Files in Rhtslib

HTSlib high-throughput sequencing library as an R package

README.md

NEWS

NAMESPACE

DESCRIPTION

build/vignette.rds

src/R_init_Rhtslib.c

src/Makevars.common

src/Makevars.win

src/Makevars

src/htslib-1.7/vcf.5

src/htslib-1.7/htslib_vars.mk

src/htslib-1.7/vcfutils.c

src/htslib-1.7/hts_os.c

src/htslib-1.7/configure.ac

src/htslib-1.7/hfile_net.c

src/htslib-1.7/textutils_internal.h

src/htslib-1.7/bcf_sr_sort.c

src/htslib-1.7/hfile.c

src/htslib-1.7/realn.c

src/htslib-1.7/bcf_sr_sort.h

src/htslib-1.7/hfile_internal.h

src/htslib-1.7/tabix.1

src/htslib-1.7/synced_bcf_reader.c

src/htslib-1.7/bgzf.c

src/htslib-1.7/hfile_s3.c

src/htslib-1.7/faidx.c

src/htslib-1.7/tbx.c

src/htslib-1.7/htslib.pc.in

src/htslib-1.7/vcf_sweep.c

src/htslib-1.7/version.sh

src/htslib-1.7/hts_internal.h

src/htslib-1.7/textutils.c

src/htslib-1.7/thread_pool.c

src/htslib-1.7/plugin.c

src/htslib-1.7/errmod.c

src/htslib-1.7/hts.c

src/htslib-1.7/tabix.c

src/htslib-1.7/multipart.c

src/htslib-1.7/probaln.c

src/htslib-1.7/htslib.mk

src/htslib-1.7/hfile_libcurl.c

src/htslib-1.7/configure

src/htslib-1.7/md5.c

src/htslib-1.7/hfile_gcs.c

src/htslib-1.7/vcf.c

src/htslib-1.7/NEWS

src/htslib-1.7/thread_pool_internal.h

src/htslib-1.7/config.h.in

src/htslib-1.7/sam.c

src/htslib-1.7/Makefile

src/htslib-1.7/INSTALL

src/htslib-1.7/.appveyor.yml

src/htslib-1.7/Makefile.Rhtslib.win

src/htslib-1.7/config.h

src/htslib-1.7/Makefile.Rhtslib

src/htslib-1.7/README

src/htslib-1.7/config.mk.in

src/htslib-1.7/sam.5

src/htslib-1.7/bgzip.c

src/htslib-1.7/kfunc.c

src/htslib-1.7/faidx.5

src/htslib-1.7/regidx.c

src/htslib-1.7/htsfile.c

src/htslib-1.7/htsfile.1

src/htslib-1.7/knetfile.c

src/htslib-1.7/kstring.c

src/htslib-1.7/LICENSE

src/htslib-1.7/htslib/vcf_sweep.h

src/htslib-1.7/htslib/hfile.h

src/htslib-1.7/htslib/kseq.h

src/htslib-1.7/htslib/kfunc.h

src/htslib-1.7/htslib/faidx.h

src/htslib-1.7/htslib/synced_bcf_reader.h

src/htslib-1.7/htslib/thread_pool.h

src/htslib-1.7/htslib/hts_log.h

src/htslib-1.7/htslib/sam.h

src/htslib-1.7/htslib/klist.h

src/htslib-1.7/htslib/hts_defs.h

src/htslib-1.7/htslib/regidx.h

src/htslib-1.7/htslib/bgzf.h

src/htslib-1.7/htslib/ksort.h

src/htslib-1.7/htslib/vcf.h

src/htslib-1.7/htslib/cram.h

src/htslib-1.7/htslib/khash.h

src/htslib-1.7/htslib/kstring.h

src/htslib-1.7/htslib/hts_os.h

src/htslib-1.7/htslib/khash_str2int.h

src/htslib-1.7/htslib/hts.h

src/htslib-1.7/htslib/kbitset.h

src/htslib-1.7/htslib/tbx.h

src/htslib-1.7/htslib/vcfutils.h

src/htslib-1.7/htslib/knetfile.h

src/htslib-1.7/htslib/hts_endian.h

