Files in Rbowtie

R bowtie wrapper

README.md

NAMESPACE

DESCRIPTION

LICENSE

build/vignette.rds

src/aligner_23mm.h

src/search_seeded_phase3.c

src/ebwt_search_util.cpp

src/bowtie

src/hit_set.cpp

src/pat.cpp

src/range_chaser.h

src/bitpack.h

src/processor_support.h

src/edit.cpp

src/ebwt_search_util.h

src/color_dec.cpp

src/ref_aligner.cpp

src/log.cpp

src/sequence_io.h

src/aligner_0mm.h

src/pool.h

src/tinythread.cpp

src/color_dec.h

src/endian_swap.h

src/blockwise_sa.h

src/threading.h

src/sstring.h

src/ccnt_lut.cpp

src/aligner_1mm.h

src/search_23mm_phase3.c

src/search_exact.c

src/hit.h

src/zbox.h

src/ref_aligner.h

src/range_source.h

src/MANUAL

src/bitset.h

src/row_chaser.h

src/reference.h

src/timer.h

src/search_1mm_phase2.c

src/aligner_metrics.h

src/hit_set.h

src/cpu_numa_info.h

src/bowtie-inspect

src/range_cache.h

src/search_1mm_phase1.c

src/cpu_numa_info.cpp

src/MANUAL.markdown

src/chaincat.cpp

src/btypes.h

src/search_23mm_phase1.c

src/color.h

src/word_io.h

src/TUTORIAL

src/range.h

src/shmem.h

src/sam.h

src/qual.cpp

src/ebwt_search.h

src/alphabet.h

src/color.cpp

src/ebwt_search.cpp

src/hit.cpp

src/edit.h

src/sam.cpp

src/pat.h

src/bowtie-build

src/search_seeded_phase1.c

src/log.h

src/ebwt.cpp

src/search_seeded_phase2.c

src/ref_read.cpp

src/NEWS

src/assert_helpers.h

src/Makefile.win

src/ebwt_build.cpp

src/tokenize.h

src/ref_read.h

src/bowtie_build_main.cpp

src/bowtie_main.cpp

src/AUTHORS

src/random_test.cpp

src/multikey_qsort.h

src/qual.h

src/shmem.cpp

src/Makefile

src/ebwt_search_backtrack.h

src/search_23mm_phase2.c

src/diff_sample.h

src/random_source.h

src/aligner.h

src/alphabet.cpp

src/auto_array.h

src/ebwt.h

src/str_util.h

src/VERSION

src/README

src/tinythread.h

src/bowtie_inspect.cpp

src/formats.h

src/search_seeded_phase4.c

src/fast_mutex.h

src/aligner_seed_mm.h

src/filebuf.h

src/search_globals.h

src/binary_sa_search.h

src/mm.h

src/LICENSE

src/third_party/cpuid.h

src/SpliceMap/runSpliceMap_QuasR.h

src/SpliceMap/cfgfile.cpp

src/SpliceMap/amalgamateSAM.cpp

src/SpliceMap/SpliceMap_utils_QuasR.cpp

src/SpliceMap/params.h

src/SpliceMap/SpliceMap_utils_QuasR.h

src/SpliceMap/getSpliceMapUnmapped.cpp

src/SpliceMap/params.cpp

src/SpliceMap/fuseReorder.cpp

src/SpliceMap/sortsam.cpp

src/SpliceMap/amalgamateSAM.h

src/SpliceMap/main.cpp

src/SpliceMap/main.h

src/SpliceMap/Makefile.win

src/SpliceMap/runSpliceMap_QuasR.cpp

src/SpliceMap/Makefile

src/SpliceMap/cfgfile.h

src/SpliceMap/sortsam.h

src/SpliceMap/LICENSE

src/SeqAn-1.1/platform_linux_gcc.h

src/SeqAn-1.1/GPL.txt

src/SeqAn-1.1/LGPL.txt

src/SeqAn-1.1/README.txt

src/SeqAn-1.1/platform_windows_mingw.h

src/SeqAn-1.1/platform_windows_vs.h

src/SeqAn-1.1/seqan/basic.h

src/SeqAn-1.1/seqan/file.h

src/SeqAn-1.1/seqan/sequence.h

src/SeqAn-1.1/seqan/platform.h

src/SeqAn-1.1/seqan/find.h

src/SeqAn-1.1/seqan/index.h

src/SeqAn-1.1/seqan/file/file_base.h

src/SeqAn-1.1/seqan/file/file_format_cgviz.h

src/SeqAn-1.1/seqan/file/stream_algorithms.h

src/SeqAn-1.1/seqan/file/file_format_fasta_align.h

src/SeqAn-1.1/seqan/file/stream.h

src/SeqAn-1.1/seqan/file/file_generated_forwards.h

src/SeqAn-1.1/seqan/file/file_forwards.h

src/SeqAn-1.1/seqan/file/file_array.h

src/SeqAn-1.1/seqan/file/file_format_fasta.h

src/SeqAn-1.1/seqan/file/file_format.h

src/SeqAn-1.1/seqan/file/meta.h

src/SeqAn-1.1/seqan/file/file_format_guess.h

src/SeqAn-1.1/seqan/file/file_format_raw.h

src/SeqAn-1.1/seqan/file/cstream.h

src/SeqAn-1.1/seqan/file/chunk_collector.h

src/SeqAn-1.1/seqan/sequence/segment_suffix.h

src/SeqAn-1.1/seqan/sequence/string_value_expand.h

