7cd332cfafe3fd70842a7a1724e98088 *DESCRIPTION
e4301f4b3118080ca6db567825529a25 *NAMESPACE
c4268ad0dcaf34e4280b2bd7e3b81f28 *NEWS
16c7d5862f8b5a78fc57b7e184f46df0 *R/Extract.classes.r
7b0f91b9f85c8884dc33d214e678ef30 *R/LD.r
017e83f00d14d0ba3ee5de2f35ec2312 *R/LDDist.r
166e9a51c91da1aae019abff601e1295 *R/LDMap.r
6c6b43cece684eac36993f1c1191c319 *R/MME.r
561e89239126bcc691c3ac56951a0059 *R/add.individuals.r
a96430e63dee57b8ba21a8c2f1fc6e3f *R/add.markers.r
95a5911a085786a007d5c3bb22e600e0 *R/add.pedigree.r
cc95d74f7f826e4ce02dca9e8867c3be *R/codeGeno.r
3ebf0f1946ea09b5dbaf2cbf1bf505eb *R/create.gpData.r
c52167bed3b7343cb734ad18083a2b0e *R/create.pedigree.r
db822db5f3416812878ffa27541e9ca9 *R/cross2gpData.r
e52c331d5aa5cfb6cb02ca559e333e77 *R/crossVal.r
367552329704e84ee6f2228c9a181827 *R/discard.markers.r
d841863795e4c431d73b22fc742fea45 *R/gpData2cross.r
b69294e927cfbd1efc44632f3ba3f7bd *R/gpData2data.frame.r
8f1a7fbd99360def20f82313b5da1086 *R/gpMod.r
f0ae8c14ea94437e19c0e9b764bb4ebc *R/kinship.r
b072240afb4c5df4e4190f2a09afff35 *R/manhattanPlot.r
92512eee109b976419acefa83e364922 *R/plot.LDdf.LDmat.r
bc8c1e5519c4fc9da3b224572ffa59c0 *R/plot.genMap.r
54220826e566f042e45e955be9da3f0f *R/plot.neighbourLD.r
4036194650ee1c6040e23afec5ec5621 *R/plot.pedigree.r
bf8f81050ad411bc4801c8b395876374 *R/plot.relationshipMatrix.r
5c9c613325ba791ff72d57dff5fa4ca3 *R/predict.gpMod.r
104f6c369f62b1597d0db9e0697acff8 *R/read.write.vcf.r
c5e1cb5f8055e70abc7a4fd6b1e6d08e *R/simul.pedigree.r
db72bd5ff81194207d9bfc4500328c70 *R/simul.phenotype.r
0596328a0774c72015590f6fb29e9781 *R/summary.LD.r
17ca3e96d17ebab737d211b1f8dc8c7b *R/summary.cvData.r
4d06e8ca9b587b25effe73a303a00918 *R/summary.gpData.r
0824223b421b0c2934d565055ee1d7c0 *R/summary.map.r
123a3582440892a5520d23b908f074a8 *R/summary.pedigree.r
26c14117783925d66bee204ce59e748c *R/summary.relationshipMatrix.r
2d6cfffc3dc3ab64b650ae94ebd6eb89 *R/write.beagle.r
6ac0d4115e8d99649fa605d9eb4e8ce8 *R/write.plink.r
00daa4742fb137a3dc1fefed81824ae5 *R/write.relationshipMatrix.r
e3272d2c021c4e91135e8b97b758fcdb *build/vignette.rds
2760b50da4fde441c793f37fc2956851 *demo/00Index
041a2f6f832d3294d757469d6d646625 *demo/createWheat.R
99d24a007e3a2f49fbf7c8c4e774fa70 *demo/gpMaize.R
fc32074b371983bc1fbdde1988e0348d *demo/gpTest.R
6aa8a17e6568211957d1436c1a5e3c01 *demo/kinship.R
8de21517efc83b8624d78ec2fa334847 *inst/CITATION
534fc3ff3ddd3e6676c2985ac280364f *inst/doc/IntroSyn.R
ef85847e2a99826648d598be8c735708 *inst/doc/IntroSyn.Rnw
b21e1394f2bdad971c31cca6dcd4a3e1 *inst/doc/IntroSyn.pdf
d23fbcef8707b9added46937149c3e76 *inst/java/beagle.21Jan17.6cc.jar
3b696bd0d12adffe2ce5b4edd3fa672e *java/COPYRIGHTS
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99b8853ad50f75ef50b261d0f29ee19f *java/beagle.21Jan17.6cc.src/src/beagleutil/CenteredIntIntervalTree.java
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27cf3b0a9b81d617d6628a4ae595290b *java/beagle.21Jan17.6cc.src/src/beagleutil/ChromInterval.java
0750a1ee0d1dcd6a7e5edd85a95d7bac *java/beagle.21Jan17.6cc.src/src/beagleutil/IntInterval.java
271d811a7cd269abd935a73f068bbb0b *java/beagle.21Jan17.6cc.src/src/beagleutil/IntIntervalTree.java
cb6b111c4c29b9d734a00b561bfedfa0 *java/beagle.21Jan17.6cc.src/src/beagleutil/Phase.java
