60cc2987ed75135f5ecb375d94502731 *DESCRIPTION
746afdf56b9188557396022c59a4baee *NAMESPACE
6cb9bc8c9a9433bbd92034d21728e256 *NEWS
70af0f3187383e36e6aad7f331786857 *R/AllClasses-Base.R
5842f55629fa2af69289ba38d70c7ab7 *R/AllClasses-QA.R
eef0a9490935362b9eae613b3e8dfb11 *R/AllGenerics-Base.R
af31f6c6087476e7e78974fb375019f2 *R/AllGenerics-QA.R
44e75db4ac7923539b7f96ce9bc9029e *R/AllUtilities.R
6f35988f34fda9c75eb201df097e43f2 *R/Snapshot.R
b5c62ebfe8d903fb4e9a49b44bb9fa65 *R/SnapshotFunction-helpers.R
ea498f18b755ed6ca23b7e463d81c960 *R/SnapshotFunction.R
3001af8e7f3649feae63fac298b85247 *R/SpTrellis.R
03a9d5c7c61259cd79f578414ab57b87 *R/filterFastq.R
5fde7a4699ae254be2a551f802447158 *R/methods-.QA.R
037edc498bfe04379e82ffcb4d3e877d *R/methods-.ShortReadBase.R
f6d8c83bc4c424cdc37cb9bb76d060ee *R/methods-AlignedDataFrame.R
ed0e601b0d02a0a1d0064f715e065d72 *R/methods-AlignedRead.R
383b940b918002f7e79c715cfdc554e8 *R/methods-BowtieQA.R
d7d857b2283abff14e105b6f06caab8e *R/methods-ExperimentPath.R
049e67340ece924374dce35f0fdeef6d *R/methods-FastqFile.R
484b64410f55d443f0098aa3c130a038 *R/methods-FastqFileReader.R
325875fe79099595c39b8dc5967e86f3 *R/methods-FastqQA.R
517606f8d39e69433c397dc2d6deae67 *R/methods-FastqSampler.R
6dbf6743dfca3b622fb8d7cc9cd6462a *R/methods-FastqStreamer.R
18642b19de7504ebf0c3700b748ed83b *R/methods-Intensity.R
4ef7cdd259cefa7e637c00b066e88dd6 *R/methods-MAQMapQA.R
d3300151b2390d723c02eaa98dfd7591 *R/methods-Misc.R
e4392eaac77ca1980bc9f0b45dc9ba87 *R/methods-QA.R
f433a838fc37f6da8166b7c4e78fe2ac *R/methods-QualityScore.R
66cf4a9135a719abe28497a22cba907c *R/methods-RochePath.R
de9ff4003a0be6114ca5e382dae291e6 *R/methods-RocheSet.R
d11af573b124d673f7baeae7f37897ec *R/methods-RtaIntensity.R
0f3a8865aba2f8a69ca125adfe81fc1e *R/methods-SRError.R
0e7a22f51ca5b2f26874862882963a18 *R/methods-SRFilter.R
2f1ab87bf027827e5096319a6bb14c54 *R/methods-SRFilterResult.R
bbc33e879d4a0db1611f9b41e8e4f7ab *R/methods-SRList.R
73f3f0f23a00a58292c9407f35f2ae11 *R/methods-SRSet.R
556a611c6a2a7e3a0d1472def5240fdd *R/methods-SRVector.R
4403ceb79571fa9e1627efb4700283a5 *R/methods-ShortRead.R
44f54697008f2ac545ba1d17c6f58e8f *R/methods-ShortReadFile.R
315b887611ca950dcd0e47c399ad46e7 *R/methods-ShortReadQ.R
138995501baf1e3570be6542926695ed *R/methods-SolexaExportQA.R
157612e951e4f3b4af953620337d2450 *R/methods-SolexaIntensity.R
c300e5bb015de650eee98d036836373b *R/methods-SolexaPath.R
6e0d8011409185e3fd5f44bc66a2bc47 *R/methods-SolexaRealignQA.R
a9ad5a5dc6da87eb78ca78c4516d0464 *R/methods-SolexaSet.R
89f9f74c17d51e5d1addb6104d74aafd *R/qa.R
