a65bb7ea4b66dd0ea79df67ce497a7d7 *DESCRIPTION
b0cd808fda6e1b0d5a1b5c092546e2d0 *LICENSE
16b475cdcc42e823b491e2fcc08de3d9 *NAMESPACE
3171e7651bf5e6da9e387c68fc9ae38b *NEWS.md
df6cc46bc7fae1a55b713f3d5065b35a *R/UPDhmm-package.R
563e1335711de3ec0bc375f7e56912fa *R/addOr.R
211d7a8ffcf93d81523267ef5cd9a7f8 *R/addRatioDepth.R
144b74782db5cd3f5003ebc2ebe1dfdf *R/applyViterbi.R
fd5054f8520223f0286335764f56c137 *R/asDfVcf.R
12ebd63a13c0fb23e208ea39d7936a70 *R/blocksVcf.R
ffbc47281df6f099c74f60ee5a805b6f *R/calculateEvents.R
37d56da3722f4b5322b903514dfa346a *R/collapseEvents.R
60acb0205d2fd1e6fd34f013337d2380 *R/data.R
33be34c0c9be0c2602f708d93f0e717a *R/identifyRecurrentRegions.R
fdd9eb58681c0b1bdb3dd1c676b908f4 *R/markRecurrentRegions.R
7efc1967fd7cb055b2991530535465c2 *R/processChromosome.R
5148b28ff827523e271a845db8b24690 *R/vcfCheck.R
d65a01340a841be41ab24b32477ec0fe *README.md
ed516772b0af386eb8f472cc22439a99 *build/vignette.rds
4b0748939e433b281b442c26178227ec *data/hmm.rda
b7ddfbc13203b0735d6375df1b8021ed *inst/doc/UPDhmm.R
ffcb2b95e62f36e3eec27ae4eebb296c *inst/doc/UPDhmm.Rmd
9f495c0930d4e1b1d1fa3e1ce6251e46 *inst/doc/UPDhmm.html
a547c0f5213329b1b9bb505b0fd62f06 *inst/doc/preprocessing.R
c885d1033579f62a71bfb4158dc1dc80 *inst/doc/preprocessing.Rmd
ca3155df00022be45435e3577510864b *inst/doc/preprocessing.html
56130c12f76862f6595a9fea2f650f1a *inst/extdata/SFARI.bed
a65faf60f1a582739a39a4d9adf41559 *inst/extdata/sample1.vcf.gz
d567eb45a541e997bfe2276a236f11f9 *inst/extdata/sample2.vcf.gz
d567eb45a541e997bfe2276a236f11f9 *inst/extdata/test.vcf.gz
a65faf60f1a582739a39a4d9adf41559 *inst/extdata/test_het_mat.vcf.gz
2b0958b095c603692c3310325bb26a2d *inst/scripts/cnps.bed
6ee6379e335c1a7e4b87de35b4c5cc0f *inst/scripts/extractTrioNA19675.sh
42a4748634a797bbc5912626007363ba *inst/scripts/getFilesExdata.sh
ae51d30ddbdd7506848a992e8eb62110 *inst/scripts/simulation3q.R
aa387557504a562f1997dab8dd792054 *man/UPDhmm-package.Rd
ad8d502362f2f9c52e8824873e631234 *man/addOr.Rd
404930779e9abb5cf42eb7e2cd92b17b *man/addRatioDepth.Rd
4a1a624946f6fe6ffcc0f0cd56529966 *man/applyViterbi.Rd
e40e24e1315ece42640722d05601990a *man/asDfVcf.Rd
b4fd2f1e207c0aa3e69790eb596158b2 *man/blocksVcf.Rd
fc7e8ea05a0775dcbbdad3b7cdf798c7 *man/calculateEvents.Rd
ff2b1a3aadc1a8da1ecca65b8c745e09 *man/collapseEvents.Rd
fa00cdb300b7a9006f3dd369dcf94690 *man/hmm.Rd
829e2ac3e16ca05efda7ae2b340393e4 *man/identifyRecurrentRegions.Rd
60219f0a857f0ba802d28ab2ee488f8f *man/markRecurrentRegions.Rd
3499fd78a77b2777587c6fb358603201 *man/processChromosome.Rd
f51841c39de56d29f02c2899afd9def3 *man/vcfCheck.Rd
6f35e9726d4801c10d3ec636e537e08b *tests/testthat.R
502c5f6204effb0bed0151809860f81f *tests/testthat/test-addOr.R
3f6d03b5d0d9cc28289072abd5427462 *tests/testthat/test-addRatioDepth.R
c770250806a4fe3c5dadc098e0d846b9 *tests/testthat/test-applyViterbi.R
3a3436cf1e7683ab512506f22bb8a69b *tests/testthat/test-asDfVcf.R
58afead505cab6230958bb847bc264a8 *tests/testthat/test-blocksVcf.R
a5ed4e0d5c72282b0e42d1331113b6e8 *tests/testthat/test-calculateEvents.R
9a628d53383accc1c40dd27463f0f042 *tests/testthat/test-collapseEvents.R
47fa9a4c4daf917ba6a362d028c94526 *tests/testthat/test-identifyRecurrentRegions.R
c885e69d162a33a855943340d7753585 *tests/testthat/test-markRecurrentRegions.R
e986da3127fff63940fefcf02c0cd19f *tests/testthat/test-processChromosome.R
6a032c24c9aac91f3e0511260c7a2f20 *tests/testthat/test-vcfCheck.R
ffcb2b95e62f36e3eec27ae4eebb296c *vignettes/UPDhmm.Rmd
c885d1033579f62a71bfb4158dc1dc80 *vignettes/preprocessing.Rmd
