Rhtslib: HTSlib high-throughput sequencing library as an R package

This package provides version 1.1 of the 'HTSlib' C library for high-throughput sequence analysis. The package is primarily useful to developers of other R packages who wish to make use of HTSlib. Motivation and instructions for use of this package are in the vignette, vignette(package="Rhtslib", "Rhtslib").

Author
Nathaniel Hayden [aut], Martin Morgan [aut], Bioconductor Package Maintainer [cre]
Date of publication
None
Maintainer
Bioconductor Package Maintainer <maintainer@bioconductor.org>
License
LGPL (>= 2)
Version
1.6.0
URLs

View on Bioconductor

Man pages

pkgconfig
Compiler configuration arguments for use of Rhtslib
Rhtslib-package
An R packaged HTSlib 1.1

Files in this package

Rhtslib/DESCRIPTION
Rhtslib/NAMESPACE
Rhtslib/R
Rhtslib/R/zzz.R
Rhtslib/README.md
Rhtslib/Rhtslib_build_guide.org
Rhtslib/build
Rhtslib/build/vignette.rds
Rhtslib/build_htslib_on_493_toolchain.md
Rhtslib/cleanup
Rhtslib/configure
Rhtslib/inst
Rhtslib/inst/doc
Rhtslib/inst/doc/Rhtslib.R
Rhtslib/inst/doc/Rhtslib.Rmd
Rhtslib/inst/doc/Rhtslib.html
Rhtslib/man
Rhtslib/man/Rhtslib-package.Rd
Rhtslib/man/pkgconfig.Rd
Rhtslib/src
Rhtslib/src/Makevars
Rhtslib/src/Makevars.win
Rhtslib/src/Rhtslib.c
Rhtslib/src/htslib
Rhtslib/src/htslib/.travis.yml
Rhtslib/src/htslib/INSTALL
Rhtslib/src/htslib/LICENSE
Rhtslib/src/htslib/Makefile.am
Rhtslib/src/htslib/Makefile.in
Rhtslib/src/htslib/README
Rhtslib/src/htslib/README.md
Rhtslib/src/htslib/aclocal.m4
Rhtslib/src/htslib/bgzf.c
Rhtslib/src/htslib/bgzf_faidx_config.h
Rhtslib/src/htslib/bgzip.c
Rhtslib/src/htslib/compile
Rhtslib/src/htslib/config.guess
Rhtslib/src/htslib/config.h.in
Rhtslib/src/htslib/config.sub
Rhtslib/src/htslib/configure
Rhtslib/src/htslib/configure.ac
Rhtslib/src/htslib/cram
Rhtslib/src/htslib/cram/cram.h
Rhtslib/src/htslib/cram/cram_codecs.c
Rhtslib/src/htslib/cram/cram_codecs.h
Rhtslib/src/htslib/cram/cram_decode.c
Rhtslib/src/htslib/cram/cram_decode.h
Rhtslib/src/htslib/cram/cram_encode.c
Rhtslib/src/htslib/cram/cram_encode.h
Rhtslib/src/htslib/cram/cram_index.c
Rhtslib/src/htslib/cram/cram_index.h
Rhtslib/src/htslib/cram/cram_io.c
Rhtslib/src/htslib/cram/cram_io.h
Rhtslib/src/htslib/cram/cram_samtools.c
Rhtslib/src/htslib/cram/cram_samtools.h
Rhtslib/src/htslib/cram/cram_stats.c
Rhtslib/src/htslib/cram/cram_stats.h
Rhtslib/src/htslib/cram/cram_structs.h
Rhtslib/src/htslib/cram/files.c
Rhtslib/src/htslib/cram/mFILE.c
Rhtslib/src/htslib/cram/mFILE.h
Rhtslib/src/htslib/cram/md5.c
Rhtslib/src/htslib/cram/md5.h
Rhtslib/src/htslib/cram/misc.h
Rhtslib/src/htslib/cram/open_trace_file.c
Rhtslib/src/htslib/cram/open_trace_file.h
Rhtslib/src/htslib/cram/os.h