d0a9d4e71cbab6e23359127c8630690f *R/qa_utilities.R
fb3b10a5b653fcd162a4bd968f8c8dc5 *R/readAligned.R
f01d25160bbf8bd39b22d4882646356f *R/readBaseQuality.R
30de68b0a716889f288b4844c5517fb1 *R/readBfaToc.R
20bc540f36d26c06ccfb1e9eb71e718e *R/readIntensities.R
45023e4957edd7cf20146f220f64064b *R/readPrb.R
55bf55a7640e12e31fb15d51cf4f81f6 *R/readQseq.R
a9ec19dc83b7f658f17c76d021662ebf *R/readXStringColumns.R
7c464db2b0f9958e60bbbae28ee934b3 *R/renew.R
3890c916b85bbd0f69cf2fffe04a7c8a *R/report.R
3e5098fbf98e528e34f6dea2aec5fc8d *R/spViewPerFeature.R
df9fb98cb12c609fed417219c5bd637c *R/trimEnds.R
4179504c19795c9d1857c9b56d08902a *build/vignette.rds
df665c330920d29973e9723a009da3f1 *cleanup
bad36d9aab261950813fbbdc9d9e2537 *configure
b54e22c37592ca971428cf4cb58935da *configure.ac
5642ea95b653f2522af0ba5bad9c85d5 *inst/CITATION
44ac94ff0dc6fd3050b91d09d55a84ce *inst/doc/Overview.R
98c2bba262a276b7986b96f0bc103ede *inst/doc/Overview.Rmd
adfbf0def8f468c99026429c379d96d3 *inst/doc/Overview.html
23770dfd9eb85ab715b4cc28268bbc42 *inst/extdata/Data/C1-36Firecrest/Bustard/GERALD/s_1_sequence.txt
50fe0016d5ff17f48e0d2041ae27d292 *inst/extdata/Data/C1-36Firecrest/Bustard/GERALD/s_2_export.txt
65dcb663231fdd438b35f7f66f4c60a2 *inst/extdata/Data/C1-36Firecrest/Bustard/GERALD/s_5_0001_realign.txt
af1c65c90697ec4f6ff2605c3942c829 *inst/extdata/Data/C1-36Firecrest/Bustard/s_1_0001_prb.txt
5f0ed9bc04c59bd83313e4cbe8cdf6cc *inst/extdata/Data/C1-36Firecrest/Bustard/s_1_0001_seq.txt
5025b5efc80a5a7121cd671a1e29499c *inst/extdata/Data/C1-36Firecrest/Bustard/s_1_1_0001_qseq.txt
215471c66b152b38b50c030b8eec32de *inst/extdata/Data/C1-36Firecrest/s_1_0001_int.txt
906b5821ce3c26326a0feebf14c613eb *inst/extdata/Data/C1-36Firecrest/s_1_0001_nse.txt
9537e5337bde4cfa3b600fffcae8bfc0 *inst/extdata/E-MTAB-1147/ERR127302_1_subset.fastq.gz
7da6d1a8c02b33d3e43a15d418088ec7 *inst/extdata/E-MTAB-1147/ERR127302_2_subset.fastq.gz
3c75c49857ff920db4ad7c611ca99358 *inst/extdata/bowtie/s_1_aligned_bowtie.txt
232629d5251548bf9a502ca7f280b852 *inst/extdata/maq/out.aln.1.txt
f7231ff14e6e59efe3cd70cbda22f2e2 *inst/extdata/maq/out.aln.2.txt
55302f03607b872357393d231232b833 *inst/script/qa-test.R
c6347c55d5bf125e41aa83374872e3b6 *inst/template/0000-Header.html
7cc3caf8396fb1a73007a6d43fe961f8 *inst/template/1000-Overview.html
0a67a22af1fdc06504995cf91ff7c063 *inst/template/1100-Overview-SolexaRealign.html
266198d6f66280f87259c7901258189a *inst/template/2000-RunSummary.html
5ac2cffcabdc88a6b0edf737907e9af3 *inst/template/3000-ReadDistribution.html