src/htslib-1.7/cram/pooled_alloc.c

src/htslib-1.7/cram/files.c

src/htslib-1.7/cram/mFILE.h

src/htslib-1.7/cram/cram_decode.c

src/htslib-1.7/cram/rANS_static.h

src/htslib-1.7/cram/cram_samtools.h

src/htslib-1.7/cram/cram_samtools.c

src/htslib-1.7/cram/string_alloc.h

src/htslib-1.7/cram/cram_decode.h

src/htslib-1.7/cram/sam_header.h

src/htslib-1.7/cram/cram_codecs.h

src/htslib-1.7/cram/cram_stats.c

src/htslib-1.7/cram/mFILE.c

src/htslib-1.7/cram/cram_encode.c

src/htslib-1.7/cram/open_trace_file.c

src/htslib-1.7/cram/rANS_static.c

src/htslib-1.7/cram/pooled_alloc.h

src/htslib-1.7/cram/cram.h

src/htslib-1.7/cram/cram_io.c

src/htslib-1.7/cram/cram_index.h

src/htslib-1.7/cram/rANS_byte.h

src/htslib-1.7/cram/sam_header.c

src/htslib-1.7/cram/os.h

src/htslib-1.7/cram/open_trace_file.h

src/htslib-1.7/cram/cram_encode.h

src/htslib-1.7/cram/cram_structs.h

src/htslib-1.7/cram/cram_stats.h

src/htslib-1.7/cram/misc.h

src/htslib-1.7/cram/cram_codecs.c

src/htslib-1.7/cram/cram_index.c

src/htslib-1.7/cram/cram_io.h

src/htslib-1.7/cram/string_alloc.c

src/htslib-1.7/cram/cram_external.c

src/htslib-1.7/test/c1#pad2.sam

src/htslib-1.7/test/compare_sam.pl

src/htslib-1.7/test/faidx.fa

src/htslib-1.7/test/xx.fa.fai

src/htslib-1.7/test/ce#unmap2.sam

src/htslib-1.7/test/auxf.fa

src/htslib-1.7/test/xx#large_aux2.sam

src/htslib-1.7/test/test-regidx.c

src/htslib-1.7/test/test_bgzf.c

src/htslib-1.7/test/test-vcf-sweep.out

src/htslib-1.7/test/ce#5b.sam

src/htslib-1.7/test/test-bcf-sr.pl

src/htslib-1.7/test/ce#5b_java.cram

src/htslib-1.7/test/xx#tlen.sam

src/htslib-1.7/test/ce.fa.fai

src/htslib-1.7/test/thrash_threads3.c

src/htslib-1.7/test/ce#1.sam

src/htslib-1.7/test/test-vcf-hdr-in.vcf

src/htslib-1.7/test/noroundtrip.vcf

src/htslib-1.7/test/c1.fa.fai

src/htslib-1.7/test/hfile.c

src/htslib-1.7/test/c1#pad3.sam

src/htslib-1.7/test/test-bcf-translate.c

src/htslib-1.7/test/auxf#values.sam

src/htslib-1.7/test/test-bcf-sr.c

src/htslib-1.7/test/c1#pad1.sam

src/htslib-1.7/test/thrash_threads4.c

src/htslib-1.7/test/fieldarith.sam

src/htslib-1.7/test/test-bcf-translate.out

src/htslib-1.7/test/c1#clip.sam

src/htslib-1.7/test/formatcols.vcf

src/htslib-1.7/test/bgziptest.txt.gz.gzi

src/htslib-1.7/test/formatmissing-out.vcf

src/htslib-1.7/test/thrash_threads6.c

src/htslib-1.7/test/test-vcf-api.c

src/htslib-1.7/test/cross_validate.sh

src/htslib-1.7/test/ce#tag_depadded.sam

src/htslib-1.7/test/c2.fa.fai

src/htslib-1.7/test/xx#rg.sam

src/htslib-1.7/test/thrash_threads2.c

src/htslib-1.7/test/test-logging.pl

src/htslib-1.7/test/bgziptest.txt

src/htslib-1.7/test/noroundtrip-out.vcf

