2c12443d4448ad27d42736cf21b225d3 *DESCRIPTION
ac7fe82d2ad864c20f2aae1fb82c4fe9 *NAMESPACE
05b8bce6dc4615009a2537217f24684e *NEWS
f681a987a4f42b56fb59dc89a81bdc7c *R/RcppExports.R
8402e13c3298d6afdf9240cd594bf04a *R/callMethylation.R
41c3a6a3c7b48d464e1f7dbb10450f8b *R/extractPatterns.R
1512eb2f17173a961fd90a471846a1ad *R/generateBedEcdf.R
ab697382cb9d0d9fc3c37d174839a866 *R/generateBedReport.R
cf3b1b2e0bb63a7034f644ec4b8d8673 *R/generateCytosineReport.R
58fe61d0c25cfc28c1f82510e48f3ef2 *R/generateMhlReport.R
c79fafbf6d47f81ea1db3591b4bf17b9 *R/generateVcfReport.R
978bfb0d534d4286adfb29d75422327f *R/internal.R
027261aa9a9eba84acfdc6c021780ac3 *R/plotPatterns.R
74f65ccdcac065feb82159b3757052da *R/preprocessBam.R
8a18d9ce82d0c915c8b16975761b60dd *R/preprocessGenome.R
a9b436e9174301c669e27a736e3320d7 *R/simulateBam.R
3afb6cb9d81872e8485db6d2e1640862 *README.md
4f96baedf3953c9f361ae7f5127aab18 *_pkgdown.yml
c516a3ce270f3addc07016de029a3255 *build/vignette.rds
632701b698bfd2e27a05c8ad7acac7df *inst/CITATION
01664ea050259d14f850c3dd52a5264e *inst/doc/epialleleR.R
4aef720c37fa96782ef30f37f401e346 *inst/doc/epialleleR.Rmd
d3e79b932b4056b26754170d01c15fb6 *inst/doc/epialleleR.html
6d99da2463ce194e50373aa46a46832e *inst/doc/values.R
03f85e834ce630a5931fea355ddbeb5c *inst/doc/values.Rmd
ae70ab87dc1e7aef0a55e04ff8fe4409 *inst/doc/values.html
58f833017ad83577c148c2c1e597e132 *inst/extdata/amplicon.bed
b021a04d94a76e4d8609419f929d177b *inst/extdata/amplicon.vcf.gz
fb65422720c8a20dd52b4cb349319df5 *inst/extdata/amplicon.vcf.gz.tbi
08f6f073a2b915f0cce062b75daa8c39 *inst/extdata/amplicon000meth.bam
8a9175527138cb03e08ccbb5eb1be447 *inst/extdata/amplicon010meth.bam
5090d9f275a998bf55b41295e3a9a97a *inst/extdata/amplicon100meth.bam
532c9c5addb7bb3edd980fbe8c51d680 *inst/extdata/capture.bam
8238372c018ccbc0466a6f724fbaa479 *inst/extdata/capture.bed
152066bcc0d8b507efea3a5ae073c000 *inst/extdata/capture.vcf.gz
f0b16c21dcc3c8d56799294862c6c3d7 *inst/extdata/capture.vcf.gz.tbi
eedee46794a999f6f590821b6f428021 *inst/extdata/test/bsmap-pe-namesort-zs.bam
56f6d441dd87609b5199cae6f23dd38b *inst/extdata/test/bsmap-pe-unsort-zs.bam
51e64e3834bfbd4cb8f63bcef10742f9 *inst/extdata/test/bsmap-se-unsort-zs.bam
c730ae0b3d9e8e2c17fa5451286fcfe3 *inst/extdata/test/bwameth-pe-namesort-yd.bam
39b3fe1f5a4caee160fdff98e42a7dec *inst/extdata/test/bwameth-pe-unsort-yd.bam
59ea2d42f1d52689ba1c46a32c073de2 *inst/extdata/test/bwameth-se-unsort-yd.bam
3bd4de272359f2ac18d2e5550a5b69c6 *inst/extdata/test/bwameth-se-unsort.bam
ea45fdb271bd7d05ba62784f111818f2 *inst/extdata/test/dragen-pe-namesort-xg-xm.bam
50bb3ae5e6a6917cbe29b1e3a8011e18 *inst/extdata/test/dragen-pe-namesort-xg.bam
30bbb6967b8566d660e5c165e0673095 *inst/extdata/test/dragen-pe-unsort-xg-xm.bam
e42654051562b1d37a3a881290361d1a *inst/extdata/test/dragen-pe-unsort-xg.bam
bc5d756188832c02da88a55e5c969ee1 *inst/extdata/test/dragen-pe.CX_report.txt.gz
f27b657a8644b7a190758d569a7134ca *inst/extdata/test/dragen-se-unsort-xg-xm.bam
b970b667e937f219c1037bd223174c6c *inst/extdata/test/dragen-se-unsort-xg.bam
