Files in Rbowtie2

An R Wrapper for Bowtie2 and AdapterRemoval

.BBSoptions

NAMESPACE

DESCRIPTION

build/vignette.rds

src/version_info.cpp

src/bowtie2_32.cpp

src/Makefile.win

src/Makefile

src/adapterremoval/main_adapter_rm.cc

src/adapterremoval/alignment.h

src/adapterremoval/userconfig.cc

src/adapterremoval/argparse.h

src/adapterremoval/fastq_io.h

src/adapterremoval/scheduler.cc

src/adapterremoval/strutils.cc

src/adapterremoval/fastq_enc.cc

src/adapterremoval/main.cc

src/adapterremoval/main_adapter_id.cc

src/adapterremoval/scheduler.h

src/adapterremoval/threads.cc

src/adapterremoval/debug.h

src/adapterremoval/linereader.h

src/adapterremoval/timer.h

src/adapterremoval/main_demultiplex.cc

src/adapterremoval/fastq.h

src/adapterremoval/demultiplex.cc

src/adapterremoval/statistics.h

src/adapterremoval/fastq_io.cc

src/adapterremoval/timer.cc

src/adapterremoval/adapterset.cc

src/adapterremoval/commontypes.h

src/adapterremoval/strutils.h

src/adapterremoval/alignment.cc

src/adapterremoval/main.h

src/adapterremoval/Makefile.win

src/adapterremoval/adapterset.h

src/adapterremoval/fastq_enc.h

src/adapterremoval/linereader_joined.cc

src/adapterremoval/Makefile

src/adapterremoval/demultiplex.h

src/adapterremoval/linereader.cc

src/adapterremoval/trimmed_reads.h

src/adapterremoval/trimmed_reads.cc

src/adapterremoval/threads.h

src/adapterremoval/debug.cc

src/adapterremoval/linereader_joined.h

src/adapterremoval/userconfig.h

src/adapterremoval/fastq.cc

src/adapterremoval/argparse.cc

src/adapterremoval/vecutils.h

src/bowtie2/aligner_driver.cpp

src/bowtie2/util.h

src/bowtie2/random_source.cpp

src/bowtie2/pat.cpp

src/bowtie2/ls.h

src/bowtie2/bitpack.h

src/bowtie2/processor_support.h

src/bowtie2/bt2_io.cpp

src/bowtie2/edit.cpp

src/bowtie2/bt2_util.cpp

src/bowtie2/bt2_search.cpp

src/bowtie2/aligner_seed.h

src/bowtie2/bt2_inspect.cpp

src/bowtie2/bt2_dp.cpp

src/bowtie2/aligner_swsse.h

src/bowtie2/sequence_io.h

src/bowtie2/group_walk.cpp

src/bowtie2/random_util.h

src/bowtie2/tinythread.cpp

src/bowtie2/endian_swap.h

src/bowtie2/aligner_sw.cpp

src/bowtie2/aligner_sw.h

src/bowtie2/blockwise_sa.h

src/bowtie2/threading.h

src/bowtie2/sse_util.h

src/bowtie2/sstring.h

src/bowtie2/simple_func.cpp

src/bowtie2/ccnt_lut.cpp

src/bowtie2/ival_list.h

src/bowtie2/aligner_sw_common.h

src/bowtie2/aligner_swsse_ee_i16.cpp

src/bowtie2/aligner_report.h

src/bowtie2/aligner_swsse_loc_i16.cpp

src/bowtie2/aln_sink.cpp

src/bowtie2/zbox.h

src/bowtie2/aligner_bt.h

src/bowtie2/unique.cpp

src/bowtie2/ls.cpp

src/bowtie2/reference.h

src/bowtie2/ref_coord.cpp

src/bowtie2/aligner_result.h

src/bowtie2/pe.cpp

src/bowtie2/timer.h

src/bowtie2/aligner_cache.cpp

src/bowtie2/aligner_metrics.h

src/bowtie2/limit.h

src/bowtie2/cpu_numa_info.h

src/bowtie2/ds.cpp

