e289d7f664162b06a39eb382e9ca8585 *DESCRIPTION
c2388f1e69de1b74a1b9c12131486814 *NAMESPACE
b6821ad485b2f4a5735f1e622e3b0e58 *NEWS
3767706473247547540be8dec5b18fbf *R/AMINO_ACID_CODE.R
acadeb92f84cbd9a3a2fee69c71ca01f *R/GENETIC_CODE.R
a524a99d1af44c3982c0ac841e55ff78 *R/IUPAC_CODE_MAP.R
794f34fd20087b0aca2dffec19a7d852 *R/MIndex-class.R
6dc24095345319dfce6443330cbfcd3d *R/MaskedXString-class.R
f36aad6d517f698eede2c476ed5d55ef *R/MultipleAlignment.R
62d84098fed254df624859fcdd1b0665 *R/PDict-class.R
24cce66b88b55b27e4dd7ffada6dfd62 *R/QualityScaledXStringSet.R
d7c9c2718d099e00988978f392b587cd *R/SparseList-class.R
3c38710c35506b2ab491fdc806cd53dd *R/XString-class.R
db67a4c9f6689111bf3a5428aec614f5 *R/XStringCodec-class.R
73d3c248647996376af601a646d513f0 *R/XStringPartialMatches-class.R
11eff2e73bcd43ad36554ccad71ace0d *R/XStringQuality-class.R
ff7c105494abe50638b1e1fff4c8fee4 *R/XStringSet-class.R
985998cde8df8be59637722353a0081b *R/XStringSet-comparison.R
fb9028a29dfbd49fc7604714a98f661d *R/XStringSet-io.R
458562d816bf830fd7df54080e31bb74 *R/XStringSetList-class.R
55a440cac213acb681947e2ef4e8f41a *R/XStringViews-class.R
0a7c1886456c9858da3428b51bb45ab0 *R/chartr.R
023563dfd14f6c32fd5dff3bc1b79eab *R/coloring.R
f7fdf9356065dbdd9c3bb9176fc67636 *R/dinucleotideFrequencyTest.R
edd180481b8d16b59545784d5f52026f *R/findPalindromes.R
0ba06cf4e43fef62f48a54231515cd9a *R/getSeq.R
27c2245d6c97c1e350fc610adf15d3bb *R/injectHardMask.R
5f0abf29e728af1dc74586eff0cff944 *R/letter.R
eb85b39257aae88abf66acd4a01970f3 *R/letterFrequency.R
f73da3bee343bf4b354d626f9a1fa4d1 *R/lowlevel-matching.R
d449d34cf6721a75a1003211b7f655a0 *R/maskMotif.R
023767530896a0c3bbefdc8feaeeb97d *R/match-utils.R
554c48b3ef0bfc9e95049de76ef95fc2 *R/matchLRPatterns.R
ef2ba9da87974dfe4351de1eb92333d9 *R/matchPDict.R
2d46d1cb3d6529f02af12ba9a2f131cf *R/matchPWM.R
228789eec5f3d05b2592a9782e6520c3 *R/matchPattern.R
fa47fb1ae253736d736ac24e769586a3 *R/matchProbePair.R
6608c65b298946a27911e16231365097 *R/matchprobes.R
2a2b619c096894c377b6e683fe1e7ddc *R/misc.R
fb0a8cdda2c80376dd646f9b5491397b *R/moved_to_pwalign.R
82de450c1bb361b8fb52a6d121aa27c1 *R/needwunsQS.R
ded43386f6162e95c86e60b64dcb552d *R/padAndClip.R
f11ba442ceaa39144c84060f24354bc3 *R/pmatchPattern.R
ceaa1e7baa75369dacb6435953bce5e6 *R/replaceAt.R
1e3e6a36ee39d28b4e192228b217b5a8 *R/replaceLetterAt.R
48888f11d2abbd9df19d175741037f0a *R/reverseComplement.R
baf7fef7e8a7c191c36a5d9348f3dbbd *R/seqinfo-methods.R
5109b8cee9ead170bf97023e87154a88 *R/seqtype.R
3ccd820ad31e58d08ac9d5880e53b6c9 *R/strsplit-methods.R
b1e78bf53882f403c4aa79307302c2a0 *R/toComplex.R
2853a8d9c1caa4072fcc9bc811031b37 *R/translate.R
ecd3903d7c85744f5e1a46dca42dec4c *R/trimLRPatterns.R
