ea041bf4353e193e3871e0973645cf3e *CHANGELOG
fb47f506de7f0e8b0873d824c2ebcf91 *CHANGE_IN_RELEASED_VERSION
a5ef1eaff719e5ca3e5d5949036066cb *DESCRIPTION
51cc2138ce235d14f4d61f92c2898ad9 *NAMESPACE
63ff5cdfd47fca13ad45d7e99cf3f46f *R/RsubreadUsersGuide.R
5153bd36161e72fcba2747204eb8aa68 *R/align.R
3a51de35f8ab19c92301d931dcea54e4 *R/atgcContent.R
91c838535b9b01f7ce623a547926fd1e *R/buildindex.R
97a0c056ae7461114d0834359b3474df *R/cellCounts.R
0bf4a92745ce10c42cdcb33e8c3270d8 *R/detectionCall.R
50cf5bce903d79f825142a48c8efff32 *R/detectionCallAnnotation.R
c40af4763a361c3bca01b3a817e328c2 *R/exactSNP.R
dc8a8cc1856fa7c69479259bec900fc0 *R/featureCounts.R
9036134775f8b54864847dd7db77c3d8 *R/findCommonVariants.R
99e77be7151c3c462465f2fb5a59282f *R/flattenGTF.R
8b562df81450f8f78c7f3a8cc09b0dd2 *R/getInBuiltAnnotation.R
ec600c48e2a22e4c03641a242812c875 *R/processExons.R
23ba999b6b59724da1d4c7bcc062f178 *R/promoterRegions.R
a46da7918d71fab1f4dd2ae3b55bdf2c *R/propmapped.R
04470586284afd28475ad6af96b45a1d *R/qualityScores.R
c7e34e5a1857295cc57b1a37521f44cc *R/removeDupReads.R
2a63819a83e7b19df53ad4c54518c22f *R/repair.R
106df35381f095ee76d845f78c9d3890 *R/sam2bed.R
8ee26ac133d41d2383e4df598effbf37 *R/simReads.R
4d44feb8340728e8bda15d167c480d54 *R/subjunc.R
1949f5a53b0ba351a13f20424dc84857 *R/sublong.R
4f32eeacfbdd3872b658940c10dd75a3 *R/txUnique.R
1bf18d9c216b8d95033f0bd2fe2906b2 *build/partial.rdb
a9cde6a08f259ab2804281205b025a22 *build/vignette.rds
27474be2b2fa49816d67e471bb890b81 *configure
586ddb64d5a281b9d1be98d857a9c34e *configure.win
da5dd86d628b4413d8787b1f46b8dcf5 *inst/CITATION
8eb49fed72825395b928f5c9a023d69e *inst/NEWS.Rd
0ccff75b48c76896d29ce557c803b158 *inst/annot/hg19_RefSeq_exon.txt
08d9e787ae6480d7b9c1cde05d4bdfbb *inst/annot/hg38_RefSeq_exon.txt
d8b19f0e062da6dcdc5ae32a7ceeab16 *inst/annot/mm10_RefSeq_exon.txt
c02177edfb75f810e8ffead432afd3c7 *inst/annot/mm39_RefSeq_exon.txt.gz
cb17837f0e18003cfb0f54bdb298e3de *inst/annot/mm9_RefSeq_exon.txt
da3a415b5c6fd004b9f7bf1566a88b12 *inst/doc/Rsubread.R
b502a056caf6b3d2f0da65425e16df35 *inst/doc/Rsubread.Rnw
e0a43404d48ea68ac094f6ff694bba36 *inst/doc/Rsubread.pdf
d47c7a101b7a7ba0f069094d24e7db2f *inst/doc/SubreadUsersGuide.pdf
06f2a4174973a64f3025555134c48503 *inst/extdata/longreads.txt.gz
dd811882ea60ee99824c241b8e66984d *inst/extdata/reads.txt.gz
6ac8e5f260e7b9b4e6c613b84c444ee3 *inst/extdata/reads1.txt.gz
4fb22dd42e7d167caf11e8e66d65aacc *inst/extdata/reads2.txt.gz
a3e4d671b27f0a28734ca92f9b123fde *inst/extdata/reference.fa
a17fa93fa3e77af18deaab47f4211f29 *inst/qualf/ref-quality-strings-20k-100bp-ERR2_70-SRR3045231.txt
5f3496a46fe7f4f91682b1ad80506948 *inst/qualf/ref-quality-strings-20k-75bp-ERR1_59-SRR3649332.txt
