8d96bb0582bb7105a2da94093cd2ac34 *DESCRIPTION
f5487f0e90e411fc5c3be3a1f6d503a5 *LICENSE
6ccbb6676194a8b9d1ccbc97fdd54ffd *NAMESPACE
18eedbe59310ead852ce23d5536af830 *R/bwa_aln.R
994f3da23e1c3351ed74665a9ff8b8cb *R/bwa_build_index.R
2673f0279fd499dfd5920a089335e31b *R/bwa_mem.R
1d2233a97f480ecb671a64dd7e40ea14 *R/bwa_sam.R
9fd3dc9ae24ed369eb43adfb08581963 *R/utils.R
2fd6f10be251a7f9a3c3999a2014394e *R/xa2multi.R
60e07f6e954513993313405fddd4f9c7 *build/vignette.rds
67c3a39047e878fa37afed5e35391bda *inst/CITATION
69f46801893cc0eeb53a64e3ae9dab50 *inst/NEWS.Rd
671733890120dd52e3d5240563531036 *inst/doc/Rbwa.R
be564a767602fdaa130e6116469e57be *inst/doc/Rbwa.Rmd
a5c6fe0f343473b8771ec579a92079ff *inst/doc/Rbwa.html
12598328fcee8e39246d0f775d9a8cc9 *inst/fasta/chr12.fa
a0e549ffe6ec1da08b2c82d168af66a4 *inst/fastq/process.R
c134b7832ddd8a2a98581528f29d44bb *inst/fastq/sequences.fastq
eb9060ede4ed057f9312e647ddfdee32 *inst/perl/xa2multi.pl
c27f680ca7d46a9f81ac77f0a44fdea2 *inst/reads/readme.txt
ae9e240ded9c25df4c55563b05ce62bc *inst/reads/reads1.fastq
a5ddc38c50d11073fafdbf33c152fe6e *inst/reads/reads2.fastq
e4e9ca675a0f6a0073f66b3439561794 *man/bwa_aln.Rd
91ff8c3bb6db345557c3c9a8a78de1bd *man/bwa_build_index.Rd
c8b4c7b790d89beab3c19aa7a79cdb67 *man/bwa_mem.Rd
b4f08fb0ef3c441202639387dbe69a76 *man/bwa_sam.Rd
db6034fdd104931ced62397682ce15dd *man/xa2multi.Rd
d32239bcb673463ab874e80d47fae504 *src/COPYING
c041b1a857e7d04e0b5b4e596ff24e96 *src/ChangeLog
1345dc4029b3d709535eb3b8f1e41b38 *src/Makefile
c216d281e80eae475a6ebe55022e0cab *src/NEWS.md
36d2262b44ea4dded33ac06c9ea5f041 *src/QSufSort.c
38c702d67ee01d6d11dcf7992241114f *src/QSufSort.h
3304f10b3275da2a3284c5673d7316f3 *src/README-alt.md
4e7df80c82624b1d654e5651939888e0 *src/README.md
82ade9fb90e4dcd52a10158b3128c9f3 *src/bamlite.c
e42620cd21a572d93ba121ee90fcec7c *src/bamlite.h
62077796a3784b215ad7213c235239cc *src/bntseq.c
6b0bf3860d426f577bb47bc6c79bab45 *src/bntseq.h
f2b29293b436fbc05f3ab91cfb995d99 *src/bwa.1
e812f059a2d50c1dff008d923c7a55aa *src/bwa.c
33951fee205281949c8ce9b0ab271ab0 *src/bwa.h
b45bf76dc085adeea4bce8665fcfb0e1 *src/bwamem.c
56f2c5e0faca802056290d8ebc9b3dfc *src/bwamem.h
f8b53744431776328b4ff75b9ac4275e *src/bwamem_extra.c
854b39c987ab89b5cde10010b2075a95 *src/bwamem_pair.c
f7213385aff2fd261a7957deef1b69e1 *src/bwape.c
2f9a35f92d72722d8ccf0cb7296d8085 *src/bwase.c
7a4e82c23591c11b798b4babadbb266c *src/bwase.h
56c16c0e75e9b47942afb63b04abfeb0 *src/bwaseqio.c
b4199a5605351a572e471728b2301795 *src/bwashm.c
2ec65ea1082bb843ca188211e41af353 *src/bwt.c
9ffc9aabcc3ca1e851152e683067ba09 *src/bwt.h
