2468b2e5ed049e900d13d6870452524d *DESCRIPTION
90ad6810a05cae048e31b480d20d4179 *NAMESPACE
4ee91d7bc8e08bfb3f474b386ab3fae9 *NEWS
c054b79e39678a360e18fea35ea4b0ad *R/BamTallyParam-class.R
b2f9e2debdefa43f1a132fb924c7cfb6 *R/GmapBamReader-class.R
f02f66f4ec71675badb46581f74c3126 *R/GmapGenome-class.R
d110e3fdffb3894fee6f7f9787312da4 *R/GmapGenomeDirectory-class.R
1175604754cc4d769e972b34fc93582e *R/GmapOutput-class.R
b886758a9fcb195904b8f7c14bca60b2 *R/GmapParam-class.R
9bdf672147eb17e2cd9eff8d2a6ff7d9 *R/GmapSnpDirectory-class.R
8ed98d97b10c60ac64a35f5186d846f5 *R/GmapSnps-class.R
68250d3b48ef1d7e81e7dd6f01cc7965 *R/GsnapOutput-class.R
170e0bb3845b58617b41274c39b72dec *R/GsnapParam-class.R
46b9432d99ba05ecbf96c3623f2957b0 *R/TP53Genome.R
5edc66c2011c19d002fb7cab9b3e62ef *R/asSystemCall.R
fe6b2bb6d1c53eb440c78d853205b68e *R/atoiindex-command.R
b40b67da61abbab38149e64e9137c826 *R/bam_tally-command.R
c513c80f731cf1ffadef8aaec7ba0dcc *R/cmetindex-command.R
f31a69c9e23d37ca02cd271a4c9af4fd *R/get-genome-command.R
d3cf8ecd946db33e21089e381c4a1039 *R/gmap-command.R
b0d76c423b0d7bbdb66769d776e9a2ac *R/gmap_build-command.R
aa6ee1bd0cc5ce73912950f4f66ebbae *R/gsnap-command.R
e57ef7959ce236ec792291febfac1495 *R/iit-format.R
d03952439de43ac3105310a5b758e4c4 *R/iit_store-command.R
d25bc4b12bcaaeae6f549a2495f4c91b *R/info.R
c886246257856cb965b99265654aa57f *R/makeGmapGenomePackage.R
09434578312207dba679722f74b95cfc *R/snpindex-command.R
beb823a6af1d09f403c74a54b05b62ae *R/system.R
ad257fc8545f36949aa379f494f78bb7 *R/test_gmapR_package.R
66612971115621d8451df1675d5d82c4 *R/utils.R
a6c6d4a74ba81be54a11c2e94cbae517 *TODO
6e0fafa7e40e9ee45f14b9ee0eaa900c *build/vignette.rds
a663bf38eaf15078db804e0728316537 *doupdate.R
d44229be3b1b194c3b71a8fcbd09b785 *inst/GmapGenomePackage-template/DESCRIPTION
7a667dd72e268f1516aca44572485cd8 *inst/GmapGenomePackage-template/NAMESPACE
0fef33b3027c30058bb7ae75a8e766b7 *inst/GmapGenomePackage-template/R/zzz.R
f0035142d4a6aeee08469a750d45e049 *inst/GmapGenomePackage-template/man/package.Rd
1440e58fab69d671b6bbd8205f12a274 *inst/doc/gmapR.R
109b15e8f334bd4e791755dde65d4bb6 *inst/doc/gmapR.Rnw
f3e9d75db2279ac2f1ee7b8414f63259 *inst/doc/gmapR.pdf
beb498e61482cd3975ead7669779befe *inst/extdata/bam_tally_test.bam
f36977846d7dcc639a7e7640a8994275 *inst/extdata/bam_tally_test.bam.bai
54fd38fa1f825c52b5abdf221ea77801 *inst/extdata/hg19.p53.fasta
4f1dcf254f8199e07deb97faf0768893 *inst/extdata/p53Variants.vcf
a2e67e810342a9b17acda05cf83ed991 *inst/extdata/test_data_aln/test_data_aln.concordant_mult.bam
95641ecdf644e7f5f4a4af16b7c5d640 *inst/extdata/test_data_aln/test_data_aln.concordant_mult.bam.bai
9099499579de56bc7d36bb37650c19de *inst/extdata/test_data_aln/test_data_aln.concordant_transloc.bam
1cde8e6f8a5488b7cd6303414439f236 *inst/extdata/test_data_aln/test_data_aln.concordant_transloc.bam.bai
63b4cb60bf0c04a872ccbc42ad8f321c *inst/extdata/test_data_aln/test_data_aln.concordant_uniq.bam
fdbde01c45b4c05154ef19ba49fb7c62 *inst/extdata/test_data_aln/test_data_aln.concordant_uniq.bam.bai
f4e172916ff451dca8e24595d1cddd0b *inst/extdata/test_data_aln/test_data_aln.halfmapping_mult.bam
ae9f627e1a07065f86bb2afdf6da2243 *inst/extdata/test_data_aln/test_data_aln.halfmapping_mult.bam.bai
9099499579de56bc7d36bb37650c19de *inst/extdata/test_data_aln/test_data_aln.halfmapping_transloc.bam
