d53e447598f6b00ad92955f8012f443f *DESCRIPTION
e1736ab0ba84a1d7fff71c14fd699da0 *INSTALL
8adf14a998733081b8a038a0de48899c *LICENSE
ba6a5aa3204f4422364f24541fde709f *NAMESPACE
14b7838922ae4c06d3da4777995c530e *NEWS
53f4713655c2ae3d6d9f1ac2c3909574 *R/bam.R
607dee9a05706e15d235fc046af8c4c2 *R/bed.R
ec9d4c3df84b41e8ebf812369c286729 *R/bigBed.R
998266c9153b1d3a71fb0899bf31eaa8 *R/bigWig.R
46fc727ec5ab7d5da34ae0fe056e912b *R/browser.R
5db88800ecc8977b4abea75fbc134b55 *R/chain.R
14c05d4aade1768a2b80124fb3de05ac *R/fasta.R
210e2f319fba6d55faecbb1333edb7a7 *R/gff.R
3c26b0ab2666feb3b80b9118e4623709 *R/igv.R
a7ef1fed3313ff15850b37f36cd4af9c *R/index.R
a502abd7a5f88bb3be937d00fb893926 *R/io.R
8132aa8d42e94b5d5737b4b8cfabe900 *R/ncbi.R
f9d59c90d99684deced6ad7c2a4614aa *R/quickload.R
8c64fd1ddb26a16e6966087cb87ada06 *R/ranges.R
07356c22720e87b9e38edfd3f58d525c *R/readGFF.R
02f417ecbfe06f77ddc24eddb4c0a1ff *R/tabix.R
ead92bf0177f6085a5fa0611cef09755 *R/test_rtracklayer_package.R
e9f89d88f066437ea580fad49af49a45 *R/trackDb.R
a19878a8c574d5a7a4aeb0a040d5209c *R/trackTable.R
cfa9c993f84421b5a4eee39ae0f72568 *R/trackhub.R
364e671c4bd78cc32c1ca4bcdd42a196 *R/twobit.R
6f98beab97b207158eddc3ae30af65f9 *R/ucsc.R
30f9b21a18d4b6cfcf9d4e0d4dc9e78a *R/utils.R
a63ec50a72b655531bc666cc4d0d4606 *R/web.R
b8f60df639b4e616ad9d72f4f2aa3293 *R/wig.R
06b6babd88c05365704ea6abe5c6934c *R/zzz.R
492aeccc850f5ea08db1b96ab7988b7c *TODO
af3ae5daf1f92dd3811b3e69fa576515 *build/vignette.rds
df665c330920d29973e9723a009da3f1 *cleanup
f1c6559b35fff813365d80f250b8fee5 *configure
8ff5e2bccac0835b96272cda647f5396 *configure.ac
40b2812d6b3ed936d3f45c13d99d73b6 *data/cpneTrack.rda
97c8cf543f7363ac5813ecbeb641a759 *data/targets.rda
62a457ade06a9b2377d2908711654ff4 *demo/00Index
fd76458bb1995a0761de52efd2d38c48 *demo/targets.R
ba50970d99ec3f5f8a3b7970a2e52b21 *inst/CITATION
20208a37f0faf278be721842a65ce541 *inst/doc/rtracklayer.R
1334f525ef4e10e8e54cd739fb52c4a3 *inst/doc/rtracklayer.Rnw
7f51506ee01399d42572e2051cbe936e *inst/doc/rtracklayer.pdf
627f7757022fcc8ef63a494fdb92e78b *inst/extdata/demo.narrowPeak.gz
45a3511bd993b3b72fc33209ac5b8b75 *inst/notes/design.org
a1dceea3fa363d468c17d90e4b52bc4a *inst/notes/requirements.tex
1ed04c41046c9bc79f80bd65e9d8e6f1 *inst/notes/use-cases.tex
8fdc046b8313f9af91dbdc21d02f4a23 *inst/scripts/cpneTrack.R
5d600a101c281bf037769c8cb082ae03 *inst/scripts/twobit.R
