Files in gmapR

An R interface to the GMAP/GSNAP/GSTRUCT suite

doupdate.R

TODO

.BBSoptions

NEWS

NAMESPACE

DESCRIPTION

papers/appnote/gmapR.Rnw

build/vignette.rds

src/gmapR.h

src/iit.c

src/bytestream.h

src/variantsummary.c

src/genome.h

src/genome.c

src/bamreader.c

src/R_init_gmapR.c

src/Makefile

src/bamtally.c

src/iit.h

src/gstruct/configure.ac

src/gstruct/ChangeLog

src/gstruct/Makefile.in

src/gstruct/Makefile.am

src/gstruct/COPYING

src/gstruct/configure

src/gstruct/NEWS

src/gstruct/AUTHORS

src/gstruct/INSTALL

src/gstruct/VERSION

src/gstruct/README

src/gstruct/config.site

src/gstruct/aclocal.m4

src/gstruct/config/depcomp

src/gstruct/config/config.guess

src/gstruct/config/ax_gcc_x86_cpuid.m4

src/gstruct/config/ax_check_compile_flag.m4

src/gstruct/config/expand.m4

src/gstruct/config/lt~obsolete.m4

src/gstruct/config/struct-stat64.m4

src/gstruct/config/libtool.m4

src/gstruct/config/ax_ext.m4

src/gstruct/config/madvise-flags.m4

src/gstruct/config/ltmain.sh

src/gstruct/config/perl.m4

src/gstruct/config/ax_gcc_x86_avx_xgetbv.m4

src/gstruct/config/acx_pthread.m4

src/gstruct/config/compile

src/gstruct/config/config.sub

src/gstruct/config/ltsugar.m4

src/gstruct/config/ltoptions.m4

src/gstruct/config/install-sh

src/gstruct/config/sse2_shift_defect.m4

src/gstruct/config/asm-bsr.m4

src/gstruct/config/acx_mmap_fixed.m4

src/gstruct/config/ltversion.m4

src/gstruct/config/mmap-flags.m4

src/gstruct/config/missing

src/gstruct/config/fopen.m4

src/gstruct/config/pagesize.m4

src/gstruct/config/acx_mmap_variable.m4

src/gstruct/src/uinttable.h

src/gstruct/src/mem.h

src/gstruct/src/access.c

src/gstruct/src/mismatchpool.h

src/gstruct/src/except.c

src/gstruct/src/littleendian.c

src/gstruct/src/tableuint.c

src/gstruct/src/expr.c

src/gstruct/src/dynprog_cigar.h

src/gstruct/src/list.h

src/gstruct/src/getline.h

src/gstruct/src/sequence.c

src/gstruct/src/Makefile.in

src/gstruct/src/fopen.h

src/gstruct/src/genomicpos.h

src/gstruct/src/chrom.h

src/gstruct/src/listdef.h

src/gstruct/src/datadir.c

src/gstruct/src/tally.c

src/gstruct/src/dynprog_simd.h

src/gstruct/src/tally.h

src/gstruct/src/matchpool.h

src/gstruct/src/complement.h

src/gstruct/src/matchpool.c

src/gstruct/src/samflags.h

src/gstruct/src/types.h

src/gstruct/src/md5.h

src/gstruct/src/mismatchdef.h

src/gstruct/src/chrnum.c

src/gstruct/src/uintlist.c

src/gstruct/src/littleendian.h

src/gstruct/src/expr.h

src/gstruct/src/bigendian.h

src/gstruct/src/Makefile.am

src/gstruct/src/chrnum.h

src/gstruct/src/iit-write.c

src/gstruct/src/sequence.h

src/gstruct/src/table.c

src/gstruct/src/genomicpos.c

src/gstruct/src/bamread.h

src/gstruct/src/genome.h

src/gstruct/src/bool.h

src/gstruct/src/mem.c

src/gstruct/src/intlist.h

src/gstruct/src/iit-read.h