56309b4dcaad9a14a2a162f7d1511b37 *inst/template/4000-CycleSpecific.html
64ae7235f64173888da41840bf758b50 *inst/template/5000-PerTile.html
3e17ac6b09ee71640bb52787031deb3d *inst/template/6000-Alignment.html
6ad71e3ba5fc22d7145058b71586d125 *inst/template/7000-MultipleAlignment.html
6e982e5ef04463d6b2655e85cd569dee *inst/template/8000-DepthOfCoverage.html
f03bc6549ffc8e707922a71b8f592582 *inst/template/9000-AdapterContamination.html
767b7cae4a8be39ecf01e3d42410d592 *inst/template/9999-Footer.html
1ecefa60dc28198866dca2b989aced1c *inst/template/QA.css
cd1f28c7f2f16b3a75fb77e8fe93b7a7 *inst/template/QAAdapterContamination.html
4e6c4ecee2935d6411750d964c7ca30d *inst/template/QAFiltered.html
1bc581b2277b65fd2083b24cff8f5581 *inst/template/QAFlagged.html
767b7cae4a8be39ecf01e3d42410d592 *inst/template/QAFooter.html
49790c5d89d5672a288545704910c81f *inst/template/QAFrequentSequence.html
33749d7179aaf6e0c1cfd8e21cae1ef5 *inst/template/QAHeader.html
ed02baf43103ec97ce464a48afdd218f *inst/template/QANucleotideByCycle.html
8c05cf59cba63d7a0f82ac723a729672 *inst/template/QANucleotideUse.html
088d8bb4d91e63c2b73aba067ada22a7 *inst/template/QAQualityByCycle.html
0a9697a0bfef58948d924ff7e5ff26de *inst/template/QAQualityUse.html
e5ebfcf6cdc9d9ed7d8aedc041fdda99 *inst/template/QAReadQuality.html
f06ca05cf9af6432b854ff5c7d05a6ee *inst/template/QASequenceUse.html
781dd0e496f07c1bd30147a4672c6f80 *inst/template/QASources.html
11fb73cf477086fa8d8b036e3b867fb0 *inst/template/image/bioclogo-small.gif
59272f98d70e5b7a024d50e6a836c4c7 *inst/template/qa_solexa.Rnw
775fb1d2ab22c4469320a142652101c3 *inst/unitTests/cases/PE_export.txt.gz
591ffef33bb7cbb7a01221d875609fee *inst/unitTests/cases/s_1_0001_int_head.txt.p
7d4e2884d7ae260d890eb4cbee762199 *inst/unitTests/cases/s_1_0001_nse_head.txt.p
16b2deef00b698bd241e570ecdd3bf10 *inst/unitTests/cases/s_1_0001_pos_head.txt
c4c9f40222b9fe6d281416602e4cc3fc *inst/unitTests/cases/s_1_results_head.txt
3f9c75ff7843a3f9a8ef24fb82fbfe8d *inst/unitTests/cases/s_1_sequence.8_lines_illegal_nucleotide.txt
6bde5fc88cf2cc76b843ee379d52657a *inst/unitTests/cases/s_1_sequence.8_lines_read_mismatch.txt
5c6ace57877560731c3f8accea436214 *inst/unitTests/cases/s_1_sequence.8_lines_read_quality_mismatch.txt
5e9cdace2bfd935d508454b3a2767809 *inst/unitTests/cases/s_1_sequence.9_lines.txt
23770dfd9eb85ab715b4cc28268bbc42 *inst/unitTests/cases/s_1_sequence.txt
7dc84327cf8f61e8e0091358cd702cf6 *inst/unitTests/cases/s_2_0001_realign_3col_head.txt
efdb3e0a3fdc0f75d31dcd635b2dd8bd *inst/unitTests/cases/s_2_0001_realign_head.txt
