Files in Rhisat2

R Wrapper for HISAT2 Aligner

README.md

NEWS

NAMESPACE

DESCRIPTION

LICENSE

build/vignette.rds

src/aligner_driver.cpp

src/spliced_aligner.h

src/util.h

src/random_source.cpp

src/pat.cpp

src/hisat2-inspect

src/ls.h

src/bitpack.h

src/processor_support.h

src/edit.cpp

src/aligner_seed.h

src/aligner_swsse.h

src/sequence_io.h

src/group_walk.cpp

src/splice_site_mem.h

src/random_util.h

src/tinythread.cpp

src/endian_swap.h

src/aligner_sw.cpp

src/hi_aligner.h

src/aligner_sw.h

src/blockwise_sa.h

src/threading.h

src/sse_util.h

src/sstring.h

src/simple_func.cpp

src/ccnt_lut.cpp

src/ival_list.h

src/aligner_sw_common.h

src/aligner_swsse_ee_i16.cpp

src/hisat2_extract_snps_haplotypes_VCF.py

src/splice_site.h

src/aligner_report.h

src/aligner_swsse_loc_i16.cpp

src/aln_sink.cpp

src/zbox.h

src/MANUAL

src/hisatgenotype.py

src/aligner_bt.h

src/unique.cpp

src/splice_site_new.cpp

src/tp.h

src/hisat2.cpp

src/ls.cpp

src/reference.h

src/ref_coord.cpp

src/aligner_result.h

src/pe.cpp

src/timer.h

src/aligner_cache.cpp

src/aligner_metrics.h

src/gfm.h

src/limit.h

src/ds.cpp

src/bp_aligner.h

src/aligner_swsse.cpp

src/extract_splice_sites.py

src/aligner_seed2.h

src/multikey_qsort.cpp

src/aligner_seed.cpp

src/MANUAL.markdown

src/hisat2_inspect.cpp

src/outq.h

src/simple_func.h

src/splice_site.cpp

src/btypes.h

src/aligner_cache.h

src/word_io.h

src/extract_exons.py

src/TUTORIAL

src/aligner_bt.cpp

src/hisatgenotype_extract_reads.py

src/hgfm.h

src/read.h

src/presets.cpp

src/shmem.h

src/get_info.cpp

src/dp_framer.h

src/sam.h

src/outq.cpp

src/qual.cpp

src/mask.cpp

src/hier_idx_common.h

src/aligner_seed_policy.h

src/aligner_sw_driver.cpp

src/aln_sink.h

src/alphabet.h

src/ds.h

src/classifier_li.h

src/pe.h

src/aligner_seed2.cpp

src/edit.h

src/pat.h

src/hisatgenotype_hla_cyp.py

src/hisat2

src/sse_util.cpp

src/ref_read.cpp

src/hisat2_simulate_reads.py

src/NEWS

src/group_walk.h

src/dp_framer.cpp

src/aligner_swsse_loc_u8.cpp

src/hisat2_main.cpp

src/hisat2_build.cpp

src/assert_helpers.h

src/Makefile.win

src/aligner_sw_nuc.h

src/tokenize.h

src/aligner_swsse_ee_u8.cpp

src/hisat2_extract_exons.py

src/unique.h

src/ref_read.h

src/gbwt_graph.h

src/alt.h

src/random_util.cpp

src/AUTHORS

src/multikey_qsort.h

src/qual.h

src/shmem.cpp

src/limit.cpp

src/read_qseq.cpp

src/hisat2-build

src/hisatgenotype_extract_vars.py

src/Makefile

src/aligner_result.cpp

src/opts.h

src/diff_sample.h

src/random_source.h

src/aligner_seed_policy.cpp

src/hisat2_build_main.cpp

src/alphabet.cpp

src/reference.cpp

src/diff_sample.cpp

src/str_util.h

src/radix_sort.h

src/VERSION

src/ref_coord.h

src/hisatgenotype_build_genome.py

src/tinythread.h

src/mem_ids.h

src/banded.h

src/presets.h

src/formats.h

src/ival_list.cpp

src/hisat_bp.cpp

src/hisat2_extract_splice_sites.py

src/fast_mutex.h

src/hisat2_extract_snps_haplotypes_UCSC.py

src/sstring.cpp

src/gp.h

src/aligner_driver.h

src/scoring.h

src/banded.cpp

src/hisatgenotype_locus.py

src/aligner_sw_driver.h

src/filebuf.h

src/search_globals.h

src/mask.h

src/binary_sa_search.h

src/gfm.cpp

src/scoring.cpp

src/mm.h

src/LICENSE

src/doc/manual.inc.html

src/doc/strip_markdown.pl

src/doc/style.css

src/doc/README

src/hisatgenotype_scripts/compare_HLA_Omixon.py