0ce0183f156d1f20b61f27c3ef5bc04b *R/utils.R
4477247ec0fe4f241dab2671552d58b4 *R/xscat.R
6a9c5e9ad4e445a7bc7e09526f2194da *R/zzz.R
8da387ddb8ca8ada8edc516ec13f92c5 *README.md
1ea01a92598d4424d134c8593608a556 *TODO
86e3323effb532ab142515272806067b *build/vignette.rds
441b87511bbfaea649eeddd3d4212c8e *data/BLOSUM100.rda
c7ae01c201f35890c59d6f62245420de *data/BLOSUM45.rda
01aa6e8033e6bf55f154f1defd2bd24a *data/BLOSUM50.rda
6f0b46abeac2afd6dd16bf51653efa10 *data/BLOSUM62.rda
a21a0aaccf40d218de51f1c0f1ce7539 *data/BLOSUM80.rda
4bb649b15a1c70fdc6beb4ea37ca8d58 *data/HNF4alpha.rda
a94e88f77afe478396b8d80340cf1713 *data/PAM120.rda
e29224d302945e3c48b40e1f910672f2 *data/PAM250.rda
313e58bed938d7d51bd164d5671681e0 *data/PAM30.rda
8791e84a693566bc6b95dc4f24936852 *data/PAM40.rda
6029c9d4f1d67f91615db1c0217178d0 *data/PAM70.rda
e566417a897993c19e4b81e517778b6c *data/yeastSEQCHR1.rda
d2e048a4811776d76ac83a3eefa224e3 *inst/doc/Biostrings2Classes.R
d7f69eedb9db937ef0b727cd1d558b8d *inst/doc/Biostrings2Classes.Rnw
7ad81a4a6eb82d6a4acdd915ba13937e *inst/doc/Biostrings2Classes.pdf
914c59556f47bccd6cd6ca993e5602a2 *inst/doc/BiostringsQuickOverview.Rnw
ba8f47da591fcf5de32648adb8ab630e *inst/doc/BiostringsQuickOverview.pdf
9522b2668945e9ebe526be27fc5ff60c *inst/doc/MultipleAlignments.R
6b16dd26215cc04bcf6740ac4ea71eb6 *inst/doc/MultipleAlignments.Rmd
9d1701cd5d6e9e83300149f872109c19 *inst/doc/MultipleAlignments.html
d03120926755c6cc3dce7540bfe729ae *inst/doc/PairwiseAlignments.Rnw
5b261ed6784c7de6b44f613367765e91 *inst/doc/PairwiseAlignments.pdf
653147def9a6c371aaff27859c98bd42 *inst/doc/matchprobes.R
45f77251e91f040403c4b3f3b0f67d3c *inst/doc/matchprobes.Rmd
d085ad085566179f1adfe37fe7b49a06 *inst/doc/matchprobes.html
78e8db3ebcbc095287e6fd8ccfe0e1a2 *inst/extdata/Phylip.txt
fce14be25eab8521b6ee474b4c36a7df *inst/extdata/README
24604bc9ec4790d5d590a623edea5548 *inst/extdata/Sc.fa
1a6fe1b8caec191eb16265cc5b1d7563 *inst/extdata/Sp.fa
11861abec072717c887a753e28f05f56 *inst/extdata/dm3_upstream2000.fa.gz
cfea9d61b851d60768c0751e17ab9937 *inst/extdata/fastaEx.fa
c4114941da5b3499beff7b3f87c84166 *inst/extdata/hg18chr8_gap.txt
76897b4820e1ed23b787a171ae4d3b5a *inst/extdata/hg18chrY_gap.txt
3f5e79e34a204b72bb52b2e5d2b79f19 *inst/extdata/msx2_mRNA.aln
23770dfd9eb85ab715b4cc28268bbc42 *inst/extdata/s_1_sequence.txt
6210f3d073b676bc7bed60172a72c3e3 *inst/extdata/someORF.fa
2fc0b8e9625d6ebebf8fca9cb7737ebd *inst/extdata/someORF.fa.gz
018adb74d849e8af2c0137070a885e7a *inst/include/Biostrings_defines.h
6cd7a305bab4ec77eaa03fbb356b1516 *inst/include/Biostrings_interface.h
d54e5d2d6c744c489a5f871d079b62d2 *inst/include/_Biostrings_stubs.c