1ecc1e6e021094cb5f94b4bc8745bc93 *inst/tests/bed.bw
8ad4283420c99289c21f4ce5440c226f *inst/tests/bed.wig
1e1f741e29717865afd71d9528c041b5 *inst/tests/genes.gff3
7b877a421abbc8c96a46c13cf8a0b011 *inst/tests/gtf.gff
51ae60628faadce25d5f17b328f96e92 *inst/tests/multi.wig
b8ddf817a4a4978ece1e22596f91a7cc *inst/tests/quickload/T_species_Oct_2011/T_species_Oct_2011.2bit
79ebfcd92aade3af546fa01048090fd0 *inst/tests/quickload/T_species_Oct_2011/annots.xml
f4fa4faa479b4ac5c907c1fff6ef5f56 *inst/tests/quickload/T_species_Oct_2011/bedData.bed.gz
5b0ad4880e8f7187338f5958c78c803c *inst/tests/quickload/T_species_Oct_2011/bedData.bed.gz.tbi
d41d8cd98f00b204e9800998ecf8427e *inst/tests/quickload/T_species_Oct_2011/bedGraphData.bw
7f656d0b19bdb05090e9c7f25f76636c *inst/tests/quickload/T_species_Oct_2011/mod_chromInfo.txt
f565227b82d1e2cc765c51dab2e85cc5 *inst/tests/quickload/contents.txt
a77aae8c92190371f0268bdd78b3fba3 *inst/tests/step.wig
da3448dc4bbd468e18bca8196d922835 *inst/tests/test.2bit
d7b044db64836c0e56b94c9a319ac95e *inst/tests/test.R
4dbda14562f0ed064f8f8ffb2ac8fb34 *inst/tests/test.bb
dacd53f71b88f4f15445474366745a7b *inst/tests/test.bed
69b3ec0ad8da42fc565da37f29c61866 *inst/tests/test.bed15
90367c22016c9fbe166bbc507b989f18 *inst/tests/test.bedGraph
303e7896894bdf47578fdcd15fecba02 *inst/tests/test.bedpe
e669ad7e1ee3266bcc418e059848a99b *inst/tests/test.bw
2133526a93413c6bbb02a5b7b7b1738a *inst/tests/test.gtf
b3d553636cb877aa650238028cc2bbc1 *inst/tests/test.xmfa
0e1a6f36d34f630340a0ef38889db0d1 *inst/tests/trackhub/genomes.txt
830c6ebe60aaef5346265a84e27fdb06 *inst/tests/trackhub/hg19/trackDb.txt
4dbda14562f0ed064f8f8ffb2ac8fb34 *inst/tests/trackhub/hg19/wgEncodeUWDukeDnaseGM12878.fdr01peaks.hg19.bb
4a9a04118d41220387ee5f1b4ded7af3 *inst/tests/trackhub/hub.txt
080abe08c56da02903b687b1c79c3395 *inst/tests/v1.gff
a81499cbeeebab1ef1979865a90f901b *inst/tests/v2.gff
c4b27d58615bef3a82d20e9ec62fe88f *inst/tests/v3.gff
4da2d3a1434b5e5e8120fd52b8c2a4b7 *inst/tests/variableStep.bw
932eab3fcb811671c46fcfff5a43da27 *inst/tests/variableStep.wig
9e5e5730d5f23d9f7a74ad3bf0c6968d *inst/unitTests/test_bb.R
8802f6517f013b0f9f3c8a41a734f252 *inst/unitTests/test_bed.R
7d357013c5048c347602a5d551e0a0c9 *inst/unitTests/test_bedGraph.R
f5d26a8b18d3d26c895daf59ec08d29a *inst/unitTests/test_bw.R
ca2ceb51e309cd2a4a374458ede0fc8a *inst/unitTests/test_gff.R