src/bowtie2/aligner_swsse.cpp

src/bowtie2/aligner_seed2.h

src/bowtie2/multikey_qsort.cpp

src/bowtie2/aligner_seed.cpp

src/bowtie2/cpu_numa_info.cpp

src/bowtie2/outq.h

src/bowtie2/simple_func.h

src/bowtie2/btypes.h

src/bowtie2/aligner_cache.h

src/bowtie2/word_io.h

src/bowtie2/aligner_bt.cpp

src/bowtie2/read.h

src/bowtie2/presets.cpp

src/bowtie2/shmem.h

src/bowtie2/dp_framer.h

src/bowtie2/sam.h

src/bowtie2/outq.cpp

src/bowtie2/qual.cpp

src/bowtie2/mask.cpp

src/bowtie2/aligner_seed_policy.h

src/bowtie2/aligner_sw_driver.cpp

src/bowtie2/aln_sink.h

src/bowtie2/alphabet.h

src/bowtie2/ds.h

src/bowtie2/pe.h

src/bowtie2/aligner_seed2.cpp

src/bowtie2/edit.h

src/bowtie2/sam.cpp

src/bowtie2/pat.h

src/bowtie2/bt2_search.h

src/bowtie2/sse_util.cpp

src/bowtie2/ref_read.cpp

src/bowtie2/group_walk.h

src/bowtie2/dp_framer.cpp

src/bowtie2/aligner_swsse_loc_u8.cpp

src/bowtie2/assert_helpers.h

src/bowtie2/Makefile.win

src/bowtie2/aligner_sw_nuc.h

src/bowtie2/tokenize.h

src/bowtie2/aligner_swsse_ee_u8.cpp

src/bowtie2/unique.h

src/bowtie2/ref_read.h

src/bowtie2/bowtie_build_main.cpp

src/bowtie2/bowtie_main.cpp

src/bowtie2/random_util.cpp

src/bowtie2/multikey_qsort.h

src/bowtie2/qual.h

src/bowtie2/shmem.cpp

src/bowtie2/limit.cpp

src/bowtie2/read_qseq.cpp

src/bowtie2/Makefile

src/bowtie2/aligner_result.cpp

src/bowtie2/opts.h

src/bowtie2/diff_sample.h

src/bowtie2/random_source.h

src/bowtie2/aligner_seed_policy.cpp

src/bowtie2/alphabet.cpp

src/bowtie2/bt2_idx.h

src/bowtie2/reference.cpp

src/bowtie2/diff_sample.cpp

src/bowtie2/str_util.h

src/bowtie2/ref_coord.h

src/bowtie2/tinythread.h

src/bowtie2/mem_ids.h

src/bowtie2/banded.h

src/bowtie2/bt2_idx.cpp

src/bowtie2/presets.h

src/bowtie2/bt2_build.cpp

src/bowtie2/formats.h

src/bowtie2/ival_list.cpp

src/bowtie2/fast_mutex.h

src/bowtie2/sstring.cpp

src/bowtie2/aligner_driver.h

src/bowtie2/scoring.h

src/bowtie2/banded.cpp

src/bowtie2/aligner_sw_driver.h

src/bowtie2/filebuf.h

src/bowtie2/search_globals.h

src/bowtie2/mask.h

src/bowtie2/binary_sa_search.h

src/bowtie2/scoring.cpp

src/bowtie2/mm.h

src/bowtie2/third_party/cpuid.h

R/bowtie2.R R/checkUtils.R R/adapterremoval.R vignettes/Rbowtie2-Introduction.Rmd man/remove_adapters.Rd man/adapterremoval_usage.Rd man/identify_adapters.Rd man/adapterremoval_version.Rd man/bowtie2_usage.Rd man/bowtie2_version.Rd man/bowtie2_build_usage.Rd man/bowtie2-build.Rd man/bowtie2.Rd

inst/NEWS

inst/CITATION

inst/doc/Rbowtie2-Introduction.Rmd

inst/doc/Rbowtie2-Introduction.html

inst/doc/Rbowtie2-Introduction.R

inst/extdata/bt2/refs/lambda_virus.fa

inst/extdata/bt2/reads/reads_1.fastq

inst/extdata/bt2/reads/reads_2.fastq

inst/extdata/adrm/reads_1.fq

inst/extdata/adrm/reads_2.fq

Rbowtie2 documentation built on Nov. 8, 2020, 5:35 p.m.