958b1ce872a2853895c3b475eddf5815 *inst/extdata/test/dragen-se.CX_report.txt.gz
7f81afe3a9442594661d37749f32d9b5 *inst/extdata/test/empty.bam
50c39c99240cbde64a078c5141b7bd25 *inst/extdata/test/reference.fasta.gz
7c064ec257d0c934b8715dd7b2ff4973 *inst/extdata/test/reference.fasta.gz.fai
7dea362b3fac8e00956a4952a3d4f474 *inst/extdata/test/reference.fasta.gz.gzi
c6488bb9ece988cdd1ae8e7a8a46f5b5 *inst/unitTests/test_callMethylation.R
a8690a788937f92bb8e8594b3f7a3536 *inst/unitTests/test_extractPatterns.R
7d58c77c7a24dcf649b5c367c7c2cb5c *inst/unitTests/test_generateBedEcdf.R
cc3b30eef6fe5fcb2242414220575adb *inst/unitTests/test_generateBedReport.R
1834e36a5ba23a706b7410c843bf10e8 *inst/unitTests/test_generateCytosineReport.R
f0f1a83f94db3fe65ca942334e817cd9 *inst/unitTests/test_generateMhlReport.R
6ae098b505f772523affe99dc3dd138d *inst/unitTests/test_generateVcfReport.R
3c5a0a9b2910244bee495afd52267c32 *inst/unitTests/test_internals.R
2828c778c4a87a848156c0928ecc005e *inst/unitTests/test_plotPatterns.R
b4117f11523453d0e3bec73291f3b889 *inst/unitTests/test_preprocessBam.R
8211b224e9c7328761b03b5e2b548a50 *inst/unitTests/test_preprocessGenome.R
b74fa5f432d9faf62cca3f1580efbf8e *inst/unitTests/test_simulateBam.R
610008be2666bf4185b5b3b4781b4ce0 *man/callMethylation.Rd
57dd9de0ae9529a1dbd8e8360382943d *man/extractPatterns.Rd
a8d26ce5ac7abf8a50dc677abf56a764 *man/generateBedEcdf.Rd
ecb333dfc40b81a71ed13eb546306e2a *man/generateBedReport.Rd
08612a3e8dd6edbe2038bd4f39620345 *man/generateCytosineReport.Rd
f3964fbd5b1aa5167f35308d5420eb59 *man/generateMhlReport.Rd
8afe8e83b200a25211a41f5bedc7030a *man/generateVcfReport.Rd
aa9a1a5e6138ecb1dd61420f34ac3a01 *man/plotPatterns.Rd
b58bf3f270b199a55bfff8c5a14b2d7d *man/preprocessBam.Rd
2845a22ffaed7797fb81adbbcea35f88 *man/preprocessGenome.Rd
793fe59178b3a583c2f31024acce9ec2 *man/simulateBam.Rd
64754d18bce35230845e5affa14b9a2b *src/Makevars
52eb92993292072e3c49afd8e691a4f7 *src/RcppExports.cpp
4af7203260d9b7f911025308017fc086 *src/epialleleR.h
4b130e690d357a6007c25aba6f7561d6 *src/rcpp_call_methylation.cpp
4a3708c7a53ef3717b97bdc594116157 *src/rcpp_check_bam.cpp
2d34f292db1b3d30201756ab7266b2f2 *src/rcpp_cx_report.cpp
b8fab67a1fbd4e5c2ef753f2f0f0ed42 *src/rcpp_extract_patterns.cpp
a775b52ec145db5e88b069ed789589de *src/rcpp_fep.cpp
f17c0c42f5e4334405abf26620f018c7 *src/rcpp_get_base_freqs.cpp
406cc41fc1cc7ca1a28005980e848dfb *src/rcpp_get_xm_beta.cpp
b4b6df0845de7d0063666e0cc4f6948f *src/rcpp_match_target.cpp
32172388e9e39f89a33cb85790e73a31 *src/rcpp_mhl_report.cpp
3385623e9b31771201b55381d0429e3e *src/rcpp_read_bam.cpp
50bcf40fe1efce78fc823b5c9f9e7f12 *src/rcpp_read_genome.cpp
87fe163e510d06a050565e6d66ab27f1 *src/rcpp_simulate_bam.cpp
95e721c414a85f463f984278e3c4d6a4 *src/rcpp_threshold_reads.cpp
243f280624b0908b4eed25aadc2f286b *tests/runTests.R
4aef720c37fa96782ef30f37f401e346 *vignettes/epialleleR.Rmd
9aa6139b3da4297f4007e93d413df028 *vignettes/epialleleR_logo.svg
46692a59acd8e4075bc5949db5af41da *vignettes/epialleles.png
03f85e834ce630a5931fea355ddbeb5c *vignettes/values.Rmd