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ea8aa71f618aea7e5de4c15d87492312 *java/beagle.21Jan17.6cc.src/src/beagleutil/Samples.java
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c20090d8210805acd534ec0faf053e8c *java/beagle.21Jan17.6cc.src/src/blbutil/IntList.java
ca4d5e94b85a1cf3d01935ce57c2d5f4 *java/beagle.21Jan17.6cc.src/src/blbutil/IntPair.java
2d9169ca4f96a401b60d3f887520e421 *java/beagle.21Jan17.6cc.src/src/blbutil/IntSet.java
424a212979d56a258c8205ec06954f7f *java/beagle.21Jan17.6cc.src/src/blbutil/SampleFileIt.java
9e1d233e523bc0e552827cafef8d14d9 *java/beagle.21Jan17.6cc.src/src/blbutil/ShiftedByteIndexArray.java
e43f8a2d988d2ee80e773280d02b8562 *java/beagle.21Jan17.6cc.src/src/blbutil/StringUtil.java
004735d4b3d14d2eb9bb8b8ec275efcf *java/beagle.21Jan17.6cc.src/src/blbutil/Utilities.java
9cc931b6697e5ad5eee47b343f44a5e3 *java/beagle.21Jan17.6cc.src/src/blbutil/Validate.java
a5b39eea4a0e68e55873e5932af2d083 *java/beagle.21Jan17.6cc.src/src/blbutil/WrappedIntArray.java
8b64f7e2094fe232abca3ceaedb78fad *java/beagle.21Jan17.6cc.src/src/dag/Dag.java
a478ed0b9e1836c3df17847e568eccbf *java/beagle.21Jan17.6cc.src/src/dag/DagLevel.java
62f6604964f7a4c4f6a589a4cb9be051 *java/beagle.21Jan17.6cc.src/src/dag/DagUtil.java
8cfc94be849fab771b6617be7a0c6a15 *java/beagle.21Jan17.6cc.src/src/dag/HighCapacityDagLevel.java
8cf7450cfbf57084da699b5833062b45 *java/beagle.21Jan17.6cc.src/src/dag/ImmutableDag.java
65f652bcdc3cdda7e7be94f02c018ee8 *java/beagle.21Jan17.6cc.src/src/dag/LinkageEquilibriumDag.java
098158c8966c2ea3c5e00276f81e8892 *java/beagle.21Jan17.6cc.src/src/dag/LowCapacityDagLevel.java
e8b341f96d93190f914f5334f8996a5c *java/beagle.21Jan17.6cc.src/src/dag/MergeableDag.java
5ff00de22051e5a1aec735685bb015cb *java/beagle.21Jan17.6cc.src/src/dag/MergeableDagLevel.java
aa7df89bfc342c76d779bd89c2ceddd2 *java/beagle.21Jan17.6cc.src/src/dag/Score.java
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e898aacd9a1772a66a47f91f9034039e *java/beagle.21Jan17.6cc.src/src/haplotype/BasicHapPairs.java
73349c8f4b276e2d8307a8f0d63f0b9e *java/beagle.21Jan17.6cc.src/src/haplotype/BasicSampleHapPairs.java
fe909f1b8e23d19df82c1a7e3a2880ad *java/beagle.21Jan17.6cc.src/src/haplotype/BitHapPair.java
dc11071215bed6e73ae6026be38d91b3 *java/beagle.21Jan17.6cc.src/src/haplotype/ConsensusPhaser.java
1284febe75348fa376ff65c58f907797 *java/beagle.21Jan17.6cc.src/src/haplotype/GLSampleHapPairs.java
3edfb06b39dbd409737487be7ace52e8 *java/beagle.21Jan17.6cc.src/src/haplotype/GenotypeCorrection.java
4a33be0431cced10ff475db89d263152 *java/beagle.21Jan17.6cc.src/src/haplotype/HapPair.java
2a89c2173ff06493cee15ff473002316 *java/beagle.21Jan17.6cc.src/src/haplotype/HapPairs.java
24becb7447276c8a1cfc01adfc6d45ad *java/beagle.21Jan17.6cc.src/src/haplotype/HapsMarkerIterator.java
52045e9b0658bd7f41f333ea431a3b9a *java/beagle.21Jan17.6cc.src/src/haplotype/RefHapPairs.java
b6b6cf49b959fefaaa47a2c1e875fd98 *java/beagle.21Jan17.6cc.src/src/haplotype/RevHapPair.java
2dbf822297434162fc6e6153653dc827 *java/beagle.21Jan17.6cc.src/src/haplotype/RevHapPairs.java
563e33e5ce3200b9231c5609a9d910dd *java/beagle.21Jan17.6cc.src/src/haplotype/RevSampleHapPairs.java
