d374cf3fc887d63f8f4f9fa00484bbf2 *ChangeLog
e02b060577a3faddee13b4497b8cb43c *DESCRIPTION
50c28547d51e8cbb9a908e6696fedb86 *LICENSE
3afbb52bd93205aa6fbf940ae4e9d567 *NAMESPACE
c73956e4acc00b9d651f02ae9df0b159 *R/genMakefile.R
8a4439844ac1e5ada5153ed7f563ff43 *R/seqminer.R
8570f7b85f02dd1c3d21b834e1224ae8 *README.md
131a236039d88977475269c6ee6c6e2c *cleanup
f43e526f7804acf3b0fdc8f10bbbbd4c *configure
62d8f6d197a5152ba0d05836fa2c6bf2 *configure.ac
68b329da9893e34099c7d8ad5cb9c940 *configure.win
a7aa8e76f7e4646af6b644cdf37f2cb7 *demo/00Index
34ab676ae0614287c6170163dbcc0c44 *demo/annotate.R
80afcb0fa924316b839b3d56655d05fe *demo/meta.workflow.R
076b6535f57410f9475402c8748869cf *demo/vcf.workflow.R
783f30a03b947ade65eb1006c46de1b7 *inst/CITATION
1c96de0a2112c8f4cc6fbdb911a29912 *inst/doc/Manual.html
751c636c82b643e5a9498591b5218032 *inst/rvtests/cfh.refFlat.txt
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
f3c9e5e6899c4ad42aa59cb70084b6ee *inst/rvtests/rvtest.MetaScore.assoc.gz
a5b24886972d5f229068eee3449f076c *inst/rvtests/rvtest.MetaScore.assoc.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
9ccb5566cb9036a08c53ae6a1fa27481 *man/SeqMiner.Rd
72462dd67ebda295c444e0636591dd83 *man/addJob.Rd
3e98ec5b369f45de929ebb2b69b0c55e *man/annotateGene.Rd
5e6db86db6f27965cfdbcf2845180a90 *man/annotatePlain.Rd
842f28a8b18ce98362d6efb40cbc2d67 *man/annotateVcf.Rd
fdafce474324e4d9105dba67e81f6ccd *man/download.annotation.resource.Rd
a060c4b7f738e87e84b86fe350409b1e *man/getCovPair.Rd
a7cc8e980742fc176da410a1b50a8329 *man/getRefBase.Rd
fa4aa16a8a499446437c9bc4403799f7 *man/hasIndex.Rd
c4f58c9516bca88a7dd3366e8c6e940a *man/isDirWritable.Rd
cc170606016d436b7053dd3c1f065ce1 *man/isInRange.Rd
25231c6da3e4160286dbafa5b2c1c84e *man/isTabixRange.Rd
a67af89739b1d41f1e5632310ecbeec4 *man/isURL.Rd
b2a36b2b83a60f3549899af99370c665 *man/makeAnnotationParameter.Rd
e635839227d6e17c60e95c6572a228a0 *man/newJob.Rd
1deb46b3aa47beb9206c5a55079eb62b *man/newWorkflow.Rd
e6f4b191ef196055bc8f3b228726b116 *man/readVCFToListByGene.Rd
2b01d9f5668149d9da4ea7f3815c17bd *man/readVCFToListByRange.Rd
c06b3834458ead5d74be1ebb6dedb792 *man/readVCFToMatrixByGene.Rd
c4c6678903ea9a7e0682e3fe5b243550 *man/readVCFToMatrixByRange.Rd
63d514ee1702d98cfb026c5f7dafec0c *man/rvmeta.readCovByRange.Rd
5184d0732bd93c5f25aa092adf4bf567 *man/rvmeta.readDataByGene.Rd
51e1882eae4f8ae10e2fc5dc6997d50d *man/rvmeta.readDataByRange.Rd
fcdb20fb09b4d95c0f095ff6b1a3e224 *man/rvmeta.readNullModel.Rd
35de05e9c57af52f29448dcfc228b01e *man/rvmeta.readScoreByRange.Rd
6275ac5c59057b67af1dae65a970cd3e *man/rvmeta.readSkewByRange.Rd
8f65ca44c82395e251c4eb81356ff86b *man/rvmeta.writeCovData.Rd
7f984db6e41e10e7fdca87cde34be561 *man/rvmeta.writeScoreData.Rd
a68df3869e57b049ca6b2abe7187a310 *man/tabix.createIndex.Rd
e64c6c46ac051a97cc23618c16064362 *man/tabix.createIndex.meta.Rd
b576fce1423a3eae42a48cde9f82e7b9 *man/tabix.createIndex.vcf.Rd
ad9940dd92479de2b06de852b94e4283 *man/tabix.read.Rd
9ad696975628068f5542d07d37c1244f *man/tabix.read.header.Rd
0045ef182d071efc0711eff12ecc0096 *man/tabix.read.table.Rd
0c5f4bdb4aed0aa16f80dfee2ab9a383 *man/validateAnnotationParameter.Rd
021b351bc4475ef77ad098e4d05291fc *man/verifyFilename.Rd
db7687209bb81b41da4a42932c6acbe8 *man/writeWorkflow.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
d7443100bde6685827500cf3c99e7cfc *src/Makevars.in