16f044e2cdb85f2d44f501610554df57 *inst/unitTests/test_MultipleAlignment.R
1437c2c15ae9d298a46c40bdc46455f9 *inst/unitTests/test_XString.R
5a4fe6582d86f20f68c627d1efd511c0 *inst/unitTests/test_matchDNAPattern.R.FIXME
62d897d440c6daa94f020fef0857b89a *inst/unitTests/test_seqinfo-methods.R
407a2929d7f9fce74bd30e731a492477 *inst/unitTests/test_twoWayAlphabetFrequency.R
20b18c4a8cba0dea8284e32c1172d70e *legacy/CHANGES_Biostrings_2_vs_Biostrings_1
4fcc6eb7667a2be633cbb264c9d6ce91 *legacy/rgrep-tip.txt
e729bcd364ac85f16c9a8f8eb373eda5 *man/AAString-class.Rd
5e5ad86dc570b91d327b9d83505b29f7 *man/AMINO_ACID_CODE.Rd
0203fbe055852cba742756721236436f *man/Biostrings-internals.Rd
bc22a99689875866f580703a631087c6 *man/DNAString-class.Rd
2e9adaf389adb192a86194c4cc9d2a11 *man/GENETIC_CODE.Rd
beb20155e6e4d2dc6b00b726bb634bda *man/HNF4alpha.Rd
f648dbb3de0af8cf5f88261293bf83cb *man/IUPAC_CODE_MAP.Rd
2f621538c5c8c706009d3543caa85c35 *man/MIndex-class.Rd
dd6c8713b218a920b4f0df8525b63158 *man/MaskedXString-class.Rd
d39e151ebdb80fa975a6da4472a78c62 *man/MultipleAlignment-class.Rd
b10b691835827e834afd15118977b784 *man/PDict-class.Rd
4b5555ac3361f49477e04e8548733925 *man/QualityScaledXStringSet-class.Rd
dcfc58404a98b9cc66f2aa2f51f616ff *man/RNAString-class.Rd
6651662b1a3a8bf360d0fb1a0b0c72f6 *man/XString-class.Rd
42b31b828aad065d9ce3beaf30f5a6f0 *man/XStringPartialMatches-class.Rd
d3e3d5bdebaf88465d3fb62064e9b0d0 *man/XStringQuality-class.Rd
2dcbcf328551e93434603a0b31b4796f *man/XStringSet-class.Rd
a19306f477c125253327f44625b1f158 *man/XStringSet-comparison.Rd
7cd7b5433936721db9798a9cdfe8bf21 *man/XStringSet-io.Rd
f52a85b16f775710376333c159fb2204 *man/XStringSetList-class.Rd
dbeab6ba45b3139723e05c1728dbdfd1 *man/XStringViews-class.Rd
7d295c53a4b99186ffcf797e51053f86 *man/chartr.Rd
727bb87cc465d16c427943abd6c99824 *man/detail.Rd
5f781a6b008b9d83d820a932f4054baf *man/dinucleotideFrequencyTest.Rd
f5a7b03a7ef4ff284f9eaa1a0d51b137 *man/findPalindromes.Rd
8794675d5cf141a7e05c1652b084f037 *man/getSeq.Rd
fc4f6959663e8576933307f096b3969b *man/gregexpr2.Rd
539ddc28efe9696bdadbccd09720d1e0 *man/injectHardMask.Rd
5fd3c56146c808cc910e4569b7688a93 *man/letter.Rd
d1a611948aee94fe303f180e11a41ee5 *man/letterFrequency.Rd
74df42d37dd3aedb8b64b0ac2c12a914 *man/longestConsecutive.Rd
37c401e38b13870ba44a1f007f1fef1a *man/lowlevel-matching.Rd
2d2664836688d580c39b3e3e567e5e4d *man/maskMotif.Rd
d70f98a26a6bd1af38d9f9c3e00b11bb *man/match-utils.Rd
178c7ea52bd620224d6a22faa4307494 *man/matchLRPatterns.Rd
5764d39c7a814d75b674f7cc93540945 *man/matchPDict-exact.Rd
74134d0f1959ba038f20ef0d5b649651 *man/matchPDict-inexact.Rd
45a8242cf1d4f0215b21b966561010e8 *man/matchPWM.Rd
83e86039b00bd5084eb6f8dd6c593709 *man/matchPattern.Rd