src/hisatgenotype_scripts/hisatgenotype_locus_samples.py

src/hisatgenotype_scripts/hisatgenotype_HLA_genotyping_PGs.py

src/hisatgenotype_scripts/extract_Omixon_HLA.py

src/hisatgenotype_scripts/get_haplotype_ILMN_StrandSeq.py

src/scripts/gen_2b_occ_lookup.pl

src/scripts/make_grcm38.sh

src/scripts/gen_solqual_lookup.pl

src/scripts/make_grch37_snp.sh

src/scripts/make_sc3.sh

src/scripts/make_mm9.sh

src/scripts/make_grch38_snp_tran.sh

src/scripts/make_grcm38_snp.sh

src/scripts/make_grcm38_snp_tran.sh

src/scripts/make_ce10.sh

src/scripts/make_r64.sh

src/scripts/make_dm6.sh

src/scripts/make_a_thaliana_tair.sh

src/scripts/make_bdgp6_tran.sh

src/scripts/convert_quals.pl

src/scripts/make_grch38_snp.sh

src/scripts/make_rnor6_tran.sh

src/scripts/make_hg38_allsnp.sh

src/scripts/make_grch38_tran.sh

src/scripts/gen_occ_lookup.pl

src/scripts/make_mm10.sh

src/scripts/make_rn6.sh

src/scripts/make_grch37_snp_tran.sh

src/scripts/make_hg19.sh

src/scripts/make_e_coli.sh

src/scripts/make_r64_tran.sh

src/scripts/make_wbcel235_tran.sh

src/scripts/make_wbcel235.sh

src/scripts/make_zm3_snp_tran_ercc.sh

src/scripts/make_rnor6.sh

src/scripts/make_grch38_snp_tran_ercc.sh

src/scripts/make_grch38.sh

src/scripts/make_canFam2.sh

src/scripts/make_b_taurus_UMD3.sh

src/scripts/make_grcm38_tran.sh

src/scripts/make_bdgp6.sh

src/scripts/make_hg38_snp_tran.sh

src/scripts/make_grch37_tran.sh

src/scripts/make_hg38.sh

src/scripts/make_grch37.sh

src/scripts/make_grch37_snp_tran_ercc.sh

src/scripts/make_rn4.sh

src/scripts/make_hg38_snp.sh

src/scripts/infer_fraglen.pl

src/example/reference/22_20-21M.snp

src/example/reference/22_20-21M.fa

src/example/reads/reads_2.fa

src/example/reads/reads_1.fa

src/example/index/22_20-21M_snp.8.ht2

src/example/index/22_20-21M_snp.7.ht2

src/example/index/22_20-21M_snp.2.ht2

src/example/index/22_20-21M_snp.3.ht2

src/example/index/22_20-21M_snp.4.ht2

src/example/index/22_20-21M_snp.1.ht2

src/example/index/22_20-21M_snp.5.ht2

src/example/index/22_20-21M_snp.6.ht2

src/hisatgenotype_modules/hisatgenotype_typing_common.py

src/hisatgenotype_modules/hisatgenotype_convert_codis.py

src/hisatgenotype_modules/hisatgenotype_extract_cyp_data.py

src/hisatgenotype_modules/hisatgenotype_assembly_graph.py

src/hisatgenotype_modules/hisatgenotype_gene_typing.py

src/hisatgenotype_modules/__init__.py

src/hisatgenotype_modules/hisatgenotype_extract_codis_data.py

R/Rhisat2.R R/Rhisat2-package.R R/extract_splice_sites.R R/helpers.R

vignettes/rhisat2.bib

vignettes/Rhisat2.Rmd man/hisat2.Rd man/dot-createFlags.Rd man/Rhisat2-package.Rd man/hisat2_usage.Rd man/hisat2_build_usage.Rd man/hisat2_build.Rd man/extract_splice_sites.Rd man/dot-hisat2Bin.Rd man/hisat2_version.Rd tests/testthat.R tests/testthat/test-genome-generation.R tests/testthat/test-helpers.R tests/testthat/test-splice-site-extraction.R tests/testthat/test-read-alignment.R

inst/doc/Rhisat2.html

inst/doc/Rhisat2.R inst/doc/Rhisat2.Rmd

inst/extdata/refs/chr3.fa

inst/extdata/refs/hisat2_splice_sites.txt

inst/extdata/refs/chr2.fa

inst/extdata/refs/chr1.fa

inst/extdata/refs/genes_diffchr.gtf

inst/extdata/refs/genes.gtf

inst/extdata/refs/hisat2_splice_sites_diffchr.txt

inst/extdata/refs/genes.granges.rds

inst/extdata/reads/reads1.fastq

inst/extdata/reads/reads2.fastq

Rhisat2 documentation built on Nov. 8, 2020, 5:49 p.m.