d8d4eddd760e188a6cef776f728a4acf *src/Makevars.win
d9fbc638f23c8635a9fd66910e89dfd2 *src/Maximum.h
ec4ad4b37abe9e5d654ed2879e0fb200 *src/ModelParser.h
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
baf138407a38de43b7f6296e35271254 *src/Profiler.cpp
173cec97bf2ce2f144131589a8d48637 *src/Profiler.h
ac4e4cf703592a37a2bd05fd297bd4af *src/R_CPP_interface.cpp
b986750f74de29d76e2e0250728eb511 *src/R_CPP_interface.h
976c9bf0d2f8a271883f5f34cef4c2f6 *src/Range.h
c240cc9ee76c664a684d0e2b90c0b983 *src/RangeList.cpp
586681b059463845e359637d9425b9d6 *src/RangeList.h
923e0a3a4f281a76b3a99e70400873ef *src/Rannotation.cpp
640a6895fe50cf13777a73d2498986ca *src/Rannotation.h
3d1b5b685392b80254b22242a5d43a9b *src/SequenceUtil.h
387eb89d34fe3c3d18b2d93a734d582e *src/SimpleMatrix.cpp
ed89460fc7151a3bfc200b066c30ee23 *src/SimpleMatrix.h
6689621f7dbc49a740c515e216369be0 *src/SimpleTimer.h
fa26446157d7f418afe30d19f658363c *src/StringTemplate.h
5575eb01a8fcd58e0971e3fa2d29e031 *src/StringUtil.h
17a3d14fd1153f81af7b0bce22190cc0 *src/TabixData.h
bb24ce56abc3fa0ceef2a3b612afe938 *src/TabixReader.h
a6f33ff1510e19cf36b2f02223bc07b9 *src/Type.h
8daf08291f0841ac552190e1271cd0d7 *src/TypeConversion.cpp
b56e777cacf3711a769b61fe1327d7ef *src/TypeConversion.h
7e44626bee9969473c4970346f7693bb *src/Utils.cpp
5e7add4be9e3567638c29704044564cd *src/Utils.h
354557b9450e958598141e4a1ca25425 *src/VCFBuffer.h
6dd8895b1f308a6f48202f0f54ee7ad2 *src/VCFConstant.h
598a4a74569c09ad42bf6d1c340711af *src/VCFExtractor.h
cd9af145da827e809947e0f915171e1b *src/VCFFilter.h
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
560c4fe44e46997affea874779957743 *src/VCFInputFile.cpp
465d0a0528782dea287bf8260e970bdf *src/VCFInputFile.h
dc2fd142e35674a1b5acdc2045b64607 *src/VCFOutputFile.h
f847d5fd6668bec3c37e88f55d02e48f *src/VCFRecord.h
58c30e048f64b8bd851799393a7df1d5 *src/VCFUtil.cpp
e9e2d549f9cdaf5f06505e30fb64ef8e *src/VCFUtil.h
c99de6988f92eec0eb978e4298303d7d *src/VCFValue.h
aba13a3883d7d117af33a6d8fe8c1ed1 *src/bam_endian.h
eff5a085d8f36bf4a84409e3a1d6f970 *src/bcf.c
613fc63007d9a00f264af2666fea9a04 *src/bcf.h
d13f7631c0a81341a0360467c78e02e0 *src/bcf_index.c
c781f162a813b6370d385952c6fffe83 *src/bcfutils.c
16f046c04a736079b56d6800ccf137da *src/bedidx.c
88d96707db87898de91c0cbb3b8b40f6 *src/bgzf.c
abd042e94b527d534410175167a07e4a *src/bgzf.h
5fbc88f708793e02b648d0fe48fbbe06 *src/config.h.in
48cd8fc534ffa1468ad3a66fcf280712 *src/khash.h
bc4c4daf33b15e7dda3665d4ff587e28 *src/knetfile.c
1f03681d00e0cc9f8f3bd7142424f25d *src/knetfile.h
89e7b91e8dd04627d7ed7833322e8ce9 *src/kseq.h
05ffa87e772c91c82b5a7f33dea80aea *src/ksort.h
6b1b42bbbbe56cdd2bdec966f4fbc3e7 *src/kstring.c
e6fa98213a711d4a816a9c35a0a90bdb *src/kstring.h
51f0c3e192db7d673c3147978f4fb222 *src/rvMetaLoader.cpp
a82d04cdb18e2e01c7f08b979e5c44e4 *src/rvMetaLoader.h
b7bfd98edaf8764867e12fcf20ce0053 *src/seqForStat.c
48a97b0705735bf0093031dc9928304c *src/seqminer.c
9ea09d7361b319cb5e4ca2d752a70e9d *src/tabix.h
5167391521da9e03b0eb29d68714b4dd *src/tabixLoader.cpp
5c463acce24b036d6912ab184f9de454 *src/tabixLoader.h
5018bd833475834bf55d67196ba7ffc2 *src/tabix_index.c
d9cfdd322d3afb508c2a38b61091adf8 *src/vcf.c
656047f89fa33b35e733f932a891da01 *src/vcf2genoLoader.cpp
e7d01db88c60614c76e804c601770cca *src/vcf2genoLoader.h
7e96a19db60eacfeabeab2cb47973be6 *tests/tests.R