612b42e13c2dc31a51ea52a4c0969305 *src/bwt_gen.c
893d910f7311d4ba993cedb0a64de883 *src/bwt_lite.c
a65db83539995b7a426dde5b2753a559 *src/bwt_lite.h
31fd5ec11018183059fd203225078629 *src/bwtaln.c
106e4c7b6db2ffd60f0656c78f1c7465 *src/bwtaln.h
33bead40a2c00abc78aa12f38a34f63c *src/bwtgap.c
899bfa6b3e4a1118ed3d1ed0b29f79d9 *src/bwtgap.h
871715b90fde89d160394643a759418b *src/bwtindex.c
5eadee6c107f2228292426aa7b5a6294 *src/bwtsw2.h
dec2cc5958cfc9512dc33a409f06d395 *src/bwtsw2_aux.c
ee48531d1571f75bf3807f2d67112942 *src/bwtsw2_chain.c
535e3c02b20d6d509ab3d96ece8c7cf9 *src/bwtsw2_core.c
123798aa8048c1afd29e00f90ca9a12d *src/bwtsw2_main.c
34b6f1cd57ebd527bde8b24eeb1a844a *src/bwtsw2_pair.c
cf46e7af7f164667cf30790c07c0426b *src/code_of_conduct.md
e1cb4c8a1425b77f8978908a69ed27f0 *src/example.c
7a5103b261b63d0d56df12628723a76c *src/fastmap.c
a1a207d13077cd17dc84580a617047c0 *src/is.c
c60cfa13d9bc288059fc5fe5e5f9b25b *src/kbtree.h
19fca2565070a4704e5ca8e8a4fd7647 *src/khash.h
82e85a9dcdda4b70a757b782368c063c *src/kopen.c
20515954b629494051a5372397a73b32 *src/kseq.h
b5c723a6a29bfe8aeb6005f01b278b9f *src/ksort.h
580fcb0e142a8109ab3bd92d9ffa0cdb *src/kstring.c
ade30b0d72236ab9a1f02b5e5f8cb83f *src/kstring.h
2e36541a66f3a85aaf292fe72ee29aad *src/ksw.c
dca02f13f42d053edb54d178fd8911f9 *src/ksw.h
4b01a46fca12e949ee504b5db3b6fb30 *src/kthread.c
27efd5dc62af6b38c45ff50b2b9beccc *src/kvec.h
7ea70946f8535a2ac1087685a9eb9214 *src/main.c
4c7eac0df6fb73eb98cde8081f4e288c *src/malloc_wrap.c
9e472add66586a775ea949c4934c5d82 *src/malloc_wrap.h
eebd688250847e7e61a0a678c2aa3342 *src/maxk.c
64169fd7d5e8cefda292dd997266bc98 *src/neon_sse.h
61f10f3b9fed5dc86a83d8f6ae0ac51f *src/pemerge.c
492e8656e0ccb5a1f3cf7f515dabafc4 *src/qualfa2fq.pl
700ba029cc89a0839f5456045cddf8cf *src/rle.c
b4a559400b7ca652aeb77bc566b3cb8e *src/rle.h
505de81a3b663055e1a9a2e2a0a5a865 *src/rope.c
71790cd06ae3bd46515fd92edfacbb30 *src/rope.h
a6a3d555318fce01cb210a627c7f6a93 *src/scalar_sse.h
40abbf780b98ed017ff240d3333c890d *src/utils.c
f9fec3789cdf6b4acbb6ad1d0689e09e *src/utils.h
4b84eac3748f735372d7440f596fbfba *src/xa2multi.pl
94005acc98fa00afd30486cca42c9bd0 *tests/testthat.R
3080bc17fadd6264247af811dcb60219 *tests/testthat/test-bwa-aln.R
11f34116ee057c9324122502f35e24ec *tests/testthat/test-bwa-build-index.R
7832e97ec037a3fef6e0fec621f56f2b *tests/testthat/test-bwa-mem.R
d0c6152da31d58cfd971e25028efde20 *tests/testthat/test-bwa-sam.R
be43a79f00ffb00f500c0ec6ee906f4b *tests/testthat/test-bwa-xa2multi.R
be564a767602fdaa130e6116469e57be *vignettes/Rbwa.Rmd
9041a6e76bb6c7543aaa3adb04db9a4c *vignettes/refs.bib