src/gstruct/src/uintlist.h

src/gstruct/src/except.h

src/gstruct/src/mismatchpool.c

src/gstruct/src/bamread.c

src/gstruct/src/ucharlist.h

src/gstruct/src/genome.c

src/gstruct/src/bgzf.h

src/gstruct/src/md5.c

src/gstruct/src/table.h

src/gstruct/src/getopt.h

src/gstruct/src/translation.c

src/gstruct/src/dynprog_single.h

src/gstruct/src/iit-read.c

src/gstruct/src/list.c

src/gstruct/src/getline.c

src/gstruct/src/iitdef.h

src/gstruct/src/stopwatch.h

src/gstruct/src/translation.h

src/gstruct/src/ucharlist.c

src/gstruct/src/config.h.in

src/gstruct/src/samread.h

src/gstruct/src/matchdef.h

src/gstruct/src/parserange.h

src/gstruct/src/dynprog.h

src/gstruct/src/access.h

src/gstruct/src/samread.c

src/gstruct/src/interval.c

src/gstruct/src/bam.h

src/gstruct/src/stopwatch.c

src/gstruct/src/bamtally.h

src/gstruct/src/uinttable.c

src/gstruct/src/intlist.c

src/gstruct/src/assert.c

src/gstruct/src/tableuint.h

src/gstruct/src/getopt1.c

src/gstruct/src/intlistdef.h

src/gstruct/src/assert.h

src/gstruct/src/bamtally.c

src/gstruct/src/interval.h

src/gstruct/src/datadir.h

src/gstruct/src/chrom.c

src/gstruct/src/bigendian.c

src/gstruct/src/parserange.c

src/gstruct/src/dynprog_nogap.h

src/gstruct/src/bamtally_main.c

src/gstruct/src/iit-write.h

src/gstruct/src/getopt.c

src/gstruct/lib/gstruct.pc.in

src/samtools/bam.c

src/samtools/bam_lpileup.o

src/samtools/libbam.a

src/samtools/razf.c

src/samtools/kprobaln.c

src/samtools/kstring.o

src/samtools/bgzf.c

src/samtools/kseq.h

src/samtools/faidx.c

src/samtools/knetfile.o

src/samtools/bam_index.c

src/samtools/faidx.h

src/samtools/bam_sort.c

src/samtools/bam_pileup.c

src/samtools/samtools_patch.c

src/samtools/sam_header.h

src/samtools/faidx.o

src/samtools/sam.o

src/samtools/samtools_patch.h

src/samtools/sam.h

src/samtools/samtools_patch.o

src/samtools/bam_index.o

src/samtools/bgzf.h

src/samtools/kprobaln.o

src/samtools/ksort.h

src/samtools/bam_import.o

src/samtools/khash.h

src/samtools/kstring.h

src/samtools/bam_md.c

src/samtools/sam_header.c

src/samtools/bam_aux.o

src/samtools/sam.c

src/samtools/bgzf.o

src/samtools/bam.h

src/samtools/bam_import.c

src/samtools/bam_md.o

src/samtools/kaln.h

src/samtools/bam_lpileup.c

src/samtools/bam.o

src/samtools/bam_endian.h

src/samtools/bam_aux.c

src/samtools/bam_sort.o

src/samtools/sam_header.o

src/samtools/razf.h

src/samtools/bam_reheader.c

src/samtools/bam_reheader.o

src/samtools/knetfile.c

src/samtools/razf.o

src/samtools/kprobaln.h

src/samtools/kstring.c

src/samtools/knetfile.h

src/samtools/bam_pileup.o

src/gmap/configure.ac

src/gmap/ChangeLog

src/gmap/Makefile.in

src/gmap/Makefile.am

src/gmap/COPYING

src/gmap/NOTICE

src/gmap/configure

src/gmap/acinclude.m4

src/gmap/NEWS

src/gmap/AUTHORS

src/gmap/INSTALL

src/gmap/VERSION