1cde8e6f8a5488b7cd6303414439f236 *inst/extdata/test_data_aln/test_data_aln.halfmapping_transloc.bam.bai
f86777a6db34df2d0dbe4f9d00f1b571 *inst/extdata/test_data_aln/test_data_aln.halfmapping_uniq.bam
63c237286d8395555b5c1c2211792918 *inst/extdata/test_data_aln/test_data_aln.halfmapping_uniq.bam.bai
b03f9477f27af44daa8371f58b9da1ad *inst/extdata/test_data_aln/test_data_aln.nomapping.bam
fb78a3abc04ac34e7352a6dc155eece3 *inst/extdata/test_data_aln/test_data_aln.nomapping.bam.bai
9099499579de56bc7d36bb37650c19de *inst/extdata/test_data_aln/test_data_aln.paired_mult.bam
1cde8e6f8a5488b7cd6303414439f236 *inst/extdata/test_data_aln/test_data_aln.paired_mult.bam.bai
9099499579de56bc7d36bb37650c19de *inst/extdata/test_data_aln/test_data_aln.paired_uniq_inv.bam
1cde8e6f8a5488b7cd6303414439f236 *inst/extdata/test_data_aln/test_data_aln.paired_uniq_inv.bam.bai
9099499579de56bc7d36bb37650c19de *inst/extdata/test_data_aln/test_data_aln.paired_uniq_long.bam
1cde8e6f8a5488b7cd6303414439f236 *inst/extdata/test_data_aln/test_data_aln.paired_uniq_long.bam.bai
9099499579de56bc7d36bb37650c19de *inst/extdata/test_data_aln/test_data_aln.paired_uniq_scr.bam
1cde8e6f8a5488b7cd6303414439f236 *inst/extdata/test_data_aln/test_data_aln.paired_uniq_scr.bam.bai
9099499579de56bc7d36bb37650c19de *inst/extdata/test_data_aln/test_data_aln.unpaired_mult.bam
1cde8e6f8a5488b7cd6303414439f236 *inst/extdata/test_data_aln/test_data_aln.unpaired_mult.bam.bai
9099499579de56bc7d36bb37650c19de *inst/extdata/test_data_aln/test_data_aln.unpaired_transloc.bam
1cde8e6f8a5488b7cd6303414439f236 *inst/extdata/test_data_aln/test_data_aln.unpaired_transloc.bam.bai
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8ce0f8a72d00dcdcfd3ff53c8c6cbd52 *inst/unitTests/test_GmapGenome.R
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0b99433a089a3ad0f9647b06a88f13d8 *inst/usr/bin/cmetindex
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3f9a1bd7e9af10d3cad27e3e7356d7ac *inst/usr/bin/gmapl
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8a7eb51eb48d5b4aeb2cee16acb5e344 *inst/usr/bin/gtf_genes
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9deb125096b25ddba4bab97c178a6541 *inst/usr/bin/uniqscan
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2255a31f9be6dd9bfe09b1b121f1dc85 *inst/usr/include/gstruct/bamread.h
9829006d556ce5231f614bc18ef23d55 *inst/usr/include/gstruct/bamtally.h
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8effdf5b6a6a03aecbd98143191754f3 *inst/usr/include/gstruct/chrom.h
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9e175d4f5291cd9aafe006e42cb359cb *inst/usr/include/gstruct/dynprog_simd.h
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158b4d9bfcfe80e83e802ad816e480d5 *inst/usr/include/gstruct/matchdef.h
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9956a30b3c2c527bfad5945c670bfdd2 *man/GmapGenome-class.Rd
832e0a1a82a9e5624c8ffdd10d6ed677 *man/GmapGenomeDirectory-class.Rd
7ee6a810692cacaaa5098cbf60c32978 *man/GmapSnpDirectory-class.Rd
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2398e2a42db63cd3d5e4ed742deceb41 *man/GsnapParam-class.Rd
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7d2ee36bca41b2741383eba94938c127 *papers/appnote/gmapR.Rnw
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