c40f0ac303d980856a90407e9be82f29 *man/matchProbePair.Rd
7e449f574876abd79e6187fc7f7d326e *man/matchprobes.Rd
a9f3be4b428467cf5a632c8f11de4461 *man/misc.Rd
9cd7656e37531e0f35e596c40e85d017 *man/moved_to_pwalign.Rd
0713a1ce08b62ed2e98b5afb574e5a3d *man/needwunsQS.Rd
aed2b722e8e09d63fb8b2820876d4af5 *man/nucleotideFrequency.Rd
8bc66c8aca209273deb5783a6ddab96a *man/padAndClip.Rd
9bf58f269a2568df90dc0a68674471d7 *man/pmatchPattern.Rd
cbf7551b10a9baa9764f4017d9b7612f *man/predefined_scoring_matrices.Rd
6a0a6f55c0b495bfaa75f5bf44d0f333 *man/replaceAt.Rd
784b72ac6e82de38120c9b0f017bb7cb *man/replaceLetterAt.Rd
b94ebc6c42c9b3514164d747d77fb0ab *man/reverseComplement.Rd
c1ede396c48ed685ea9cdd17c79c4677 *man/seqinfo-methods.Rd
60964f2085a1ae9002505db2830431c5 *man/toComplex.Rd
b644ecdb3926275d84a2911cc106a6eb *man/translate.Rd
551079253e0130101ce1e3c4364b95af *man/trimLRPatterns.Rd
bbe8b24e23563b358bd816c20f606fdc *man/xscat.Rd
0e8b29e517a35d1a0f2e09589d430030 *man/yeastSEQCHR1.Rd
73371d7927a120a44655a04e8e001fa8 *src/BAB_class.c
d0ae3257b9264aba1c5bc69c74d8aba2 *src/Biostrings.h
823fedfc4dfcff7f8768b9bd0aab9079 *src/BitMatrix.c
b0447144238dce005a1fa8a625d1563c *src/IRanges_stubs.c
deddf0409ead20db1b088677c99d2139 *src/MIndex_class.c
18f5e7a808c9e9e7edbb3ae6c2fbcbf6 *src/PreprocessedTB_class.c
6ed3649bd2a954ee7d9030d6cb601a9f *src/R_init_Biostrings.c
b7f2cec8a5ca5d8e98c1fd2b5a189657 *src/RoSeqs_utils.c
bab0b4b09cf160fa0109ae25fbb471ef *src/S4Vectors_stubs.c
56cd0cb62db491b814b6a8f766eabef4 *src/SparseList_utils.c
ca0aa90d1c194aec8015cf4907af6007 *src/XStringSetList_class.c
8f18b99309c38800ed8466422af4b854 *src/XStringSet_class.c
d9cc9ad52f999bc1c87ff5b3b428114d *src/XString_class.c
07fbf9ef7d1a296302e6de26aa821a44 *src/XVector_stubs.c
c602fb8cf8b36570331e51b0ddd432d2 *src/find_palindromes.c
56e0d09bf0b4b5e375fcfb9561e254ed *src/gtestsim.c
1086178ce353a876ca3d5e11557fa0af *src/inject_code.c
68ab53654734519946216736903eb7cb *src/letter_frequency.c
57d6d1cd41733839f49e081e316f04fe *src/lowlevel_matching.c
7fd8d92887db38763411e5fd14ea41c3 *src/match_PWM.c
6688280e0dcde10598400a196bd2de6e *src/match_pattern.c
45699c371ae782de7ae288fcf5d61548 *src/match_pattern_boyermoore.c
5862ee121eb67c942110d5b311ae987e *src/match_pattern_indels.c
4dbffc10dd966af56ed20a78e035bf63 *src/match_pattern_shiftor.c
c686c66f33c8ffe3a101ad6d29f4dd6e *src/match_pdict.c
e02fe796e48897e02ba1dbddf689ca60 *src/match_pdict_ACtree2.c
7afe974adbdb9fb197649f183733f387 *src/match_pdict_Twobit.c
ca3b1b293c436f2ffcb87cd69bf7a16a *src/match_pdict_utils.c
6953c7914b57856bc9c680c7b7445e9d *src/match_reporting.c
25a4cc378d4d6036790890d1847f63fa *src/matchprobes.c
639bf7ad015dc41dcd8483177e41ab2b *src/pmatchPattern.c