Rhtslib/src/htslib/cram/pooled_alloc.c
Rhtslib/src/htslib/cram/pooled_alloc.h
Rhtslib/src/htslib/cram/rANS_byte.h
Rhtslib/src/htslib/cram/rANS_static.c
Rhtslib/src/htslib/cram/rANS_static.h
Rhtslib/src/htslib/cram/sam_header.c
Rhtslib/src/htslib/cram/sam_header.h
Rhtslib/src/htslib/cram/string_alloc.c
Rhtslib/src/htslib/cram/string_alloc.h
Rhtslib/src/htslib/cram/thread_pool.c
Rhtslib/src/htslib/cram/thread_pool.h
Rhtslib/src/htslib/cram/vlen.c
Rhtslib/src/htslib/cram/vlen.h
Rhtslib/src/htslib/cram/zfio.c
Rhtslib/src/htslib/cram/zfio.h
Rhtslib/src/htslib/depcomp
Rhtslib/src/htslib/faidx.5
Rhtslib/src/htslib/faidx.c
Rhtslib/src/htslib/hfile.c
Rhtslib/src/htslib/hfile_internal.h
Rhtslib/src/htslib/hfile_net.c
Rhtslib/src/htslib/hts.c
Rhtslib/src/htslib/htsfile.c
Rhtslib/src/htslib/htslib
Rhtslib/src/htslib/htslib.mk
Rhtslib/src/htslib/htslib.pc.in
Rhtslib/src/htslib/htslib/bgzf.h
Rhtslib/src/htslib/htslib/faidx.h
Rhtslib/src/htslib/htslib/hfile.h
Rhtslib/src/htslib/htslib/hts.h
Rhtslib/src/htslib/htslib/hts_defs.h
Rhtslib/src/htslib/htslib/kfunc.h
Rhtslib/src/htslib/htslib/khash.h
Rhtslib/src/htslib/htslib/khash_str2int.h
Rhtslib/src/htslib/htslib/klist.h
Rhtslib/src/htslib/htslib/knetfile.h
Rhtslib/src/htslib/htslib/kseq.h
Rhtslib/src/htslib/htslib/ksort.h
Rhtslib/src/htslib/htslib/kstring.h
Rhtslib/src/htslib/htslib/regidx.h
Rhtslib/src/htslib/htslib/sam.h
Rhtslib/src/htslib/htslib/synced_bcf_reader.h
Rhtslib/src/htslib/htslib/tbx.h
Rhtslib/src/htslib/htslib/vcf.h
Rhtslib/src/htslib/htslib/vcf_sweep.h
Rhtslib/src/htslib/htslib/vcfutils.h
Rhtslib/src/htslib/htslib_vars.mk
Rhtslib/src/htslib/install-sh
Rhtslib/src/htslib/kfunc.c
Rhtslib/src/htslib/knetfile.c
Rhtslib/src/htslib/kstring.c
Rhtslib/src/htslib/lib
Rhtslib/src/htslib/lib/Makefile.am
Rhtslib/src/htslib/lib/Makefile.in
Rhtslib/src/htslib/lib/alloca.c
Rhtslib/src/htslib/lib/alloca.in.h
Rhtslib/src/htslib/lib/arpa_inet.in.h
Rhtslib/src/htslib/lib/close.c
Rhtslib/src/htslib/lib/dup2.c
Rhtslib/src/htslib/lib/errno.in.h
Rhtslib/src/htslib/lib/fcntl.c
Rhtslib/src/htslib/lib/fcntl.in.h
Rhtslib/src/htslib/lib/fd-hook.c
Rhtslib/src/htslib/lib/fd-hook.h
Rhtslib/src/htslib/lib/fdatasync.c
Rhtslib/src/htslib/lib/fsync.c
Rhtslib/src/htslib/lib/getdtablesize.c
Rhtslib/src/htslib/lib/getpagesize.c
Rhtslib/src/htslib/lib/gettimeofday.c
Rhtslib/src/htslib/lib/inttypes.in.h
Rhtslib/src/htslib/lib/msvc-inval.c
Rhtslib/src/htslib/lib/msvc-inval.h
Rhtslib/src/htslib/lib/msvc-nothrow.c
Rhtslib/src/htslib/lib/msvc-nothrow.h
Rhtslib/src/htslib/lib/netdb.in.h
Rhtslib/src/htslib/lib/recv.c
Rhtslib/src/htslib/lib/send.c
Rhtslib/src/htslib/lib/signal.in.h
Rhtslib/src/htslib/lib/stdalign.in.h