src/gmap/README

src/gmap/config.site

src/gmap/aclocal.m4

src/gmap/config/depcomp

src/gmap/config/config.guess

src/gmap/config/ax_gcc_x86_cpuid.m4

src/gmap/config/ax_check_compile_flag.m4

src/gmap/config/expand.m4

src/gmap/config/lt~obsolete.m4

src/gmap/config/struct-stat64.m4

src/gmap/config/libtool.m4

src/gmap/config/ax_ext.m4

src/gmap/config/madvise-flags.m4

src/gmap/config/ltmain.sh

src/gmap/config/perl.m4

src/gmap/config/acx_pthread.m4

src/gmap/config/builtin.m4

src/gmap/config/compile

src/gmap/config/config.sub

src/gmap/config/test-driver

src/gmap/config/ltsugar.m4

src/gmap/config/ltoptions.m4

src/gmap/config/install-sh

src/gmap/config/asm-bsr.m4

src/gmap/config/acx_mmap_fixed.m4

src/gmap/config/ltversion.m4

src/gmap/config/mmap-flags.m4

src/gmap/config/missing

src/gmap/config/fopen.m4

src/gmap/config/pagesize.m4

src/gmap/config/acx_mmap_variable.m4

src/gmap/src/tableint.c

src/gmap/src/bitpack64-access.h

src/gmap/src/uinttable.h

src/gmap/src/iit_dump.c

src/gmap/src/changepoint.c

src/gmap/src/oligo.c

src/gmap/src/result.h

src/gmap/src/mem.h

src/gmap/src/access.c

src/gmap/src/match.c

src/gmap/src/except.c

src/gmap/src/stage3.h

src/gmap/src/genome-write.h

src/gmap/src/diagpool.c

src/gmap/src/littleendian.c

src/gmap/src/saca-k.c

src/gmap/src/oligoindex_hr.c

src/gmap/src/chimera.h

src/gmap/src/maxent_hr.h

src/gmap/src/smooth.c

src/gmap/src/tableuint.c

src/gmap/src/goby.c

src/gmap/src/boyer-moore.h

src/gmap/src/gmap.c

src/gmap/src/tableuint8.c

src/gmap/src/indexdb_hr.h

src/gmap/src/oligoindex_hr.h

src/gmap/src/diagdef.h

src/gmap/src/splicetrie_build.h

src/gmap/src/splicetrie_build.c

src/gmap/src/sarray-write.h

src/gmap/src/mode.h

src/gmap/src/splicestringpool.h

src/gmap/src/oligoindex.h

src/gmap/src/list.h

src/gmap/src/bitpack64-access.c

src/gmap/src/compress.c

src/gmap/src/pbinom.h

src/gmap/src/sequence.c

src/gmap/src/stage1.c

src/gmap/src/Makefile.in

src/gmap/src/fopen.h

src/gmap/src/iit-write-univ.h

src/gmap/src/substring.h

src/gmap/src/genomicpos.h

src/gmap/src/chrom.h

src/gmap/src/sense.h

src/gmap/src/listdef.h

src/gmap/src/spanningelt.h

src/gmap/src/result.c

src/gmap/src/datadir.c

src/gmap/src/goby.h

src/gmap/src/splicetrie.h

src/gmap/src/tableint.h

src/gmap/src/stage3hr.c

src/gmap/src/genome-write.c

src/gmap/src/compress.h

src/gmap/src/stage1hr.h

src/gmap/src/stage2.h

src/gmap/src/orderstat.h

src/gmap/src/matchpool.h

src/gmap/src/complement.h

src/gmap/src/stage1hr.c

src/gmap/src/get-genome.c

src/gmap/src/gregion.c

src/gmap/src/matchpool.c

src/gmap/src/indexdb.h

src/gmap/src/bitpack64-read.h

src/gmap/src/samflags.h

src/gmap/src/splicetrie.c

src/gmap/src/maxent.c

src/gmap/src/reader.c

src/gmap/src/types.h

src/gmap/src/sarray-read.h

src/gmap/src/md5.h

src/gmap/src/uint8list.c