a9002d874702f284f308b5354dc5f9ed *man/RsubreadUsersGuide.Rd
8f36e0d5bbfeace5af2d27e0df64940d *man/align.Rd
c079376b00164897d762b6bba3ec7038 *man/atgcContent.Rd
ed5752c54e2d1daf9e52abc0e137b517 *man/buildindex.Rd
5967597ed7295c439efc9f8f672cb152 *man/cellCounts.Rd
a561b5816972684ce211f593b922254c *man/detectionCall.Rd
137fef54d6267e13e3923167420f04f6 *man/detectionCallAnnotation.Rd
58534853fca1163ca957320a0a554b94 *man/exactSNP.Rd
5ae6684261887abc229ab58752732ed5 *man/featureCounts.Rd
7d7415d5bd39b62c766d7e55a402d6f3 *man/findCommonVariants.Rd
6af5a2f002722af0383e104160ba2389 *man/flattenGTF.Rd
3eef43e97be7edb0485843ada53a6156 *man/getInBuiltAnnotation.Rd
6ee31c8d378611510cdec21b0323f24d *man/processExons.Rd
fcb42835ddcbf38dff95e356668110cd *man/promoterRegions.Rd
69a635c9b9c62e09c8fc0790ff23e3c9 *man/propmapped.Rd
229c5585e8b235a1ebf1e7ac6c0b7241 *man/qualityScores.Rd
61415b60faf4d40b7558911855b93864 *man/removeDupReads.Rd
87620dc41bf0ecbd948dba8c167e4856 *man/repair.Rd
5426c279e20b98685bb22e73460360c6 *man/sam2bed.Rd
a9e5d405c6cfce6ac13c8ebf532177e5 *man/simReads.Rd
e6e90bd0827780a3ee72b364fd11c16d *man/sublong.Rd
72dbb7268fe0fa4a5dda215ba97ff377 *man/txUnique.Rd
f0ddb3e60b68fc4ee702dc77ea773ee2 *src/HelperFunctions.c
a84ca4239b6648c63dac7dfe2ec07f0b *src/HelperFunctions.h
3b199237f97faeb6514f09500aeb4f8a *src/LRMbase-index.c
1bbaf5c3899dd5c3871af20e94291698 *src/LRMbase-index.h
abf92654c243a0b778777f7874bc0507 *src/LRMchro-event.c
45413a07df514c2cc0753cc26f15229c *src/LRMchro-event.h
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643c3181ff580d93e82647e6ce157e83 *src/LRMhashtable.c
4660106b6281a4d8346ae8b35671211a *src/LRMhashtable.h
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ab45f16e17ef1700ecfa63d700dae9da *src/LRMhelper.h
33ed9459b2064d76754b4aff4ee3adf6 *src/LRMseek-zlib.c
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ab1fb32cdf5c60de471ac4ac97a3c65a *src/LRMsorted-hashtable.h
bbc9034c91e581cca3b16c49fb5b1050 *src/Makevars
a7728f9c45be03404e8a2702caf212e2 *src/Makevars.FreeBSD
bbaf0eeeda8ec308f82ffd0d7c9f8507 *src/Makevars.Linux
c4e9899e99d6896af4521397ca806bff *src/Makevars.MacOS
c4e9899e99d6896af4521397ca806bff *src/Makevars.SunOS
ec19c361201163756d2a7d781a77f56c *src/Makevars.Windows
e9f34de6c4cc10090fbeb63099989b66 *src/R_wrapper.c
af2ff66d239e68042d5d334142c05012 *src/RsimReads.c
eb88f7e394c4ed19e99f2d3e4bb8abab *src/SNPCalling.c
4779638267e9fa9a81855cd9a77d911d *src/SNPCalling.h
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e7d42fc049b789c4a4c3cd0f02ad8a3e *src/atgcContent.c
1d9c59e76be07f80252e6f0481bae098 *src/build-sam-index.c
e6b095eb349d6b8769b9f414150bbaf0 *src/cell-counts.c
cc5f2ac0568078913d6d1a21710dd2fb *src/core-bigtable.c
