e5002540e91e24ad2c071c9b3f9101e6 *CHANGELOG
fb47f506de7f0e8b0873d824c2ebcf91 *CHANGE_IN_RELEASED_VERSION
4b4bfcc3c1a549e5a1387838628c248a *DESCRIPTION
51cc2138ce235d14f4d61f92c2898ad9 *NAMESPACE
63ff5cdfd47fca13ad45d7e99cf3f46f *R/RsubreadUsersGuide.R
5153bd36161e72fcba2747204eb8aa68 *R/align.R
3a51de35f8ab19c92301d931dcea54e4 *R/atgcContent.R
91c838535b9b01f7ce623a547926fd1e *R/buildindex.R
7910a1162f082ee79b43082d16f407e1 *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
4817bc7cf35c6fd3cb43114393ae8bf4 *R/simReads.R
4d44feb8340728e8bda15d167c480d54 *R/subjunc.R
1949f5a53b0ba351a13f20424dc84857 *R/sublong.R
4f32eeacfbdd3872b658940c10dd75a3 *R/txUnique.R
533839446f70bde34a1050627ce80586 *build/partial.rdb
922916c44b54be2ab7620aa67dcc1f61 *build/vignette.rds
27474be2b2fa49816d67e471bb890b81 *configure
586ddb64d5a281b9d1be98d857a9c34e *configure.win
da5dd86d628b4413d8787b1f46b8dcf5 *inst/CITATION
8eb49fed72825395b928f5c9a023d69e *inst/NEWS.Rd
0ccff75b48c76896d29ce557c803b158 *inst/annot/hg19_RefSeq_exon.txt
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d8b19f0e062da6dcdc5ae32a7ceeab16 *inst/annot/mm10_RefSeq_exon.txt
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cb17837f0e18003cfb0f54bdb298e3de *inst/annot/mm9_RefSeq_exon.txt
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b502a056caf6b3d2f0da65425e16df35 *inst/doc/Rsubread.Rnw
7b59a975094905adcc261387575b9b9a *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
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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
ba993a39ae04dda542050c485173c461 *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
d9d1129eb5bc2148ecc59c9b0e743444 *man/simReads.Rd
e6e90bd0827780a3ee72b364fd11c16d *man/sublong.Rd
72dbb7268fe0fa4a5dda215ba97ff377 *man/txUnique.Rd
741a6499d84539bb7ff2667426d09c35 *src/HelperFunctions.c
193fb7ed8f95713ba411ba11b796d148 *src/HelperFunctions.h
3b199237f97faeb6514f09500aeb4f8a *src/LRMbase-index.c
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ab1fb32cdf5c60de471ac4ac97a3c65a *src/LRMsorted-hashtable.h
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6d70f5c10140a980179bba707d48905b *src/Makevars.Linux
c4e9899e99d6896af4521397ca806bff *src/Makevars.MacOS
c4e9899e99d6896af4521397ca806bff *src/Makevars.SunOS
ec19c361201163756d2a7d781a77f56c *src/Makevars.Windows
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4779638267e9fa9a81855cd9a77d911d *src/SNPCalling.h
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1d9c59e76be07f80252e6f0481bae098 *src/build-sam-index.c
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7bbf0fa9a41e1a2c4ad80c8667214dc5 *src/core-bigtable.h
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8424983ba4b4f04343d8fba11151b724 *src/fusion-align.c
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8b026ba35caab43c1a1b6de827e5b958 *src/input-blc.h
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e4257a4cb0e262989be0f880a7780500 *src/propmapped.c
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1d9f4dc8bd923c2e451b96515d6e37c0 *src/removeDupReads.h
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5ff9c48fcda555791464da77d9f49ea0 *src/sambam-file.h
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1c0a16768af95eae9e60c4afd34c6c94 *src/sublog.h
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fc03ab636032294a105dfa337be3bcd1 *src/tx-unique.c
31da5cf7488badf47d8a4d71c520e3e1 *src/tx-unique.h
b502a056caf6b3d2f0da65425e16df35 *vignettes/Rsubread.Rnw