src/gmap/src/chimera.c

src/gmap/src/chrnum.c

src/gmap/src/uintlist.c

src/gmap/src/littleendian.h

src/gmap/src/indexdb.c

src/gmap/src/separator.h

src/gmap/src/atoiindex.c

src/gmap/src/uniqscan.c

src/gmap/src/pbinom.c

src/gmap/src/indel.c

src/gmap/src/indexdbdef.h

src/gmap/src/bigendian.h

src/gmap/src/genome_hr.h

src/gmap/src/tableuint8.h

src/gmap/src/genome_hr.c

src/gmap/src/cmet.h

src/gmap/src/Makefile.am

src/gmap/src/chrnum.h

src/gmap/src/iit-write.c

src/gmap/src/sequence.h

src/gmap/src/compress-write.h

src/gmap/src/request.c

src/gmap/src/table.c

src/gmap/src/oligo.h

src/gmap/src/indexdb-write.h

src/gmap/src/genomicpos.c

src/gmap/src/genome.h

src/gmap/src/maxent_hr.c

src/gmap/src/request.h

src/gmap/src/iit_get.c

src/gmap/src/diagpool.h

src/gmap/src/bool.h

src/gmap/src/mem.c

src/gmap/src/mapq.c

src/gmap/src/intlist.h

src/gmap/src/pair.h

src/gmap/src/bzip2.h

src/gmap/src/shortread.h

src/gmap/src/iit-read.h

src/gmap/src/bzip2.c

src/gmap/src/shortread.c

src/gmap/src/stage3.c

src/gmap/src/uintlist.h

src/gmap/src/resulthr.h

src/gmap/src/maxent.h

src/gmap/src/except.h

src/gmap/src/atoi.c

src/gmap/src/splice.h

src/gmap/src/stage2.c

src/gmap/src/substring.c

src/gmap/src/univinterval.c

src/gmap/src/samheader.c

src/gmap/src/mapq.h

src/gmap/src/indexdb-write.c

src/gmap/src/compress-write.c

src/gmap/src/gbuffer.h

src/gmap/src/genome.c

src/gmap/src/diagnostic.c

src/gmap/src/samprint.h

src/gmap/src/outbuffer.h

src/gmap/src/iit-read-univ.c

src/gmap/src/intron.h

src/gmap/src/dynprog.c

src/gmap/src/md5.c

src/gmap/src/spanningelt.c

src/gmap/src/table.h

src/gmap/src/getopt.h

src/gmap/src/translation.c

src/gmap/src/changepoint.h

src/gmap/src/smooth.h

src/gmap/src/sarray-write.c

src/gmap/src/gmapindex.c

src/gmap/src/iit-read.c

src/gmap/src/diag.h

src/gmap/src/pairdef.h

src/gmap/src/cellpool.h

src/gmap/src/splice.c

src/gmap/src/cellpool.c

src/gmap/src/doublelist.c

src/gmap/src/pairpool.h

src/gmap/src/stage1.h

src/gmap/src/diag.c

src/gmap/src/oligoindex.c

src/gmap/src/chrsubset.c

src/gmap/src/list.c

src/gmap/src/iitdef.h

src/gmap/src/iit-read-univ.h

src/gmap/src/stopwatch.h

src/gmap/src/translation.h

src/gmap/src/config.h.in

src/gmap/src/matchdef.h

src/gmap/src/parserange.h

src/gmap/src/genome_sites.h

src/gmap/src/iit_store.c

src/gmap/src/dynprog.h

src/gmap/src/access.h

src/gmap/src/interval.c

src/gmap/src/inbuffer.h

src/gmap/src/snpindex.c

src/gmap/src/resulthr.c

src/gmap/src/indel.h

src/gmap/src/cmetindex.c

src/gmap/src/atoi.h

src/gmap/src/bitpack64-write.h

src/gmap/src/samprint.c

src/gmap/src/pair.c

src/gmap/src/chrsubset.h

src/gmap/src/diagnostic.h

src/gmap/src/stopwatch.c

src/gmap/src/doublelist.h

src/gmap/src/uint8list.h

src/gmap/src/gregion.h

src/gmap/src/gsnap.c

src/gmap/src/orderstat.c

