9fe7c15d02ab199c1b3d41aa812d15a5 *ChangeLog
d77f567e49da6c39e3b3d84e82f64158 *DESCRIPTION
50c28547d51e8cbb9a908e6696fedb86 *LICENSE
1bbde4ac4ad752ce23129a7fdd274238 *NAMESPACE
41221a2583cced774e19dcb98cb385ea *R/seqminer.R
ca26fe4095537700c16fd206f4981d1e *README.md
131a236039d88977475269c6ee6c6e2c *cleanup
fb5ab8978d07fbd4bf0c1fc697a82992 *configure
9ae2d4052422c8a79c0e0b4be9f55aac *configure.ac
62e8ae8f7711c3681d616f7c01e667eb *configure.win
7bb67b9779288c68f4983a0663a2d262 *demo/00Index
e39927036debbb6042ebcf8920d82a23 *demo/workflow.R
cbbe73bf76dae8a277a19879144cca6b *inst/CITATION
1c96de0a2112c8f4cc6fbdb911a29912 *inst/doc/Manual.html
b94af6795e947307028d232aee84d501 *inst/rvtests/rvtest.MetaCov.assoc.gz
6ed4d335152649bfe88ce972d23440e5 *inst/rvtests/rvtest.MetaCov.assoc.gz.tbi
6e9beac74bc1ec51eeead95a58c2e57c *inst/rvtests/rvtest.MetaScore.assoc.anno.gz
543690c148fb9bccb7e8b3e05826f5f6 *inst/rvtests/rvtest.MetaScore.assoc.anno.gz.tbi
99237619851543e09bc2906e6a66c2d7 *inst/rvtests/rvtest.MetaSkew.assoc.gz
a2d22ed038bcdd63b2200f8a495ce0d8 *inst/rvtests/rvtest.MetaSkew.assoc.gz.tbi
e3b70c9d450ffc3505f6b60025605363 *inst/tabanno/codon.txt
587f0fb382bf9328f31d9c0b48dc63ba *inst/tabanno/input.100.vcf.gz
fdb819f529759c78b5023b530904974f *inst/tabanno/input.demo.vcf
cddf8f9094beb0f87332bee2abb860b8 *inst/tabanno/input.test.plain.txt
5da124f1fde1b084dafcf5a870f46b1e *inst/tabanno/input.test.vcf
7e51a21043ce478b9cd506e0b8162697 *inst/tabanno/priority.epact.txt
23e5d1b21219abad05b0503e88af00be *inst/tabanno/priority.txt
e68c266d8b91871bee9d06053fc338b3 *inst/tabanno/test.bed
d29bd9d0fefcb9559e3b3b649007b3b6 *inst/tabanno/test.dbNSFP.gz
cead2c0cb02fe1fd2ed7cd610c38bc3d *inst/tabanno/test.dbNSFP.gz.tbi
04b35b0c9a1d2799782d2ad34fa0684c *inst/tabanno/test.fa
54932744e3eed15da9808ea28475cc98 *inst/tabanno/test.fa.fai
ed581f9cebe1457335b2fd0463f88f58 *inst/tabanno/test.gene.txt
1da7da33635f876f5633bee3f0225ed9 *inst/tabanno/tmp.vcf
9053a4d846251aa8123bebaaf4805153 *inst/tests/correct.Rdata
96c027f72b597640d7ae4059a5b37e9c *inst/tests/testthat.R
e95e6420f0b8bdf2306dc87628a2c9b5 *inst/vcf/1000g.phase1.20110521.CFH.var.anno.vcf.gz
8e1e8a6b0944b906b913d315aa4f8fe0 *inst/vcf/1000g.phase1.20110521.CFH.var.anno.vcf.gz.tbi
30b34178034c34db61e46eeaf01fe863 *inst/vcf/all.anno.filtered.extract.bcf.gz
da2e7fb5756f4e027cf076ddcdb5eade *inst/vcf/all.anno.filtered.extract.bcf.gz.bci
a30627f5fed64983816d94ff2f90369c *inst/vcf/all.anno.filtered.extract.vcf.gz
eebfb3d8260a7def9f29034931b7f9e2 *inst/vcf/all.anno.filtered.extract.vcf.gz.tbi
9cc4f5122bb2e3b0b6b519f8c00d4fd7 *inst/vcf/refFlat_hg19_6col.txt.gz
51222ed1e3a90db6bb96daa83d386836 *man/SeqMiner.Rd
644d51732a21ea27c80fe792528dd5c8 *man/annotateGene.Rd
c79082589793f31b4f93fa6a77b57841 *man/annotatePlain.Rd
085779c971e7d43497d1ebcb0ca29ea9 *man/annotateVcf.Rd
1bfbae9add31f27e3463d4cc1451563f *man/getCovPair.Rd
d44bf7e81f3b868eebdd1f7d32adf584 *man/getRefBase.Rd
11fbed3577ba760ccb02db9b123d2512 *man/hasIndex.Rd