Rhtslib/src/htslib/lib/stddef.in.h
Rhtslib/src/htslib/lib/stdint.in.h
Rhtslib/src/htslib/lib/stdlib.in.h
Rhtslib/src/htslib/lib/string.in.h
Rhtslib/src/htslib/lib/sys_select.in.h
Rhtslib/src/htslib/lib/sys_socket.c
Rhtslib/src/htslib/lib/sys_socket.in.h
Rhtslib/src/htslib/lib/sys_stat.in.h
Rhtslib/src/htslib/lib/sys_time.in.h
Rhtslib/src/htslib/lib/sys_types.in.h
Rhtslib/src/htslib/lib/sys_uio.in.h
Rhtslib/src/htslib/lib/time.in.h
Rhtslib/src/htslib/lib/unistd.c
Rhtslib/src/htslib/lib/unistd.in.h
Rhtslib/src/htslib/lib/w32sock.h
Rhtslib/src/htslib/ltmain.sh
Rhtslib/src/htslib/m4
Rhtslib/src/htslib/m4/00gnulib.m4
Rhtslib/src/htslib/m4/absolute-header.m4
Rhtslib/src/htslib/m4/alloca.m4
Rhtslib/src/htslib/m4/arpa_inet_h.m4
Rhtslib/src/htslib/m4/close.m4
Rhtslib/src/htslib/m4/dup2.m4
Rhtslib/src/htslib/m4/errno_h.m4
Rhtslib/src/htslib/m4/extensions.m4
Rhtslib/src/htslib/m4/extern-inline.m4
Rhtslib/src/htslib/m4/fcntl-o.m4
Rhtslib/src/htslib/m4/fcntl.m4
Rhtslib/src/htslib/m4/fcntl_h.m4
Rhtslib/src/htslib/m4/fdatasync.m4
Rhtslib/src/htslib/m4/fsync.m4
Rhtslib/src/htslib/m4/getdtablesize.m4
Rhtslib/src/htslib/m4/getpagesize.m4
Rhtslib/src/htslib/m4/gettimeofday.m4
Rhtslib/src/htslib/m4/gnulib-cache.m4
Rhtslib/src/htslib/m4/gnulib-common.m4
Rhtslib/src/htslib/m4/gnulib-comp.m4
Rhtslib/src/htslib/m4/gnulib-tool.m4
Rhtslib/src/htslib/m4/include_next.m4
Rhtslib/src/htslib/m4/inttypes-pri.m4
Rhtslib/src/htslib/m4/inttypes.m4
Rhtslib/src/htslib/m4/libtool.m4
Rhtslib/src/htslib/m4/longlong.m4
Rhtslib/src/htslib/m4/ltoptions.m4
Rhtslib/src/htslib/m4/ltsugar.m4
Rhtslib/src/htslib/m4/ltversion.m4
Rhtslib/src/htslib/m4/lt~obsolete.m4
Rhtslib/src/htslib/m4/msvc-inval.m4
Rhtslib/src/htslib/m4/msvc-nothrow.m4
Rhtslib/src/htslib/m4/multiarch.m4
Rhtslib/src/htslib/m4/netdb_h.m4
Rhtslib/src/htslib/m4/off_t.m4
Rhtslib/src/htslib/m4/signal_h.m4
Rhtslib/src/htslib/m4/socketlib.m4
Rhtslib/src/htslib/m4/socklen.m4
Rhtslib/src/htslib/m4/sockpfaf.m4
Rhtslib/src/htslib/m4/ssize_t.m4
Rhtslib/src/htslib/m4/stdalign.m4
Rhtslib/src/htslib/m4/stddef_h.m4
Rhtslib/src/htslib/m4/stdint.m4
Rhtslib/src/htslib/m4/stdlib_h.m4
Rhtslib/src/htslib/m4/string_h.m4
Rhtslib/src/htslib/m4/sys_select_h.m4
Rhtslib/src/htslib/m4/sys_socket_h.m4
Rhtslib/src/htslib/m4/sys_stat_h.m4
Rhtslib/src/htslib/m4/sys_time_h.m4
Rhtslib/src/htslib/m4/sys_types_h.m4
Rhtslib/src/htslib/m4/sys_uio_h.m4
Rhtslib/src/htslib/m4/time_h.m4
Rhtslib/src/htslib/m4/unistd_h.m4
Rhtslib/src/htslib/m4/warn-on-use.m4
Rhtslib/src/htslib/m4/wchar_t.m4
Rhtslib/src/htslib/missing
Rhtslib/src/htslib/regidx.c
Rhtslib/src/htslib/run_tests.sh
Rhtslib/src/htslib/sam.5
Rhtslib/src/htslib/sam.c
Rhtslib/src/htslib/snippet
Rhtslib/src/htslib/snippet/_Noreturn.h