ef55258125ae998e07656b4513d15cec *java/beagle.21Jan17.6cc.src/src/haplotype/SampleHapPairs.java
db3f38135b0f8b2a7f9bcd54cd4747d9 *java/beagle.21Jan17.6cc.src/src/haplotype/Weights.java
38d7792985eb95a9bb04e3f91c671b95 *java/beagle.21Jan17.6cc.src/src/haplotype/WrappedHapPair.java
f551418070f3941ef6a12dc5fbcaaeed *java/beagle.21Jan17.6cc.src/src/ibd/HapSegment.java
d20ef8b3ed46c46aabeb87d660da8afc *java/beagle.21Jan17.6cc.src/src/ibd/HaploidIbd.java
6363adad063f0893a0d25e134d680790 *java/beagle.21Jan17.6cc.src/src/ibd/Haplotype.java
6c548b3161fc2664097eb5305eba2015 *java/beagle.21Jan17.6cc.src/src/ibd/IbdBaum.java
5d9bdfc22e45e569ec384ff821a9b374 *java/beagle.21Jan17.6cc.src/src/ibd/IbdSegment.java
04863c3b3a2dd94a1ca8cf6e45c29f0f *java/beagle.21Jan17.6cc.src/src/ibd/IbsHapSegments.java
e04643ed1000d7ed56177e570a1430e4 *java/beagle.21Jan17.6cc.src/src/main/AlleleProbs.java
f29b5b418efe6d2e57eaf68e68d1d69f *java/beagle.21Jan17.6cc.src/src/main/BasicAlleleProbs.java
5c1240a429fa09c0d59a79a5425f7f91 *java/beagle.21Jan17.6cc.src/src/main/BasicGenotypeValues.java
dbeb0aa66c9ed983afd7575b5ee430a8 *java/beagle.21Jan17.6cc.src/src/main/ConstrainedAlleleProbs.java
21ff0b04703f21e0fa93d838b38474e5 *java/beagle.21Jan17.6cc.src/src/main/CurrentData.java
610f1d38f3f16302b68ca56e3b01babb *java/beagle.21Jan17.6cc.src/src/main/GeneticMap.java
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7620b24d6c5bca10084f97d3a66ec512 *java/beagle.21Jan17.6cc.src/src/main/HapAlleleProbs.java
678f032388b7d2a710adfe3d95940f9b *java/beagle.21Jan17.6cc.src/src/main/HapPairSampler.java
7025e0dfe67bbc639e9516b6a275e8ad *java/beagle.21Jan17.6cc.src/src/main/LiAndStephensHapSampler.java
32ee4e41003e09c390dd5af487ea4945 *java/beagle.21Jan17.6cc.src/src/main/LowMemHapAlleleProbs.java
cf5ffa60c21194c6cf66759704d2bf78 *java/beagle.21Jan17.6cc.src/src/main/Main.java
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11ba04402ac6febec035aa9f745d9621 *java/beagle.21Jan17.6cc.src/src/main/NuclearFamilies.java
67de3eaf78dd020332904ad902869604 *java/beagle.21Jan17.6cc.src/src/main/Par.java
df4b5eb01d4c5f6c21a0378870ca0753 *java/beagle.21Jan17.6cc.src/src/main/PlinkGeneticMap.java
02f98cf472847bec457938410a525ce4 *java/beagle.21Jan17.6cc.src/src/main/PositionMap.java
265110bcc569f75258b9f44de3972330 *java/beagle.21Jan17.6cc.src/src/main/RecombHapPairSampler.java
39bbd0be3e46485384d5255f3f0f3b8e *java/beagle.21Jan17.6cc.src/src/main/RevGenotypeValues.java
8829256a225638dae502f51e5c16789b *java/beagle.21Jan17.6cc.src/src/main/RunStats.java
fdcb8c922f7e39011a988a2f2c8817de *java/beagle.21Jan17.6cc.src/src/main/SampleGenotypeValues.java
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23ab233cc2ca5608673af812c20170a6 *java/beagle.21Jan17.6cc.src/src/main/WindowWriter.java
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446434c2798eefb812e6285c691b96b7 *java/beagle.21Jan17.6cc.src/src/net/sf/samtools/SAMFormatException.java
613730e18d45191e959e09eb080487b2 *java/beagle.21Jan17.6cc.src/src/net/sf/samtools/util/BinaryCodec.java
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616473c41da398c1321b8542075a1434 *java/beagle.21Jan17.6cc.src/src/net/sf/samtools/util/BlockCompressedOutputStream.java