src/gmap/src/splicestringpool.c

src/gmap/src/uinttable.c

src/gmap/src/match.h

src/gmap/src/intlist.c

src/gmap/src/univinterval.h

src/gmap/src/assert.c

src/gmap/src/reader.h

src/gmap/src/samheader.h

src/gmap/src/comp.h

src/gmap/src/tableuint.h

src/gmap/src/sarray-read.c

src/gmap/src/indexdb_hr.c

src/gmap/src/getopt1.c

src/gmap/src/iit-write-univ.c

src/gmap/src/bitpack64-write.c

src/gmap/src/intlistdef.h

src/gmap/src/assert.h

src/gmap/src/gbuffer.c

src/gmap/src/boyer-moore.c

src/gmap/src/block.h

src/gmap/src/saca-k.h

src/gmap/src/segmentpos.h

src/gmap/src/stage3hr.h

src/gmap/src/inbuffer.c

src/gmap/src/interval.h

src/gmap/src/bitpack64-read.c

src/gmap/src/datadir.h

src/gmap/src/chrom.c

src/gmap/src/cmet.c

src/gmap/src/outbuffer.c

src/gmap/src/segmentpos.c

src/gmap/src/bigendian.c

src/gmap/src/parserange.c

src/gmap/src/scores.h

src/gmap/src/block.c

src/gmap/src/genome_sites.c

src/gmap/src/intron.c

src/gmap/src/iit-write.h

src/gmap/src/getopt.c

src/gmap/src/fastlog.h

src/gmap/src/pairpool.c

src/gmap/tests/align.test.ok

src/gmap/tests/Makefile.in

src/gmap/tests/map.test.ok

src/gmap/tests/coords1.test.ok

src/gmap/tests/setup.ref123positions.ok

src/gmap/tests/setup.genomecomp.ok

src/gmap/tests/iittest.iit.ok

src/gmap/tests/Makefile.am

src/gmap/tests/align.test.in

src/gmap/tests/iit.test.in

src/gmap/tests/fa.iittest

src/gmap/tests/coords1.test.in

src/gmap/tests/iit_get.out.ok

src/gmap/tests/ss.her2

src/gmap/tests/setup1.test.in

src/gmap/tests/defs

src/gmap/tests/ss.chr17test

src/gmap/util/gmap_uncompress.pl.in

src/gmap/util/gvf_iit.pl.in

src/gmap/util/gmap_compress.pl.in

src/gmap/util/Makefile.in

src/gmap/util/gmap_setup.pl.in

src/gmap/util/gmap_reassemble.pl.in

src/gmap/util/gff3_splicesites.pl.in

src/gmap/util/gtf_genes.pl.in

src/gmap/util/gtf_introns.pl.in

src/gmap/util/fa_coords.pl.in

src/gmap/util/Makefile.am

src/gmap/util/gff3_genes.pl.in

src/gmap/util/vcf_iit.pl.in

src/gmap/util/dbsnp_iit.pl.in

src/gmap/util/gmap_process.pl.in

src/gmap/util/gff3_introns.pl.in

src/gmap/util/psl_splicesites.pl.in

src/gmap/util/psl_introns.pl.in

src/gmap/util/psl_genes.pl.in

src/gmap/util/md_coords.pl.in

src/gmap/util/gmap_build.pl.in

src/gmap/util/gtf_splicesites.pl.in

R/gmap-command.R R/info.R R/GmapSnps-class.R R/BamTallyParam-class.R R/iit_store-command.R R/GmapOutput-class.R R/system.R R/utils.R R/TP53Genome.R R/GmapGenomeDirectory-class.R R/iit-format.R R/bam_tally-command.R R/GmapBamReader-class.R R/get-genome-command.R R/makeGmapGenomePackage.R R/snpindex-command.R R/GmapGenome-class.R R/GsnapParam-class.R R/GmapSnpDirectory-class.R R/gmap_build-command.R R/GmapParam-class.R R/atoiindex-command.R R/GsnapOutput-class.R R/asSystemCall.R R/test_gmapR_package.R R/cmetindex-command.R R/gsnap-command.R