5b5e33d895aebbc2772b9b736e8256c7 *man/isInRange.Rd
c78309c57475bf16429f43eba1c1d03f *man/makeAnnotationParameter.Rd
c3fbcbeee112655c33a7b33300b99405 *man/readVCFToListByGene.Rd
86bb67b698b57861f67c05538ea4a8b2 *man/readVCFToListByRange.Rd
8d600b7276b76ae23d1ec0f17251fac0 *man/readVCFToMatrixByGene.Rd
12efcfea63e337e24889b56ca8dbc0d1 *man/readVCFToMatrixByRange.Rd
64a1a33b6e026290fb670d6f09e68ceb *man/rvmeta.readCovByRange.Rd
65adccb4aeb5f07c2faffb9c05cdf5bf *man/rvmeta.readDataByGene.Rd
39669f356266ddd5fe13dc2755aaebc5 *man/rvmeta.readDataByRange.Rd
3e36a839b166130448ac3aeb8793a733 *man/rvmeta.readNullModel.Rd
c0eacc2c20089df41342e99184f7eec8 *man/rvmeta.readScoreByRange.Rd
b19f0239243cd9107ebbb1d68ed3aad0 *man/rvmeta.readSkewByRange.Rd
0c2479b6f1bd5f5b9691456deaa569cb *man/rvmeta.writeCovData.Rd
cdea3b459197bad6c30729a6345a37fd *man/rvmeta.writeScoreData.Rd
8b23831eb3357bcdab4ddab9bb078ce6 *man/tabix.createIndex.Rd
fc7ce315132fc3595c92274405611b8d *man/tabix.createIndex.meta.Rd
4c5924fb5d8f255acf32d35bc65476aa *man/tabix.createIndex.vcf.Rd
178eae1c41df6cafbdc567d308b47d53 *man/tabix.read.Rd
43517c5dba796b5ccde652765eae891c *man/tabix.read.header.Rd
3baee3e3f00a607afc2ddde6d8d61a9b *man/tabix.read.table.Rd
0fff6f7ce66c2d5460744fd24f07d618 *man/validateAnnotationParameter.Rd
7d5d1a014c9780ae010fa734625636ff *src/AnnotationController.h
d85b92c76dcb55444027a6a8d99e27cf *src/AnnotationInputFile.h
6021462af480441309bfb226d4d29cc8 *src/AnnotationOutput.h
3184b057843a5dfda16318b9d4d713da *src/AnnotationOutputFile.h
a118eaa3a82b335229fe08221d59165d *src/AnnotationResult.h
50cd872876c6e5d4a70c59bdcc32f9e5 *src/AnnotationResultCollection.h
c51a61dc863f832884d5bf5e118f7002 *src/AnnotationString.h
6a1db02fef8e1ed053dc9ad2ade1c872 *src/BCFReader.cpp
a8302e38cecdde63fe299db71d42dd21 *src/BCFReader.h
b447cc997ea9c74318ed9cf784a42940 *src/BedReader.h
90a67bdcbf2ebeb6866f2c91e43e6833 *src/Codon.h
d69a4a44faf4874925b39227b01a447b *src/Common.h
f2dfc84a2dfd0290c2dc8d910bee0b53 *src/Exception.cpp
be9a7201c6ec40825118cd53f50f677f *src/Exception.h
a35ca7176ce98a73cc231422dde7923a *src/FileFormat.h
a95e5ec7ace400494ce16d20bc1d3ada *src/FreqTable.h
d2592825b8f3bd8ace8d350859568488 *src/Gene.h
5fb3d1bfb17ad3abd83d0d30cd905b0f *src/GeneAnnotation.h
222b54973e8c0f6de708737c566e73c9 *src/GeneFormat.h
7e2b3c5bff8130ef64ecb6af89ea3c85 *src/GeneLoader.cpp
54e44e25de3378d5c46a8c0330f56320 *src/GeneLoader.h
7b66f7778a8a3888845b5456dddb100f *src/GenomeScore.h
893125d6779ed7e5035a31fba769e79f *src/GenomeSequence.h
47e38da7377fc11ba10b374a6a4c13a8 *src/HiCExtract.h
b7d9dfdfe8afaee484c6633309deeaf6 *src/IO.cpp
4d1b969552cde23c382f9250f8f85bb5 *src/IO.h
422d83b84e05058cdff9a2032fc2b196 *src/LogFile.h
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1d24c1cf530f5b3dfbcdc4940c032b25 *src/Makevars.win
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9279857f27d2551483166caab8cbc1b0 *src/OrderedMap.h
a0cb740bd8ce684c99351d099e4bc26c *src/PatternMatch.cpp
