a0b7bdb5ab9158fad99363230a5bffa2 *DESCRIPTION
ac7fe82d2ad864c20f2aae1fb82c4fe9 *NAMESPACE
adf358c4414db8cf3098ff985af30a01 *NEWS
927fbf3774f13fc0ca158e1dd64ab626 *R/RcppExports.R
8402e13c3298d6afdf9240cd594bf04a *R/callMethylation.R
6ae7fac3b309fdb0fef9de999aa4075b *R/extractPatterns.R
1512eb2f17173a961fd90a471846a1ad *R/generateBedEcdf.R
8a0574afde52e14f5d640ca33ad5458e *R/generateBedReport.R
06f653b18baf469b59e686233a1be3f1 *R/generateCytosineReport.R
08f11d94ec14e60168c7217014d5ff6b *R/generateMhlReport.R
1d5fcdde1ded9fb902617c5a81be7a49 *R/generateVcfReport.R
2f9f490560b7e53e3c98150c46a9c5d3 *R/internal.R
027261aa9a9eba84acfdc6c021780ac3 *R/plotPatterns.R
f2dbfa265d901063dd41c977dec3d17a *R/preprocessBam.R
8a18d9ce82d0c915c8b16975761b60dd *R/preprocessGenome.R
a9b436e9174301c669e27a736e3320d7 *R/simulateBam.R
f6f854ee45577c7daf14ab51c1775df4 *README.md
4f96baedf3953c9f361ae7f5127aab18 *_pkgdown.yml
403b6a293842f61874156c71f710da6a *build/vignette.rds
632701b698bfd2e27a05c8ad7acac7df *inst/CITATION
ca851f33f8eabaac5dd2d1820d3b5253 *inst/doc/epialleleR.R
9003ef5a29e2b9964deb11dc9ca0aee6 *inst/doc/epialleleR.Rmd
68c72ac7cac9314e65ccb0e753f7c58a *inst/doc/epialleleR.html
7eed7238643e7f72b905223c93a98063 *inst/doc/values.R
7acf39369eb00556a0251f12f4ccdd86 *inst/doc/values.Rmd
e487eb4a9c5b0610a35af43de437abe4 *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
33b29026ee19c7d8720719d9e8b70c52 *inst/extdata/longread.bam
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
85652f1a461433aaa354591e0f801cea *inst/unitTests/test_extractPatterns.R
7d58c77c7a24dcf649b5c367c7c2cb5c *inst/unitTests/test_generateBedEcdf.R
620e5821ff4df91c57218ee80923be3e *inst/unitTests/test_generateBedReport.R
348fd1fc756857aa7e058e0a79f8e360 *inst/unitTests/test_generateCytosineReport.R
f77c7c2f30907f6d05e1a8ac30b3047e *inst/unitTests/test_generateMhlReport.R
158c1157e9ab7ce6b810ca33c5915c47 *inst/unitTests/test_generateVcfReport.R
3c5a0a9b2910244bee495afd52267c32 *inst/unitTests/test_internals.R
2828c778c4a87a848156c0928ecc005e *inst/unitTests/test_plotPatterns.R
e0b79e9ca015cc7614142e4b4181d6be *inst/unitTests/test_preprocessBam.R
8211b224e9c7328761b03b5e2b548a50 *inst/unitTests/test_preprocessGenome.R
b74fa5f432d9faf62cca3f1580efbf8e *inst/unitTests/test_simulateBam.R
610008be2666bf4185b5b3b4781b4ce0 *man/callMethylation.Rd
30ff3b4acaab7e0dfa065da868cc42b2 *man/extractPatterns.Rd
a8d26ce5ac7abf8a50dc677abf56a764 *man/generateBedEcdf.Rd
c15baa9cf845e59a17f7b61f28682e89 *man/generateBedReport.Rd
adbd35f56bcc59d07f098c1f189229cd *man/generateCytosineReport.Rd
a7dbd1272e85a37f31930497e15a68e9 *man/generateMhlReport.Rd
0605e205cb0a0da796932ef07471b02c *man/generateVcfReport.Rd
aa9a1a5e6138ecb1dd61420f34ac3a01 *man/plotPatterns.Rd
368bbd85a7310c2e547dee180a066953 *man/preprocessBam.Rd
2845a22ffaed7797fb81adbbcea35f88 *man/preprocessGenome.Rd
793fe59178b3a583c2f31024acce9ec2 *man/simulateBam.Rd
64754d18bce35230845e5affa14b9a2b *src/Makevars
57f1b58416c6360f962ef2027ebfbc39 *src/RcppExports.cpp
4af7203260d9b7f911025308017fc086 *src/epialleleR.h
4b130e690d357a6007c25aba6f7561d6 *src/rcpp_call_methylation.cpp
4a3708c7a53ef3717b97bdc594116157 *src/rcpp_check_bam.cpp
96811ef718f8fda96f69454a1aa5ca53 *src/rcpp_cx_report.cpp
d51ec5597e27d19523495d78346a4dc5 *src/rcpp_extract_patterns.cpp
a775b52ec145db5e88b069ed789589de *src/rcpp_fep.cpp
4bd151455170f7b930d357e6e8993e38 *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
b54fc68dda0c5e45948f787f59d95494 *src/rcpp_read_bam.cpp
50bcf40fe1efce78fc823b5c9f9e7f12 *src/rcpp_read_genome.cpp
b9152405efd2197bdaa9f85355369fdd *src/rcpp_simulate_bam.cpp
d235de34feb776c358b393ffb376ba4b *src/rcpp_threshold_reads.cpp
243f280624b0908b4eed25aadc2f286b *tests/runTests.R
9003ef5a29e2b9964deb11dc9ca0aee6 *vignettes/epialleleR.Rmd
9aa6139b3da4297f4007e93d413df028 *vignettes/epialleleR_logo.svg
46692a59acd8e4075bc5949db5af41da *vignettes/epialleles.png
7acf39369eb00556a0251f12f4ccdd86 *vignettes/values.Rmd