4c1eac82661bebb0404993709faed253 *inst/unitTests/cases/s_2_export_run_as_factor.txt
af36fb2e8781dff40399be7d03678c5d *inst/unitTests/cases/s_2_export_toIUPAC.txt
c75212a1278b1dc7f06f6b5d83197185 *inst/unitTests/cases/sanger.fastq
bd9f99a60a3e6f02833670b82f8daa13 *inst/unitTests/cases/soap.txt
5935f0094ff6c8e0b73091312c8edf8f *inst/unitTests/cases/solexa.fastq
a7cd71a158c7033dce312e3e3fc0937f *inst/unitTests/test_AlignedRead.R
ba2451c216f1739716065e09eb8093ba *inst/unitTests/test_AllClasses.R
9aabb94ccacf98f9e924a7ea67f11118 *inst/unitTests/test_FastqFile.R
1751f46c71f778ff9c7321f86a846ea6 *inst/unitTests/test_Intensity.R
7520890e2c723080df9c469ef4604313 *inst/unitTests/test_SRError.R
c76e58147669abfc298bfb3c33be7b54 *inst/unitTests/test_SRFilter.R
3f19ec0b57a6205cd299e1533354be8e *inst/unitTests/test_SRFilterResult.R
abfe15e905cfdfd02109fd8bb86e301f *inst/unitTests/test_SRList.R
d03f1bda8212637092948012b511fa13 *inst/unitTests/test_SRVector.R
895c15b844968178d9ba1467a24d8865 *inst/unitTests/test_ShortRead.R
6487af0848302841bdfdae33d963bc9f *inst/unitTests/test_ShortReadQ.R
bbd73177b90388aae680b6ef14c9458e *inst/unitTests/test_SolexaIntensity.R
28ff7428a1d9fe243550378e73d0d7a8 *inst/unitTests/test_append.R
4b7f9bd51b98341f6a74e9bf32b59caa *inst/unitTests/test_coverage.R
3878ed20ebf62a8feaf68c7eb26eed54 *inst/unitTests/test_filterFastq.R
7d507346db44c4dbf33bc335c35e397d *inst/unitTests/test_functions.R
e3315aa7f10257c6475bc5bdbdd7e4bc *inst/unitTests/test_qa.R
83080a9b1d04081ea78d27fd93b1b795 *inst/unitTests/test_readPrb.R
289c8e2f0c2821df49344f231e4e7769 *inst/unitTests/test_readQseq.R
acda1ecb23e81f359a6d848ef435ba80 *inst/unitTests/test_readXStringColumns.R
b81b7db9cb4f2bd428c8c236c8399e5e *inst/unitTests/test_renew.R
3680a10534fbdb7957a224043751b760 *inst/unitTests/test_trimEnds.R
132a346dcd383197636e8722bae670c0 *inst/unitTests/test_trimTails.R
089c7704c6f8806d56ee243bb34e1ff9 *inst/unitTests/test_writeFastq.R
5993e5a7bc28ed9e2787a618cbc0abb1 *issue-10.R
2f259eec97fe5e447d3cb51992e146eb *man/AlignedDataFrame-class.Rd
2b7c3507a57aeee96c7b9b78ffdc5c86 *man/AlignedDataFrame.Rd
29961c558db7650575344f26b14e02c4 *man/AlignedRead-class.Rd
b9a2c034a7c92d9838436a9b9a5cf9c1 *man/AlignedRead.Rd
b074b2b9e8e4e85a0b367d655218e28b *man/BowtieQA-class.Rd
ff7410e62b284f3866bc7e9aed17455b *man/ExperimentPath-class.Rd
09971e8ba2de093cd0cf83db576b1b3f *man/FastqQA-class.Rd
5082bb7cf5eb30bbe13e173b181090b3 *man/Intensity-class.Rd
47d5cc827b8f026684631c7a9ef24f57 *man/MAQMapQA-class.Rd
1173c239cdd758ecd5a6b2d55217236d *man/QA-class.Rd
