ae68be652f27dc0deb5122ef2e5252f3 *DESCRIPTION
c57cb37009a2ae19f6fef02250ed3bc0 *NAMESPACE
3fac0080f522372290c7203e4dfd9319 *R/applyTallies.R
8606ad245030d71fe736a731404ed0bb *R/call.variants.R
9ea4e9ce14165fb0ecc76b72e4280a23 *R/call.variants.fisher.R
06f6fb0dadfa75261daea01c3398822a *R/call.variants.single.R
a6ab29254eb7ae25f2cb8739627fb3ca *R/coverage.R
4ee02a9995c14b7a8b35d2a7e719837d *R/get.sample.metadata.R
2f476ef119ecc0cc8b98cd4c22c02d6e *R/getChromSize.R
d827119398768031449d520c8d589f74 *R/h5apply.R
0b3249f7b44337e2bae932748d2a8ded *R/h5readBlock.R
dbf88daa21164d6d31f1668fb6d0b6ee *R/helpers.R
a573e1d88a98825ca7248a6156f2a025 *R/mergeTallyFiles.r
1fef4b5ab111e21978173536cc91d68b *R/mutation.spectrum.R
fee361e9ea3d399922b4160cb4852095 *R/plotting.R
40e6b48ec9bc1fed6ae1f38bc0386a1b *R/prepareForHDF5.R
7603f4249129d42cdb2c446831c07245 *R/prepareTallyFile.R
2855cff05e8f4b45f8601b74f1be9579 *R/set.sample.metadata.R
f587151923ac5c4625d1ca96cd7171ae *R/tally.in.ranges.r
f369b598579fbaefee4a58f1c15b61a1 *R/tallyBAM.R
853505513343ced7002c4049075e990f *R/write.reference.R
6525bddd6cccbacdf4af5382aaa6862a *build/vignette.rds
c2945e1af51fac5b5c325587ab05a31c *data/bases.rda
b4d0858b7a50534150c713036c926e54 *inst/CITATION
09991dd1e000f55b142821da4df6de9f *inst/doc/bioc_adapted.css
45c76c8edcaeeabd3d2c68c008b4212d *inst/doc/h5vc.simple.genome.browser.R
22397e70b40c7a5d1efd37dd698da5fa *inst/doc/h5vc.simple.genome.browser.Rmd
f00ea336f9d10fc947aa4ea73bc15f46 *inst/doc/h5vc.simple.genome.browser.html
80d380875083567bb68e9284deffca40 *inst/doc/h5vc.tour.R
6833ce0c16219b1e0b76557c7c60cf6e *inst/doc/h5vc.tour.Rmd
cf84570fdb4610664c2c672dd333b00d *inst/doc/h5vc.tour.html
73ceca9b4a72b1a83d37905ad4d3a529 *inst/unitTests/expected.counts.txt
0a627b8638aee4ce1659079fc42c0946 *inst/unitTests/insert.bam
ef4f5cd7f5833fc619d370bc0f94459e *inst/unitTests/insert.bam.bai
a862e66c570a6d9f7e4d3f00031c5b9d *inst/unitTests/test_tallyBAM.R
be840394c755b27c4f93a7f62979be41 *man/applyTallies.Rd
2913d5536cc18abc3ff2388e72296398 *man/batchTallies.Rd
5074a5fe925436dbdfd53cbeb6764600 *man/binGenome.Rd
b3c53eb53bc586c073b2bed86ce7fc5b *man/binnedAFs.Rd
0c8c1aa0bc68cdbee7a7f6d97191a5ef *man/callVariants.Rd
1ade547754cf04414a481f53a2772c32 *man/callVariantsFisher.Rd
aba095683137eff68fcbdd608a4c5b2c *man/callVariantsSingle.Rd
7d151c705e59ab10bda98c86a98665e3 *man/coverage.Rd
ade539c34dc2cc4517be144dc2dd995e *man/geom_h5vc.Rd
90b2007f5bac79a8581b099228048f69 *man/getSampleData.Rd
ffbe939019996c45c7e645863332dae5 *man/h5dapply.Rd
7578b1e5090e95162636d3574b3e3d78 *man/h5readBlock.Rd
ba858736d29bb920d50a52f87b371d40 *man/h5vc-package.Rd
bd124b46eaf1d40111270d6ba8f50a92 *man/helpers.Rd
2fbf0b9684021c6d778843517e0a91c5 *man/mergeTallies.Rd
689350002dec8192a1c4a47860ad3748 *man/mergeTallyFiles.Rd
949dd744141779559db7b5e48e8d379e *man/mismatchPlot.Rd
656a15515227728b1bafe2f25fc3d69f *man/mutationSpectrum.Rd
27a1727d7718474640976bdaae90eebf *man/plotMutationSpectrum.Rd
26cfd79e0551f378295838aee11f7419 *man/prepareForHDF5.Rd
f5af04fcc297299bb448f202bfed8221 *man/prepareTallyFile.Rd
6abee1e36ccc5d8e672d557998bd230d *man/tallyBAM.Rd
0bce5e293827bfe8c31b71ab33b3faf4 *man/tallyRanges.Rd
4cd96af88e0bbb12d856d36536109588 *man/writeReference.Rd
7de5e3fe53be3a18ea15f563bef9a3be *man/writeToTallyFile.Rd
7b8d1c2c8939e293615971dd97729f83 *src/Makevars
c0cb60ff823f5cd21c36e84827a196a4 *src/Makevars.win
b6f4b3f91a93e5a5b9d3019ee537bb64 *src/bam_plbuf.c
c4c6c93857a981c4485dd3e522a4b13d *src/tallyBAM.cpp
ae2f9f9cea154da8dd4142a23c023d95 *tests/runTests.R
a0eddf26a500c77851cd332199a6e621 *vignettes/bioc_adapted.css
735aa91e9cbd14172924c392e5731add *vignettes/example.plot.1.png
74554e88b984604e2c3ac2599e886228 *vignettes/example.plot.2.png
192d999d399d76f167db3f0b335e5d8e *vignettes/example.plot.3.png
a307b8db4cfbc99a385356189ae5e677 *vignettes/example.plot.4.png
3ec41a850c861409e653a02743feb6a4 *vignettes/example.plot.5.png
22397e70b40c7a5d1efd37dd698da5fa *vignettes/h5vc.simple.genome.browser.Rmd
6833ce0c16219b1e0b76557c7c60cf6e *vignettes/h5vc.tour.Rmd
797e9ce64132650117fa3b59ddd67738 *vignettes/mutation.spectrum.example.png
02a48ac9182c4cf99ff1ccf7da160abd *vignettes/tally.file.layout.png