src/SeqAn-1.1/seqan/sequence/string_base.h

src/SeqAn-1.1/seqan/sequence/sequence_multiple.h

src/SeqAn-1.1/seqan/sequence/string_stack.h

src/SeqAn-1.1/seqan/sequence/string_alloc.h

src/SeqAn-1.1/seqan/sequence/std_string.h

src/SeqAn-1.1/seqan/sequence/segment_prefix.h

src/SeqAn-1.1/seqan/sequence/string_cstyle.h

src/SeqAn-1.1/seqan/sequence/segment_infix.h

src/SeqAn-1.1/seqan/sequence/string_packed.h

src/SeqAn-1.1/seqan/sequence/string_pointer.h

src/SeqAn-1.1/seqan/sequence/sequence_shortcuts.h

src/SeqAn-1.1/seqan/sequence/string_array.h

src/SeqAn-1.1/seqan/sequence/sequence_forwards.h

src/SeqAn-1.1/seqan/sequence/sequence_generated_forwards.h

src/SeqAn-1.1/seqan/sequence/lexical.h

src/SeqAn-1.1/seqan/sequence/sequence_interface.h

src/SeqAn-1.1/seqan/sequence/segment_base.h

src/SeqAn-1.1/seqan/basic/basic_tag.h

src/SeqAn-1.1/seqan/basic/basic_allocator_singlepool.h

src/SeqAn-1.1/seqan/basic/basic_iterator_adapt_std.h

src/SeqAn-1.1/seqan/basic/basic_debug.h

src/SeqAn-1.1/seqan/basic/basic_alphabet_trait_basic.h

src/SeqAn-1.1/seqan/basic/basic_allocator_to_std.h

src/SeqAn-1.1/seqan/basic/basic_generated_forwards.h

src/SeqAn-1.1/seqan/basic/basic_pointer.h

src/SeqAn-1.1/seqan/basic/basic_allocator_interface.h

src/SeqAn-1.1/seqan/basic/basic_counted_ptr.h

src/SeqAn-1.1/seqan/basic/basic_compare.h

src/SeqAn-1.1/seqan/basic/basic_volatile_ptr.h

src/SeqAn-1.1/seqan/basic/basic_alphabet_interface2.h

src/SeqAn-1.1/seqan/basic/basic_profile.h

src/SeqAn-1.1/seqan/basic/basic_operator.h

src/SeqAn-1.1/seqan/basic/basic_iterator_adaptor.h

src/SeqAn-1.1/seqan/basic/basic_type.h

src/SeqAn-1.1/seqan/basic/basic_alphabet_interface.h

src/SeqAn-1.1/seqan/basic/basic_metaprogramming.h

src/SeqAn-1.1/seqan/basic/basic_aggregates.h

src/SeqAn-1.1/seqan/basic/basic_forwards.h

src/SeqAn-1.1/seqan/basic/basic_allocator_multipool.h

src/SeqAn-1.1/seqan/basic/basic_host.h

src/SeqAn-1.1/seqan/basic/basic_alphabet_simple_tabs.h

src/SeqAn-1.1/seqan/basic/basic_alphabet_simple.h

src/SeqAn-1.1/seqan/basic/basic_holder.h

src/SeqAn-1.1/seqan/basic/basic_definition.h

src/SeqAn-1.1/seqan/basic/basic_iterator_base.h

src/SeqAn-1.1/seqan/basic/basic_proxy.h

src/SeqAn-1.1/seqan/basic/basic_iterator_simple.h

src/SeqAn-1.1/seqan/basic/basic_allocator_simple.h

src/SeqAn-1.1/seqan/basic/basic_iterator_position.h

src/SeqAn-1.1/seqan/basic/basic_converter.h

src/SeqAn-1.1/seqan/basic/basic_iterator.h

src/SeqAn-1.1/seqan/basic/basic_transport.h

src/SeqAn-1.1/seqan/index/index_manual_forwards.h

src/SeqAn-1.1/seqan/index/index_qgram_find.h

src/SeqAn-1.1/seqan/index/shape_gapped.h

src/SeqAn-1.1/seqan/index/shape_predefined.h

src/SeqAn-1.1/seqan/index/index_sa_lss.h

src/SeqAn-1.1/seqan/index/index_find.h

src/SeqAn-1.1/seqan/index/index_generated_forwards.h

src/SeqAn-1.1/seqan/index/shape_base.h

src/SeqAn-1.1/seqan/index/index_base.h

src/SeqAn-1.1/seqan/find/find_generated_forwards.h

src/SeqAn-1.1/seqan/find/find_multi.h

src/SeqAn-1.1/seqan/find/find_set_horspool.h

src/SeqAn-1.1/seqan/find/find_multiple_shiftand.h

src/SeqAn-1.1/seqan/find/find_horspool.h

src/SeqAn-1.1/seqan/find/find_score.h

src/SeqAn-1.1/seqan/find/find_base.h

R/Rbowtie.R R/SpliceMap.R vignettes/Rbowtie-Overview.Rmd

vignettes/Rbowtie-refs.bib

man/Rbowtie.Rd man/SpliceMap.Rd man/Rbowtie-package.Rd

inst/NEWS

inst/CITATION

inst/doc/Rbowtie-Overview.html

inst/doc/Rbowtie-Overview.R inst/doc/Rbowtie-Overview.Rmd

inst/samples/refs/chr3.fa

inst/samples/refs/chr2.fa

inst/samples/refs/chr1.fa

inst/samples/reads/reads.fastq

Rbowtie documentation built on Nov. 8, 2020, 6:11 p.m.