fc29c2108edddc1ce3119624fadc9b6a *inst/unitTests/test_trackhub.R
0be88fe9f5763004d32ff177fc1006f6 *inst/unitTests/test_twoBit.R
d63de424604848a41458ee789ac6ddae *inst/unitTests/test_ucsc.R
25fc50759a31d583ad1ede3fa1862afa *inst/unitTests/test_wig.R
4bb49cd68c49c167425a102321edb70f *man/BEDFile-class.Rd
622562050261166eb3808247fc21aa57 *man/BamFile-methods.Rd
0488f76d779f571e3cf1e70aaeee1979 *man/Bed15TrackLine-class.Rd
1916fbd79a0548f0a4329c37db9bc29a *man/BigBedFile.Rd
6ae22bd7cfd526c5f0472c06646ac781 *man/BigBedSelection.rd
4ebfc76279bde8ea739c40fa70d55dfa *man/BigWigFile.Rd
71b9a3e3fc4c1f5899b111e35d53b15a *man/BigWigSelection-class.Rd
ce9bfc52f30b6c34a8375f04b98706db *man/BrowserViewList-class.Rd
a5486f4e178a5ac44c4c0c87afbcbb37 *man/Chain-class.Rd
18ec16db271b30103678b98a52621510 *man/FastaFile-class.Rd
23d8ba30eecb90c44d657cabb0601dbe *man/GFFFile-class.Rd
c66dc468c847805fa64ed3882478b9ef *man/GRangesForUCSCGenome.Rd
7dbe9c421cb97df7163b43a59b5afcfa *man/GenomicData.Rd
599746bdb20710abd4c1fe2bfa074e00 *man/GenomicSelection.Rd
eebbc45960f35bd45cfc0ec92c210692 *man/IntegerRangesList-methods.Rd
4f7198bb48c76dbe9f9029169abdda5c *man/Quickload-class.Rd
8e3927e05c18de944e4ab4536e30e160 *man/QuickloadGenome-class.Rd
a04e96eab2b8e716673301361f1fc56d *man/TabixFile-methods.Rd
aa54e93af9e5e2690c342c269d739e50 *man/TrackDb-class.Rd
5887249c6a6450fbda14676f587c8248 *man/TrackHub-class.Rd
15940d147906a7c7d4210538288227e2 *man/TrackHubGenome-class.Rd
3b6b12db5b6cbebd08405ecbe520ba24 *man/TwoBitFile-class.Rd
1db0c71a0931c9441f2286650b2ba22b *man/UCSCData-class.Rd
0418d963e1c654f54503240d39fc679d *man/UCSCFile-class.Rd
195b541a08243b8863f72fcabf6088fa *man/UCSCSchema-class.Rd
cf8f5d5bbd2b6c0bc2e5000c86a475d0 *man/UCSCTableQuery-class.Rd
28e156f33ae8191613873de9b50ee982 *man/WIGFile-class.Rd
69f8d0d1d033c20d4398155314409667 *man/activeView-methods.Rd
3b747d8bb6625ba70fc0b5431e9ce01a *man/asBED.Rd
c1c3f0849bbc657bfdf61dd86dbe8ee5 *man/asGFF.Rd
040a063b75ca508f085dc751ba7506c0 *man/basicTrackLine-class.Rd
eac632a9f972a562c1164ce4d171eff6 *man/blocks-methods.Rd
66df0fd2bb07618c210cf6e7c5fe2479 *man/browseGenome.Rd
d76aafb8924852fb8664c5d937d2128e *man/browserSession-class.Rd
043e81566759aec120360fcb10ebf955 *man/browserSession-methods.Rd
558961315c84ec185c95e44d020fb298 *man/browserView-class.Rd
d7e0e22430de6914277f80f44732ab26 *man/browserView-methods.Rd
80f10b808515286ed2b76352c2b094a3 *man/browserViews-methods.Rd