db6e600f67fccfb2dff94a5e60ece0cb *java/beagle.21Jan17.6cc.src/src/net/sf/samtools/util/BlockCompressedStreamConstants.java
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dd4bbb4dffd53d0026fc9a51d192f0a7 *java/beagle.21Jan17.6cc.src/src/net/sf/samtools/util/HttpUtils.java
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9bcee4792605ee9bd23cc495af93d031 *java/beagle.21Jan17.6cc.src/src/net/sf/samtools/util/RuntimeEOFException.java
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5aa69f4e5a3b2b8bff07c7302bb56b6d *java/beagle.21Jan17.6cc.src/src/net/sf/samtools/util/SeekableHTTPStream.java
0d37182d12902a0e95b4c06fc99118f5 *java/beagle.21Jan17.6cc.src/src/net/sf/samtools/util/SeekableStream.java
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a3362a8be39b7226e86e8245baecd270 *java/beagle.21Jan17.6cc.src/src/sample/ConsumeSingleSamples.java
29913e1fd1de830f93a1ad6e3b9dd24f *java/beagle.21Jan17.6cc.src/src/sample/DiploidStates.java
0b3d9e34cb15b667c01cc36a7bd48d29 *java/beagle.21Jan17.6cc.src/src/sample/DuoBaumLevel.java
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a836f83d89d8b223d67de89012682e4d *java/beagle.21Jan17.6cc.src/src/sample/HapBaumLevel.java
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753a0809e587d11b48a00f76655045be *java/beagle.21Jan17.6cc.src/src/sample/HaplotypeCoder.java
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1ea081bd21a8a4ea23601b636555fc87 *java/beagle.21Jan17.6cc.src/src/sample/LSHapBaum.java
7ce75569a23452369590df9889a619d2 *java/beagle.21Jan17.6cc.src/src/sample/RecombSingleBaum.java
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a8d9c8abddcdcd50cedf5c4421412f99 *java/beagle.21Jan17.6cc.src/src/sample/RecombSingleNodes.java
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cce3c997e3d5543f885104264c9bf13f *java/beagle.21Jan17.6cc.src/src/sample/SamplerData.java
5d9218cfdc7b4238a9cd3184bbcb59c4 *java/beagle.21Jan17.6cc.src/src/sample/SingleBaum.java
4ae6de8f8fc7a23e4ffe1114a51a3ff9 *java/beagle.21Jan17.6cc.src/src/sample/SingleBaumInterface.java
18b73de782d607b873c95877eb16513d *java/beagle.21Jan17.6cc.src/src/sample/SingleBaumLevel.java
ae25eff8e6f0b29000b573d7fd5e9fdf *java/beagle.21Jan17.6cc.src/src/sample/SingleNodes.java
be9f1840b014e9bc9429ecb523e3935e *java/beagle.21Jan17.6cc.src/src/vcf/AL.java
c446e5205af83a9e6510bf8479954658 *java/beagle.21Jan17.6cc.src/src/vcf/AllData.java
c37b07313566a6413c9c433ac0ec6fc7 *java/beagle.21Jan17.6cc.src/src/vcf/BasicGL.java
0320f8e1b4aa7b3bb997c759852c2e00 *java/beagle.21Jan17.6cc.src/src/vcf/BasicMarker.java
d3084f5c9d9922e3e3fe6632624a5bc0 *java/beagle.21Jan17.6cc.src/src/vcf/BitSetGT.java
862c4e648019b6f1dc5c95b10e006548 *java/beagle.21Jan17.6cc.src/src/vcf/BitSetRefGT.java
b4a83fca8119de84d6b7f6917b51f2e9 *java/beagle.21Jan17.6cc.src/src/vcf/Bref.java
a74734eb25d70b0193cd1884254f02f0 *java/beagle.21Jan17.6cc.src/src/vcf/BrefIt.java
2ed8db11752c56570e1749ed887ade78 *java/beagle.21Jan17.6cc.src/src/vcf/ByteArrayRefGT.java
09777154670b7708c1a041d50dc4ebc1 *java/beagle.21Jan17.6cc.src/src/vcf/Data.java
235756051a6920b8aebd9bb5b04a10f6 *java/beagle.21Jan17.6cc.src/src/vcf/FilterUtil.java
9ac94baac2af526ef7001af009e5cea5 *java/beagle.21Jan17.6cc.src/src/vcf/FuzzyGL.java
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