Rhtslib/src/htslib/snippet/arg-nonnull.h
Rhtslib/src/htslib/snippet/c++defs.h
Rhtslib/src/htslib/snippet/warn-on-use.h
Rhtslib/src/htslib/synced_bcf_reader.c
Rhtslib/src/htslib/tabix.1
Rhtslib/src/htslib/tabix.c
Rhtslib/src/htslib/tbx.c
Rhtslib/src/htslib/test
Rhtslib/src/htslib/test-driver
Rhtslib/src/htslib/test/Makefile.am
Rhtslib/src/htslib/test/Makefile.in
Rhtslib/src/htslib/test/auxf#values.sam
Rhtslib/src/htslib/test/auxf.fa
Rhtslib/src/htslib/test/auxf.fa.fai
Rhtslib/src/htslib/test/c1#bounds.sam
Rhtslib/src/htslib/test/c1#clip.sam
Rhtslib/src/htslib/test/c1#pad1.sam
Rhtslib/src/htslib/test/c1#pad2.sam
Rhtslib/src/htslib/test/c1#pad3.sam
Rhtslib/src/htslib/test/c1.fa
Rhtslib/src/htslib/test/c1.fa.fai
Rhtslib/src/htslib/test/ce#1.sam
Rhtslib/src/htslib/test/ce#2.sam
Rhtslib/src/htslib/test/ce#5.sam
Rhtslib/src/htslib/test/ce#5b.sam
Rhtslib/src/htslib/test/ce#large_seq.sam
Rhtslib/src/htslib/test/ce#tag_depadded.sam
Rhtslib/src/htslib/test/ce#tag_padded.sam
Rhtslib/src/htslib/test/ce#unmap.sam
Rhtslib/src/htslib/test/ce#unmap1.sam
Rhtslib/src/htslib/test/ce#unmap2.sam
Rhtslib/src/htslib/test/ce.fa
Rhtslib/src/htslib/test/ce.fa.fai
Rhtslib/src/htslib/test/compare_sam.pl
Rhtslib/src/htslib/test/fieldarith.c
Rhtslib/src/htslib/test/fieldarith.sam
Rhtslib/src/htslib/test/hfile.c
Rhtslib/src/htslib/test/sam.c
Rhtslib/src/htslib/test/test-regidx.c
Rhtslib/src/htslib/test/test-vcf-api.c
Rhtslib/src/htslib/test/test-vcf-api.out
Rhtslib/src/htslib/test/test-vcf-sweep.c
Rhtslib/src/htslib/test/test-vcf-sweep.out
Rhtslib/src/htslib/test/test.pl
Rhtslib/src/htslib/test/test_view.c
Rhtslib/src/htslib/test/test_view.pl
Rhtslib/src/htslib/test/xx#blank.sam
Rhtslib/src/htslib/test/xx#large_aux.sam
Rhtslib/src/htslib/test/xx#large_aux2.sam
Rhtslib/src/htslib/test/xx#minimal.sam
Rhtslib/src/htslib/test/xx#pair.sam
Rhtslib/src/htslib/test/xx#rg.sam
Rhtslib/src/htslib/test/xx#triplet.sam
Rhtslib/src/htslib/test/xx#unsorted.sam
Rhtslib/src/htslib/test/xx.fa
Rhtslib/src/htslib/test/xx.fa.fai
Rhtslib/src/htslib/vcf.5
Rhtslib/src/htslib/vcf.c
Rhtslib/src/htslib/vcf_sweep.c
Rhtslib/src/htslib/vcfutils.c
Rhtslib/src/htslib/version.h
Rhtslib/src/winlib
Rhtslib/src/winlib/i386
Rhtslib/src/winlib/i386/libhts.a
Rhtslib/src/winlib/x64
Rhtslib/src/winlib/x64/libhts.a
Rhtslib/tools
Rhtslib/tools/Makefile.in
Rhtslib/tools/compile
Rhtslib/tools/config.guess
Rhtslib/tools/config.h.in
Rhtslib/tools/config.sub
Rhtslib/tools/configure
Rhtslib/tools/depcomp
Rhtslib/tools/install-sh
Rhtslib/tools/lib_Makefile.in
Rhtslib/tools/ltmain.sh
Rhtslib/tools/missing
Rhtslib/tools/test-driver
Rhtslib/tools/test_Makefile.in
Rhtslib/vignettes
Rhtslib/vignettes/Rhtslib.Rmd