vignettes/gmapR.Rnw

man/directory.Rd man/GsnapParam-class.Rd man/GmapSnps-class.Rd man/bam_tally-methods.Rd man/GmapGenome-class.Rd man/GmapSnpDirectory-class.Rd man/gsnap-methods.Rd man/GsnapOutput-class.Rd man/TP53Genome.Rd man/cmetindex.Rd man/BamTallyParam-class.Rd man/makeGmapGenomePackage.Rd man/gmap_build-methods.Rd man/GmapGenomeDirectory-class.Rd man/internals.Rd tests/gmapR_unit_tests.R inst/doc/gmapR.pdf inst/doc/gmapR.R

inst/doc/gmapR.Rnw

inst/extdata/bam_tally_test.bam

inst/extdata/bam_tally_test.bam.bai

inst/extdata/p53Variants.vcf

inst/extdata/hg19.p53.fasta

inst/extdata/test_data_aln/test_data_aln.concordant_uniq.bam.bai

inst/extdata/test_data_aln/test_data_aln.paired_mult.bam.bai

inst/extdata/test_data_aln/test_data_aln.paired_mult.bam

inst/extdata/test_data_aln/test_data_aln.paired_uniq_inv.bam.bai

inst/extdata/test_data_aln/test_data_aln.halfmapping_uniq.bam

inst/extdata/test_data_aln/test_data_aln.paired_uniq_inv.bam

inst/extdata/test_data_aln/test_data_aln.unpaired_mult.bam.bai

inst/extdata/test_data_aln/test_data_aln.paired_uniq_long.bam.bai

inst/extdata/test_data_aln/test_data_aln.nomapping.bam

inst/extdata/test_data_aln/test_data_aln.halfmapping_mult.bam

inst/extdata/test_data_aln/test_data_aln.concordant_transloc.bam

inst/extdata/test_data_aln/test_data_aln.unpaired_transloc.bam

inst/extdata/test_data_aln/test_data_aln.paired_uniq_scr.bam

inst/extdata/test_data_aln/test_data_aln.nomapping.bam.bai

inst/extdata/test_data_aln/test_data_aln.unpaired_uniq.bam

inst/extdata/test_data_aln/test_data_aln.halfmapping_uniq.bam.bai

inst/extdata/test_data_aln/test_data_aln.unpaired_mult.bam

inst/extdata/test_data_aln/test_data_aln.halfmapping_mult.bam.bai

inst/extdata/test_data_aln/test_data_aln.concordant_mult.bam.bai

inst/extdata/test_data_aln/test_data_aln.paired_uniq_scr.bam.bai

inst/extdata/test_data_aln/test_data_aln.halfmapping_transloc.bam.bai

inst/extdata/test_data_aln/test_data_aln.concordant_transloc.bam.bai

inst/extdata/test_data_aln/test_data_aln.concordant_mult.bam

inst/extdata/test_data_aln/test_data_aln.concordant_uniq.bam

inst/extdata/test_data_aln/test_data_aln.halfmapping_transloc.bam

inst/extdata/test_data_aln/test_data_aln.unpaired_transloc.bam.bai

inst/extdata/test_data_aln/test_data_aln.paired_uniq_long.bam

inst/extdata/test_data_aln/test_data_aln.unpaired_uniq.bam.bai

inst/GmapGenomePackage-template/NAMESPACE

inst/GmapGenomePackage-template/DESCRIPTION

inst/GmapGenomePackage-template/R/zzz.R

inst/GmapGenomePackage-template/man/package.Rd

inst/usr/bin/cmetindex

inst/usr/bin/psl_introns

inst/usr/bin/gmap_process

inst/usr/bin/psl_genes

inst/usr/bin/gtf_splicesites

inst/usr/bin/psl_splicesites

inst/usr/bin/gmapl

inst/usr/bin/gff3_splicesites

inst/usr/bin/atoiindex

inst/usr/bin/vcf_iit