7059cb687f0a5f5af474fadb917f9d8d *man/cpneTrack.Rd
b2e10bc58aa5c0c50b46091a3752704a *man/genomeBrowsers.Rd
bb648844f75e3f414940415f460d7dd9 *man/laySequence-methods.Rd
89184a62faf8e0bd3f44db6f4c2c8a64 *man/layTrack-methods.Rd
9c57e6bc0f279e74dace4cae9c3ec93d *man/liftOver.Rd
605a418619f25ab3239c234715444ca0 *man/readGFF.Rd
e38abad38a406bb471393f33e09aec57 *man/targets.Rd
4960ca21ccab9a4f1c2672427b270668 *man/tracks-methods.Rd
179a091668b32ef1f2f138d98f8f67e8 *man/ucscGenomes.Rd
724d855028dd35a9bb6b9e8b0a3b30fc *man/ucscSession-class.Rd
dfe5103bc5c9ae04eb89756b07f04e42 *man/ucscTrackLine-class.Rd
8f5479909ca725aa41d9825e81ba31b8 *man/ucscTrackModes-class.Rd
213910113b5923c3b95f0dfedfcb2d1d *man/ucscTrackModes-methods.Rd
9ed8990facb5920ab343c4b7d4e336cf *man/ucscView-class.Rd
11006f53b4c1409481a98f9e073a74d9 *man/wigToBigWig.Rd
011371026f7189cfadda363c07eed9dc *man/wigTrackLine-class.Rd
89c64601544f50d62c58010dea7a4a5a *src/IRanges_stubs.c
e18beb53a44b739890a2e964f7f159b7 *src/Makevars.common
7bba46bfbf6a533e61272f25ec3bfb27 *src/Makevars.in
f28dcdd2d4c844e920df098d9e779b6f *src/Makevars.win
5f3786af33717c94d85653ceb81820b5 *src/R_init_rtracklayer.c
35b1cdedfa6e3e2842c15a35bd373ec6 *src/S4Vectors_stubs.c
a255527d3590da0bb08d05e05719c9ee *src/XVector_stubs.c
26362ccc7a18fbfd42c282930036f3fa *src/bbiHelper.c
37b9d190c7d17ff51b84494735fceb5a *src/bbiHelper.h
fe74eaf7072463348cade06d38d9d26a *src/bigBed.c
2cb2bfdcc1337d484a96ee51c9428ee4 *src/bigBed.h
8fd5003c12fa766144837acf4f1ac9cd *src/bigBedHelper.c
5a8c0642aa063b7731814ea63044c6ca *src/bigBedHelper.h
050b0f2caca65fd3a5d84dcf558a294c *src/bigWig.c
069dd41f912eecf37d79b30dd0fa52b3 *src/bigWig.h
f107495c3f90765203b4dc16b4369e81 *src/chain_io.c
028003240fc7cfd668f3036c3cdcfd70 *src/handlers.c
f376a1d2b084b6b9f46cf89db3f9ab66 *src/handlers.h
9649caba8a33ac2007c72c2d313bf9ef *src/readGFF.c
18ffb80657705842bd76b3f75c26c348 *src/readGFF.h
a761005e92e7b6a3ffa62c34ab6742e8 *src/rtracklayer.h
c61a601a2ecd1b82c071e91467e37f3c *src/twoBit.c
c4b666996d2cb407d432563cab10ada7 *src/twoBit.h
5add4b8b5c4c15ca321f4fa56e0cae0f *src/ucsc/_cheapcgi.c
b77d59a91a877b9cec4985f0a8ee1f46 *src/ucsc/_portimpl.c
d2ea68af9e4d321b1e7b3a17fd839448 *src/ucsc/_portimpl.h
81582040b2ea255b234021103d34aa3a *src/ucsc/asParse.c
4c9d6abc3a5b1f6b8aa7297a8010af6e *src/ucsc/asParse.h
210353d6b35fcb5f4467d13b7006cc4a *src/ucsc/bPlusTree.c