src/htslib-1.7/test/c1#bounds.sam

src/htslib-1.7/test/ce.fa

src/htslib-1.7/test/xx#large_aux_java.cram

src/htslib-1.7/test/xx#blank.sam

src/htslib-1.7/test/xx#minimal.sam

src/htslib-1.7/test/auxf#values_java.cram

src/htslib-1.7/test/ce#large_seq.sam

src/htslib-1.7/test/ce#2.sam

src/htslib-1.7/test/thread_pool.md

src/htslib-1.7/test/auxf.fa.fai

src/htslib-1.7/test/xx#pair.sam

src/htslib-1.7/test/md#1.sam

src/htslib-1.7/test/test-vcf-hdr.out

src/htslib-1.7/test/ce#unmap1.sam

src/htslib-1.7/test/test.pl

src/htslib-1.7/test/sam.c

src/htslib-1.7/test/c1#noseq.sam

src/htslib-1.7/test/ce#5.sam

src/htslib-1.7/test/c1.fa

src/htslib-1.7/test/thrash_threads1.c

src/htslib-1.7/test/thrash_threads5.c

src/htslib-1.7/test/xx.fa

src/htslib-1.7/test/xx#triplet.sam

src/htslib-1.7/test/c2#pad.sam

src/htslib-1.7/test/test_view.c

src/htslib-1.7/test/xx#large_aux.sam

src/htslib-1.7/test/xx#unsorted.sam

src/htslib-1.7/test/formatmissing.vcf

src/htslib-1.7/test/test-vcf-sweep.c

src/htslib-1.7/test/ce#unmap.sam

src/htslib-1.7/test/ce#supp.sam

src/htslib-1.7/test/fieldarith.c

src/htslib-1.7/test/test-vcf-api.out

src/htslib-1.7/test/md.fa.fai

src/htslib-1.7/test/xx#repeated.sam

src/htslib-1.7/test/ce#tag_padded.sam

src/htslib-1.7/test/md.fa

src/htslib-1.7/test/c1#unknown.sam

src/htslib-1.7/test/bgziptest.txt.gz

src/htslib-1.7/test/xx#tlen2.sam

src/htslib-1.7/test/c2.fa

src/htslib-1.7/test/hts_endian.c

src/htslib-1.7/test/tabix/tabix.tst

src/htslib-1.7/test/tabix/vcf_file.2.3199812.out

src/htslib-1.7/test/tabix/bed_file.bed

src/htslib-1.7/test/tabix/vcf_file.vcf

src/htslib-1.7/test/tabix/large_chr.vcf

src/htslib-1.7/test/tabix/large_chr.20.1.2147483647.out

src/htslib-1.7/test/tabix/gff_file.gff

src/htslib-1.7/test/tabix/bed_file.Y.100200.out

src/htslib-1.7/test/tabix/gff_file.X.2934832.2935190.out

src/htslib-1.7/test/tabix/vcf_file.1.3000151.out

src/htslib-1.7/test/tabix/test-tabix.sh

src/htslib-1.7/os/lzma_stub.h

src/htslib-1.7/os/rand.c

src/htslib-1.7/m4/hts_prog_cc_warnings.m4

R/zzz.R vignettes/Rhtslib.Rmd man/Rhtslib-package.Rd man/pkgconfig.Rd inst/doc/Rhtslib.Rmd inst/doc/Rhtslib.R

inst/doc/Rhtslib.html

inst/include/bam.c

inst/include/samtools.h

inst/include/version.h

inst/include/bam_cat.c

inst/include/bam_plbuf.h

inst/include/bam_sort.c

inst/include/sam_header.h

inst/include/sam.h

inst/include/sam_opts.c

inst/include/sam_opts.h

inst/include/bam_plbuf.c

inst/include/sam.c

inst/include/bam.h

inst/include/bam_endian.h

inst/include/README

inst/include/bam_aux.c

inst/include/sam_utils.c

Rhtslib documentation built on Nov. 8, 2020, 4:55 p.m.