inst/usr/bin/gmap_uncompress

inst/usr/bin/gmap_reassemble

inst/usr/bin/gtf_introns

inst/usr/bin/gsnapl

inst/usr/bin/gtf_genes

inst/usr/bin/dbsnp_iit

inst/usr/bin/gff3_genes

inst/usr/bin/gsnap

inst/usr/bin/iit_get

inst/usr/bin/snpindex

inst/usr/bin/fa_coords

inst/usr/bin/gmap_build

inst/usr/bin/md_coords

inst/usr/bin/gmap

inst/usr/bin/iit_store

inst/usr/bin/uniqscan

inst/usr/bin/gmapindex

inst/usr/bin/gvf_iit

inst/usr/bin/iit_dump

inst/usr/bin/gmap_compress

inst/usr/bin/uniqscanl

inst/usr/bin/gff3_introns

inst/usr/bin/gmap_setup

inst/usr/bin/get-genome

inst/usr/include/gstruct/uinttable.h

inst/usr/include/gstruct/mem.h

inst/usr/include/gstruct/mismatchpool.h

inst/usr/include/gstruct/dynprog_cigar.h

inst/usr/include/gstruct/list.h

inst/usr/include/gstruct/fopen.h

inst/usr/include/gstruct/genomicpos.h

inst/usr/include/gstruct/chrom.h

inst/usr/include/gstruct/listdef.h

inst/usr/include/gstruct/dynprog_simd.h

inst/usr/include/gstruct/tally.h

inst/usr/include/gstruct/matchpool.h

inst/usr/include/gstruct/complement.h

inst/usr/include/gstruct/types.h

inst/usr/include/gstruct/md5.h

inst/usr/include/gstruct/mismatchdef.h

inst/usr/include/gstruct/littleendian.h

inst/usr/include/gstruct/bigendian.h

inst/usr/include/gstruct/chrnum.h

inst/usr/include/gstruct/sequence.h

inst/usr/include/gstruct/bamread.h

inst/usr/include/gstruct/genome.h

inst/usr/include/gstruct/bool.h

inst/usr/include/gstruct/intlist.h

inst/usr/include/gstruct/iit-read.h

inst/usr/include/gstruct/uintlist.h

inst/usr/include/gstruct/except.h

inst/usr/include/gstruct/ucharlist.h

inst/usr/include/gstruct/table.h

inst/usr/include/gstruct/dynprog_single.h

inst/usr/include/gstruct/iitdef.h

inst/usr/include/gstruct/stopwatch.h

inst/usr/include/gstruct/translation.h

inst/usr/include/gstruct/samread.h

inst/usr/include/gstruct/matchdef.h

inst/usr/include/gstruct/parserange.h

inst/usr/include/gstruct/dynprog.h

inst/usr/include/gstruct/access.h

inst/usr/include/gstruct/bamtally.h

inst/usr/include/gstruct/config.h

inst/usr/include/gstruct/tableuint.h

inst/usr/include/gstruct/intlistdef.h

inst/usr/include/gstruct/assert.h

inst/usr/include/gstruct/interval.h

inst/usr/include/gstruct/datadir.h

inst/usr/include/gstruct/dynprog_nogap.h

inst/usr/include/gstruct/iit-write.h

inst/usr/lib/libgstruct-1.0.la

inst/usr/lib/libgstruct-1.0.a

inst/usr/lib/pkgconfig/gstruct-1.0.pc

inst/unitTests/test_BamTallyParam.R inst/unitTests/test_bam_tally.R inst/unitTests/test_makeGmapGenomePackage.R inst/unitTests/test_gsnap.R inst/unitTests/off_test_GmapSnpDirectory.R inst/unitTests/off_test_bam_tally.R inst/unitTests/test_GmapGenomeDirectory.R inst/unitTests/test_GsnapParam.R inst/unitTests/test_GmapGenome.R

gmapR documentation built on Nov. 8, 2020, 5:29 p.m.