045a2e41468674a2bc3b404a1826e62f *src/ucsc/bPlusTree.h
6ab3dae32e18e17e142a40f5f81d8f60 *src/ucsc/base64.c
097addf4aefef1baf4f3aa12b97bb683 *src/ucsc/base64.h
576638d55843eeb6997ac7673a722b0f *src/ucsc/basicBed.c
3239b4ee6d023eb35405e1289245f1ce *src/ucsc/basicBed.h
cddce6ac0b7646c630422afcc9c36a92 *src/ucsc/bbiFile.h
27b1cb9989ba0df4f78aaa2ef0dae422 *src/ucsc/bbiRead.c
5dbb7361c6dc834c662013d77542b031 *src/ucsc/bbiWrite.c
f7b5458032f20e0b959ecd0286538781 *src/ucsc/bigBed.c
93d659b64a46b8232bbfe4d97fb833be *src/ucsc/bigBed.h
fbcb033500d3e87f1da0078f67f9c0c9 *src/ucsc/bigWig.h
f4e3108a674cbd96bfae8b352272da12 *src/ucsc/binRange.c
81fa658c87f25a69894a0a8ea3efaa84 *src/ucsc/binRange.h
dd3c5977e23fb3818f8293aee847db5d *src/ucsc/bits.c
5f565890c5b739f74c7f418fd804cb3d *src/ucsc/bits.h
235635017c580dd191f5b1958cf019cd *src/ucsc/bwgCreate.c
8a7066f5351e59ac1cd1da5ccf454e4b *src/ucsc/bwgInternal.h
89d7d599f12938ecf738a333d16b236a *src/ucsc/bwgQuery.c
0cdc037f8e3a9b69a9b019840e500655 *src/ucsc/cheapcgi.h
a41aab6ef26489dfb7c002b0d9591dde *src/ucsc/cirTree.c
1683454212bbaa977045574e139c3ea3 *src/ucsc/cirTree.h
62f174c52da3f07fe064c907f6bbc5c5 *src/ucsc/common.c
c19ede522d07df64d8fc12e793d4659d *src/ucsc/common.h
a64e031bf82aba973f6a9ea3c9439d1e *src/ucsc/dlist.c
f2f79f1784ce9d1f99f0d3617c6c1930 *src/ucsc/dlist.h
a418978491dff0e20f770733cad89121 *src/ucsc/dnaseq.c
a3322eed24caef6e5fba60e854c34958 *src/ucsc/dnaseq.h
3c5a822c2d2b0ae21dafdf659232f1ed *src/ucsc/dnautil.c
33965260d6de1c6e0fd381d21909076c *src/ucsc/dnautil.h
c04907f5e343b652f7ff26a233508b4f *src/ucsc/dystring.c
5598665c018b00c16522bc681ecca2a8 *src/ucsc/dystring.h
1c7ec946451ad48f158986465bd87ddd *src/ucsc/errAbort.c
07caad4b96232b761b3f1015bfa0ec3c *src/ucsc/errAbort.h
2adca7a26d559f0214f28ba7db8be50b *src/ucsc/errCatch.h
588cf0cb122c5a8d238fa56336aabf0a *src/ucsc/filePath.c
71f2338ef6240404a89beed7d9f51a72 *src/ucsc/filePath.h
597cfea6cf2cfa9d3ae56e9f3b0622d5 *src/ucsc/hash.c
3dac7e987e9041d767a23541d62d0b7b *src/ucsc/hash.h
9903442dbe96665221554db3fe96f9ff *src/ucsc/hmmstats.c
80450feb27177c5cbb57ea25f740917c *src/ucsc/hmmstats.h
da7cfbac55c93e1dc54671bf442db7b9 *src/ucsc/htmlColor.c
8b86cc5942eb4399161236bb0eb1da46 *src/ucsc/htmlColor.h
bde00e96163d75617001535e8026e617 *src/ucsc/htmlPage.c
bdac756f901898f4ad95beeb348e9fb4 *src/ucsc/htmlPage.h
736849a8156470a9ac0ed4f1d4e7d439 *src/ucsc/https.c