a25d2a59b7051ac1040b412af196a2d7 *src/PatternMatch.h
10a321be45f3709dc6e77da323e0bc98 *src/PeopleSet.cpp
cbc062a62e16c021f8f7595252018847 *src/PeopleSet.h
7eefb9404550500c36612a2de43ba771 *src/PlinkInputFile.cpp
cea9d82e949f03b9094b3fa6c31c3df2 *src/PlinkInputFile.h
70bccc3a5d23fba307bccba4ae22060e *src/PlinkOutputFile.cpp
05f8aad8f969c9ab5f8366eea52da98d *src/PlinkOutputFile.h
baa046303cdb0d186d7ea8e1be042959 *src/Priority.h
7abf822e003aecddc9f3c835fedfa37c *src/Profiler.cpp
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976c9bf0d2f8a271883f5f34cef4c2f6 *src/Range.h
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586681b059463845e359637d9425b9d6 *src/RangeList.h
923e0a3a4f281a76b3a99e70400873ef *src/Rannotation.cpp
640a6895fe50cf13777a73d2498986ca *src/Rannotation.h
3d1b5b685392b80254b22242a5d43a9b *src/SequenceUtil.h
387eb89d34fe3c3d18b2d93a734d582e *src/SimpleMatrix.cpp
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17a3d14fd1153f81af7b0bce22190cc0 *src/TabixData.h
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8daf08291f0841ac552190e1271cd0d7 *src/TypeConversion.cpp
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7e44626bee9969473c4970346f7693bb *src/Utils.cpp
5e7add4be9e3567638c29704044564cd *src/Utils.h
354557b9450e958598141e4a1ca25425 *src/VCFBuffer.h
6dd8895b1f308a6f48202f0f54ee7ad2 *src/VCFConstant.h
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938cd6107b805c0c53c71202c14c9f02 *src/VCFFunction.h
117ba480aba2f66b889425ade7ff9d69 *src/VCFHeader.cpp
fd0e89070c4faa3ccb3a5aa1de32fe6c *src/VCFHeader.h
47590e10745ed94857230e87700200db *src/VCFIndividual.cpp
ff41af0fa67d5e91ccc7d9b66986a9b3 *src/VCFIndividual.h
552321d7a3b6481df8133c33e0d5c104 *src/VCFInfo.cpp
9c67c0226efd1fa4abbf983e20755859 *src/VCFInfo.h
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465d0a0528782dea287bf8260e970bdf *src/VCFInputFile.h
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a9f135cf6c369a13d43510eaff9c983b *src/bedidx.c
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48cd8fc534ffa1468ad3a66fcf280712 *src/khash.h
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1f03681d00e0cc9f8f3bd7142424f25d *src/knetfile.h
89e7b91e8dd04627d7ed7833322e8ce9 *src/kseq.h
05ffa87e772c91c82b5a7f33dea80aea *src/ksort.h
6b1b42bbbbe56cdd2bdec966f4fbc3e7 *src/kstring.c
e6fa98213a711d4a816a9c35a0a90bdb *src/kstring.h
cb1582a1de62dc12591b19ef838c5c1b *src/rvMetaLoader.cpp
a82d04cdb18e2e01c7f08b979e5c44e4 *src/rvMetaLoader.h
b7bfd98edaf8764867e12fcf20ce0053 *src/seqForStat.c
48a97b0705735bf0093031dc9928304c *src/seqminer.c
9ea09d7361b319cb5e4ca2d752a70e9d *src/tabix.h
dc5b59d84f2eb95b3f6b26818ed9e4d7 *src/tabixLoader.cpp
5c463acce24b036d6912ab184f9de454 *src/tabixLoader.h
53e6f35860621109da0de128f3207114 *src/tabix_index.c
53fc599227476643816a4a82f647e9cb *src/vcf.c
656047f89fa33b35e733f932a891da01 *src/vcf2genoLoader.cpp
e7d01db88c60614c76e804c601770cca *src/vcf2genoLoader.h
7e96a19db60eacfeabeab2cb47973be6 *tests/tests.R