459cb88436e0a4b36e4ca30c549d4974 *man/QualityScore-class.Rd
4371c8d060d827a9480c1a3a23271f13 *man/QualityScore.Rd
2daf7acf600ed7b4ea5c3191ae7d1dc3 *man/RochePath-class.Rd
3c30b4a74fb6cd51aa4af72ced1d5243 *man/RocheSet-class.Rd
ad0c43f3328711825c3d2c6bfeeaa750 *man/RtaIntensity-class.Rd
d2dedb3edad757bd157dbc23ff71a474 *man/RtaIntensity.Rd
2caa1e05f8eb155383f5b5d7257f3f37 *man/SRFilter-class.Rd
bf78ae6f6ac5833e878bb036bc644425 *man/SRFilterResult-class.Rd
1ebfe280c6696c60b83dde44efa3b43a *man/SRSet-class.Rd
baa80bce0daeca518edf4dfd3f94805f *man/SRUtil-class.Rd
860bed40ca710abc4a26c2d64156e83e *man/Sampler-class.Rd
b926e9999d73807ed90fe9f139581591 *man/ShortRead-class.Rd
eab9696eac60bfe49799f657ea85fc3b *man/ShortRead-deprecated.Rd
f23107320e946393efc81cb09816a193 *man/ShortRead-package.Rd
dec08c74f6a3acc46a1cf56aa42b26ec *man/ShortReadQ-class.Rd
c8bb2f2307bf5e4c88c649a22753b79b *man/Snapshot-class.Rd
cdc86e0ea3407e6dbadccd51d8120fc3 *man/SnapshotFunction-class.Rd
ab79f1ea3a39837cf71b211475a40f84 *man/SolexaExportQA-class.Rd
b99ba37faca3db9d09f23486cdd6a6e6 *man/SolexaIntensity-class.Rd
be82ac1431f402df00f872792ce2923f *man/SolexaIntensity.Rd
d859bc6c7dd52e9efdbf9a18b3e84234 *man/SolexaPath-class.Rd
1eb4eee9398e6d8136c67e16a5949614 *man/SolexaSet-class.Rd
4426bff173e4831475b9b22c0b7fb3e7 *man/SpTrellis-class.Rd
dc427922fc078655c707e306187fd792 *man/accessors.Rd
d6274ce0dedc90faba242c5f50278d0d *man/alphabetByCycle.Rd
bdbb316c70ed56598da5cf40ff1f6c65 *man/alphabetScore.Rd
584dcc6d2ecc23fe0d43c262bf7969db *man/clean.Rd
84286b1768f1b3947a24f5792fc65c1b *man/countLines.Rd
d57862b28bdcc1361edf471e9938d563 *man/deprecated.Rd
dd1725a79c05f2f55af232ac6fe206d4 *man/dotQA-class.Rd
41efad57a5fcaddd4e14796edfbbd084 *man/dustyScore.Rd
c5c7e8a3fcaa0cd17ae228a0f888ef6d *man/filterFastq.Rd
8697c20026c074467ce4fe3f0385aa00 *man/polyn.Rd
3f30ac1cfb92c622c9b2baecb200d54e *man/qa.Rd
872b3518c77b95140795095d378dce60 *man/qa2.Rd
0bb3fc6335c0bc7ec2d3737b4a57c1ba *man/readAligned.Rd
e0faddf219c15079f73499432ac0b9f7 *man/readBaseQuality.Rd
d47364814e7a8f92dee0cf0632d53d00 *man/readBfaToc.Rd
a0f8c92177286bd9474c56cf7a4fbc7b *man/readFasta.Rd
5f7c2cd8700e77b14ac17ec953b34a57 *man/readFastq.Rd
a159a11ee5a470a03b60ce4de183fb6c *man/readIntensities.Rd
189dfc2f66cadaa6762f9a54f21baa44 *man/readPrb.Rd
016fb147e6994301db94926261a94271 *man/readQseq.Rd
f289e1c54990518e87a5a37ab5430c93 *man/readXStringColumns.Rd
05defeb0c8e4e1a5bd7f7f7f3a4b1231 *man/renew.Rd
1739215f8d29675ea79f7361c6d8acfb *man/report.Rd
be2ae8a28c5d857308aa814841162404 *man/spViewPerFeature.Rd