7bbf0fa9a41e1a2c4ad80c8667214dc5 *src/core-bigtable.h
3b13243483936b901b70a4e235ee7e1f *src/core-indel.c
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711d33d24d7c3f70aed3d034a2200ae3 *src/core-interface-subjunc.c
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5dd7bdfcd1db4e5aae409bc3ceeb2430 *src/core-junction.h
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663e7ad98f7a6dedd75048f175ac3737 *src/detectionCall.c
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8424983ba4b4f04343d8fba11151b724 *src/exon-algorithms.c
8424983ba4b4f04343d8fba11151b724 *src/exon-algorithms.h
8424983ba4b4f04343d8fba11151b724 *src/exon-align-indel.c
8424983ba4b4f04343d8fba11151b724 *src/exon-align.c
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b0cb0939dc7b2c798c3a9ee9e8b9e968 *src/fullscan.c
8424983ba4b4f04343d8fba11151b724 *src/fusion-align.c
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0ee72192b5598bd845fe644bba1cb89a *src/gene-algorithms.h
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c03f3a01845160d61f3e7bcb43b9e30b *src/hashtable.c
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5297e088700009add005dbb93dc35d2e *src/index-builder.c
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9388fc9abe02a7c9cf2870fdafa4c943 *src/input-blc.h
f80255097a599370fe77a256a11515e5 *src/input-files.c
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22019db259502bc5741afb06970d3816 *src/interval_merge.c
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1f1661fcd4d6434801586e2e082d973c *src/long-hashtable.c
04858a4f3e2d561e59a930b2ffef13e5 *src/long-hashtable.h
05721af646a5b884bdb87d26f72d4f48 *src/longread-mapping.c
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262a82d7994c8e9b9262c9daa5f25ac2 *src/processExons.c
e4257a4cb0e262989be0f880a7780500 *src/propmapped.c
9592a2509a32619a234b195bd02de7a8 *src/qualityScores.c
ffd2d8850bae9849475e007edb541f72 *src/read-repair.c
5d4485c353d2ad263bada45cfce291d8 *src/readSummary.c
64306b4e84f1f52ea517086244e96ea8 *src/removeDupReads.c
1d9f4dc8bd923c2e451b96515d6e37c0 *src/removeDupReads.h
e4b4d09ac2b71cd2c6aa8050b2a0d985 *src/sam2bed.c
b2773f1f7b30f28790fece16fce85632 *src/sambam-file.c
5ff9c48fcda555791464da77d9f49ea0 *src/sambam-file.h
582f403a085e343274427966e6847817 *src/seek-zlib.c
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521ebfefad4985347777045963613695 *src/sorted-hashtable.c
b7a4e2ec9771d7f6318d9342c38ad95c *src/sorted-hashtable.h
339ebfd955827c07d7c293832ef2d7fe *src/sublog.c
1c0a16768af95eae9e60c4afd34c6c94 *src/sublog.h
678476555fe331efa22118c1d31108b6 *src/subread.h
fc03ab636032294a105dfa337be3bcd1 *src/tx-unique.c
31da5cf7488badf47d8a4d71c520e3e1 *src/tx-unique.h
b502a056caf6b3d2f0da65425e16df35 *vignettes/Rsubread.Rnw