7d69292ea107c370c1189648ef89ada7 *src/read_fasta_files.c
688a9b6e201f2a8b7e525faac663f170 *src/read_fastq_files.c
db65836c4cafae780225b08dfa1de343 *src/replaceAt.c
4cb337c3be55577116e8107690c72c7e *src/replace_letter_at.c
4060dc05e4df1e727ec0268a773f9ee0 *src/strutils.c
adda9dc155e8333e2dc12fc115891d29 *src/translate.c
4e065fa98bcef34b1d3c396a102c93ad *src/unstrsplit_methods.c
019dcff69462f91782cf2e238540dc98 *src/utils.c
8ddb0cacd4cea08c40f7e333c56491a3 *src/xscat.c
f4142a40ef41b9bb0a1c7c21beab277e *tests/testthat.R
905a35784f0969c07b1447cdeae5c4f2 *tests/testthat/test-MaskedXString.R
8a2f720fbc3877c33e2504d40c8a0547 *tests/testthat/test-OtherMasking.R
12a1e98e4dac7765b2d62aa91b5fcc16 *tests/testthat/test-PDict.R
2d189559f5cdf4aca2753994258ff828 *tests/testthat/test-QualityScaledXStringSet.R
77420150dfa54c3a622b72cff4b3b7da *tests/testthat/test-XString-class.R
d94ce0c6e17b4f1ce8a52d993db4dc3c *tests/testthat/test-XStringQuality.R
b723c2d22d15598c643937c4055a561c *tests/testthat/test-XStringSet-class.R
7d93ba4ad3c4a5cbf1355b7dece0e325 *tests/testthat/test-XStringSet-io.R
1114709e7d3380ba0d459c4ac86ca939 *tests/testthat/test-XStringSetList-class.R
b6dc00f913caaf1fa5ea74695482186f *tests/testthat/test-XStringSetList.R
bc6ba987b20e092d11eb3197a03abbc1 *tests/testthat/test-XStringViews.R
9a495865bb4dd7dd4ed80ac827a2d3a2 *tests/testthat/test-chartr.R
cb567a5b3eb83c5eb443e851bfc75ee6 *tests/testthat/test-dinucleotideFrequencyTest.R
aed165440757b6110150223613b9f561 *tests/testthat/test-findPalindromes.R
4548a0b9a4ade473cf9bb6f387ee9992 *tests/testthat/test-letter.R
5fb5ace3d72fb1a44350c8dd60896383 *tests/testthat/test-letterFrequency.R
5d14c979d742a61585d77426d61d514b *tests/testthat/test-matchLRPatterns.R
9ce01b50c6b8b2e35c7f449732882cc8 *tests/testthat/test-matchPDict.R
58dc48ab6c82fa0c70d68b3f2a69c5a9 *tests/testthat/test-matchPWM.R
91d08eb86e5e16dabbbcb0eaf0ec9670 *tests/testthat/test-matchPattern.R
7bfd33eb06f8342b9a68a086090df61a *tests/testthat/test-miscXStringMethods.R
e5e2eb6b9bc92d448816e47f41e91f59 *tests/testthat/test-miscellaneous.R
19439be6182d8e31bb90f40bc66f2e8d *tests/testthat/test-replaceAt.R
7eed2803431b5db7d885a9e79d41e6de *tests/testthat/test-translate.R
2f1c552b2ce95ebd5d2594fc5d576fde *tests/testthat/test-trimLRPatterns.R
d7f69eedb9db937ef0b727cd1d558b8d *vignettes/Biostrings2Classes.Rnw
914c59556f47bccd6cd6ca993e5602a2 *vignettes/BiostringsQuickOverview.Rnw
6b16dd26215cc04bcf6740ac4ea71eb6 *vignettes/MultipleAlignments.Rmd
d03120926755c6cc3dce7540bfe729ae *vignettes/PairwiseAlignments.Rnw
e2e656ffec899c4046cef4cb8d8aa885 *vignettes/SolexaYi2-benchmark.txt
45f77251e91f040403c4b3f3b0f67d3c *vignettes/matchprobes.Rmd