b9c0348e106eff279480250a08113cd3 *man/srFilter.Rd
98d400bd15120c6562463b3623e88231 *man/srdistance.Rd
7e0c53db067fdd75b58812b203fee5d8 *man/srduplicated.Rd
e9a88e179024065b16579573c125e6f7 *man/tables.Rd
e736df5115207cd480af363b5e9c1535 *man/trimTails.Rd
f1f4685a8f0afb74e19c344a86d86b22 *src/Biostrings_stubs.c
b0447144238dce005a1fa8a625d1563c *src/IRanges_stubs.c
97dc2d350ba214d976cdfdfbe8984996 *src/Makevars.in
8279f90e79c7abf2e4ca1a52d0156e2c *src/Makevars.win
6f9c7f06240c68b1dce2a295753137e3 *src/R_init_ShortRead.c
bab0b4b09cf160fa0109ae25fbb471ef *src/S4Vectors_stubs.c
c8f439b91dec8228881be598478bd45b *src/ShortRead.h
07fbf9ef7d1a296302e6de26aa821a44 *src/XVector_stubs.c
34287f144f1c8ff5b4b439fddf6a97e0 *src/alphabet.c
350d23e71bb66548d8f9eec5ae4c4621 *src/call.h
a60ccfcdb29b5ac97c8f2b3893718074 *src/const.h
09252d756b0ad2c256fa5d005ca99f98 *src/count.c
7d10e9bed16576a9f5d29d216c805c66 *src/io.c
6f286f12599f01b771f364be55a568fa *src/io_bowtie.c
0977664342065f7748e262d580037765 *src/io_soap.c
1e10e5d26e917fe6c216dce167a3ab40 *src/maqmap_m.h
5c845a026f26fbd4290308ce2e1f7ea5 *src/readBfaToc.cc
42730b486de811d536344ed41b66b2b3 *src/read_maq_map.cc
acda28f5358091f964c7b5fdf1826b4b *src/sampler.c
428b1c6cd8fe21f2645bc09b70c713f4 *src/trim.c
86fd73026569cb006e3db4359e83df16 *src/trim.h
b9458ffc1006ce77d021b2d5d37542a3 *src/util.c
177b293338336b6c75e254336b1af653 *src/xsnap.c
8eaaf14c584be7b51acde5e5601401df *tests/ShortRead_unit_tests.R
98c2bba262a276b7986b96f0bc103ede *vignettes/Overview.Rmd
7913edefa77255a6783534776062b4bc *vignettes/README
770185fa1979baa2913a0c930149abd4 *vignettes/ShortRead_and_HilbertVis.Rnw_
0ae89572ce175d8afefe7d7d6c9b0700 *vignettes/ShortRead_and_HilbertVis.pdf
515221810054ddeb635f967913cf992f *vignettes/hilbert.bib
63fb6ea8cd401802ca5061893269f033 *vignettes/images/HilbertDisplay_GUI.pdf
b83363803120fc34f84767dada820653 *vignettes/images/HilbertDisplay_GUI.png
ae58cd0f268c13b69033405c5120fcf5 *vignettes/images/HilbertPlot_H3K4me1.pdf
5b208d3ec4b026dad23841abb39a5984 *vignettes/images/HilbertPlot_H3K4me1.png
6738bb5919ad56b79daad987947b63e0 *vignettes/images/HilbertPlot_H3K4me3.pdf
a41860f3e2969b11698d3343ccd1dccd *vignettes/images/HilbertPlot_H3K4me3.png
8e50b2de8cb265a2b168bbc797f9307b *vignettes/images/Strand_and_Dir.pdf
517f309c1b9c3f094b8df6b73a75fc70 *vignettes/images/hilbert_3col.pdf
87211753f755efffefd383540d415c76 *vignettes/images/hilbert_3col.png
56a92730e47788da2babbd09ace554c7 *vignettes/qa_E-MTAB-1147.Rda
154e14137ebd674b290ed0797610a054 *vignettes/simon2.bst