ee3eb5817cf42cf92774df42daed1f6c *src/ucsc/https.h
ff9cc3c51012d98da33e9b4fb5a78e2b *src/ucsc/internet.c
bb04c17bbb06274b1037f40f67caa9b6 *src/ucsc/internet.h
caeed954ad0cbfa52cdeac44af8d0f5f *src/ucsc/linefile.c
b325decb8a07b53df3bd39766125509b *src/ucsc/linefile.h
6abd18b5ba3cfc5344eea648f588229c *src/ucsc/localmem.c
7c96d1430c3d83283ff88c0b0bca0f42 *src/ucsc/localmem.h
25152cca43ea695647993f9276e4e18e *src/ucsc/memalloc.c
f24cdb22ad283310d99bc328ac6414de *src/ucsc/memalloc.h
def37ab8e8cf8f730cc125f23e827250 *src/ucsc/memgfx.c
9626a7ca53b8d41ca3902418f16f96a6 *src/ucsc/memgfx.h
223a5ae27767d13d076a38f823347f8b *src/ucsc/net.c
85ada9ea0d54cd2d7d8f57240d822afb *src/ucsc/net.h
23cdf8d3e19aa9128c933d30186a8050 *src/ucsc/obscure.c
a153d60c74f876af250d638cc335537e *src/ucsc/obscure.h
7e0cf9aa2149aaaa28ccafc59649f96d *src/ucsc/os.c
aeeb896a116894e1456ccc50bd86dc90 *src/ucsc/osunix.c
2e369fcbf477f850127a7c8afbe5c8ed *src/ucsc/oswin9x.c
e2b651528ddd9ea9076bdb8a98312f5c *src/ucsc/portable.h
6c90cbb177f198829e58af436865d04a *src/ucsc/portimpl.h
8b33ee59964b74305bcb482fde911711 *src/ucsc/rangeTree.c
6e5493dad2f7a254de9591ffbf721a35 *src/ucsc/rangeTree.h
8f329e374f30ababb51a91c3179c5a6f *src/ucsc/rbTree.c
a3002ca77338114b35ca009fc26301d7 *src/ucsc/rbTree.h
f7f58d66cced835f83c3bb0bd60c3022 *src/ucsc/sig.h
1dc28df4482ad35248e4d073f1d60ec8 *src/ucsc/sqlList.c
b23989b172126c0c682a4d20e922a73b *src/ucsc/sqlList.h
8f1161b1841fe82958990c086266e00e *src/ucsc/sqlNum.c
35b90fabc6a18e68f634e9f0ecab6518 *src/ucsc/sqlNum.h
cc7471e009b3c0d74c07a50d483b4653 *src/ucsc/tokenizer.c
210b3477d067a2d84125b42c5b80f75a *src/ucsc/tokenizer.h
f60cd2d2a7a51c9846b43925a436af9b *src/ucsc/twoBit.c
6928145a109cc0fdaea43a0fff28b0a5 *src/ucsc/twoBit.h
704dd969e1b27b5036b656a3e7803c73 *src/ucsc/udc.c
1f57eb0a3fc8e3d669fc01727df83485 *src/ucsc/udc.h
c1ba910b09849062d907ada331b2d5a9 *src/ucsc/verbose.c
895f97eb781515b2be6069d7ccbda824 *src/ucsc/verbose.h
675a2b8d768ff1bcb4db6b81a4ff5063 *src/ucsc/wildcmp.c
379be1564efb3b7921807447bc7d9a50 *src/ucsc/zlibFace.c
0fe854153c488b613b01e1beee86f6bf *src/ucsc/zlibFace.h
52f50f63522fd0307ea6a4508de63e07 *src/utils.c
62f756e32df854864af927be8d2441ce *src/utils.h
a6e1734883d13f7d25205e5f5c20991e *tests/rtracklayer_unit_tests.R
fa36193f9c797a171b90754f3ab47070 *vignettes/example.bed
1334f525ef4e10e8e54cd739fb52c4a3 *vignettes/rtracklayer.Rnw
