Aug. 25, 2025, 5:11 p.m.

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Rapid Manipulation of the Variant Call Format (VCF)

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vcfppR
Rapid Manipulation of the Variant Call Format (VCF)

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Rapid Manipulation of the Variant Call Format (VCF)