37e3cab48b81e519e60c2ba803ff429c *DESCRIPTION
24a928ac37e1dd1ced96808d80118916 *NAMESPACE
2f09b24df75f999a618bbcf2a8fb4a27 *NEWS.md
cf8b47d2a0f31ecae80f4bbe850f943a *R/RcppExports.R
63a679bf7419493e9a302dc81c832662 *R/annot_vcf_to_476_catalog.R
26466e613ef1f34d0f6fc5c68a2a7001 *R/annot_vcf_to_83_catalog.R
00c7e15e94f828248b3e1fef1db01fc4 *R/annot_vcf_to_89_catalog.R
0bdb8c3c5efc66ba7e9c1b26b702160c *R/annotate_id_vcf.R
8953d2ad14136119c231b6e8e9e01d0a *R/annotate_sbs_or_dbs_vcf.R
aeafc646f913b2246edd9856623b11da *R/catalog_attr.R
b5da7b83547ce952be9c7cb1d993162e *R/catalog_build.R
7bcfd34141c91b410d7d7c8fbef8fe8b *R/catalog_io.R
872d707b56f7495e3f5e838128664738 *R/catalog_row_order.R
bfc513df91a3e2e0057c75fe46ed5ac1 *R/catalog_transform.R
f97a2e61e2690c7a1f7720d0bbc38b5c *R/categorize_1_justified_indel.R
2366cbd70e606b9f3ad563a674f7f384 *R/categorize_indels_in_vcf.R
87888b21da678464f905c6525782a665 *R/change_476_type_ids_to_open_intervals.R
27f9a3ad2663f55fcf8c2154f8a791e9 *R/change_89_type_ids_to_open_intervals.R
7ee460f30708949653223bc3fb62dad5 *R/chromosome_names.R
b58c34d13425cabaffb4ecacaebde676 *R/data_docs.R
4ff1efd41dfb9776a280b882241ceac9 *R/discarded_variants.R
42cdfbb508f4009564f11818684caa11 *R/explain_indel_justification.R
7b11f9d938b06e4061a9fdfe2fe15c72 *R/gen_476_type_mh_string.R
e46cc5c7e5ceee4f7459df5714824776 *R/gen_476_type_string.R
d212606c7a0570e3cecda73b0c014c73 *R/gen_83_type_string.R
611d6ce9a3bbcbc5a13f931d95eff63a *R/gen_89_type_mh_string.R
7800380cdb8deb6b8d4a2d07c5c0b6b2 *R/gen_89_type_string.R
2b7df7146f412d34e012054839c28859 *R/genome_utils.R
c3298c0d1931c26a2a8f086c209951e7 *R/justify_id_vcf.R
5aad15a54f8a97c60f22dd7d579ea20f *R/justify_indel.R
ea3ab35bd385d2af74aa5c0493d8c44c *R/justify_indels_in_id_vcf_with_contexts.R
999ed0a1d40b2bd06e97585764c5bc2e *R/lcprefix_fast.R
6904b013bdc48bdb9a486b9a5a885acb *R/mSigSpectra-package.R
94f4c93814f451948cbc6245f17bdd88 *R/quick_check_vcf.R
97f2b60421937f567e25e05ec7a68030 *R/read_vcf.R
5000dacf2c83f44be7053297fbf584d3 *R/seg_simple.R
bb69c655305dc897e172bb9a6b191d8b *R/sequence_context.R
79c9ca33d935fe3092a404bd4fe38ad1 *R/split_vcf.R
a7dc2c7ae29c92f1d09b4d37dba6dc2b *R/strand_helpers.R
7c73c05aef97f1ed7ba5cb770776c371 *R/sysdata.rda
47d3e088c30e797ac65591e26510146c *R/transcript_strand.R
7e5afd58d9c312d1233a3f8eff81fb09 *README.md
8974fccf49474c8ff955f711998be368 *build/vignette.rds
e252a32e566d6a1037e12e3b5b14354c *data/all.abundance.rda
48af61803a7500b15accc5c514aeef18 *data/trans.ranges.GRCh37.rda
117095c775bb567edeaa1283b352180b *data/trans.ranges.GRCh38.rda
38dfffb7ab31f5e7744a9d0784ab4c03 *data/trans.ranges.GRCm38.rda
f09d7e119dc4da2551ce390ab1b6dcab *inst/doc/mSigSpectra.R
7ad8d989a5f047508d5db5c3ef61f287 *inst/doc/mSigSpectra.Rmd
7b8e9f14af804ede0e09ba3c0c87b67c *inst/doc/mSigSpectra.html
e34f31c566d1b387718ba6b8007a4e4a *inst/extdata/Mutect-GRCh37/Mutect.GRCh37.s1.vcf
dbcb84d295791390a324895485755804 *inst/extdata/Strelka-ID-GRCh37/Strelka.ID.GRCh37.s1.vcf
982b3e43d5db44b6ed65ef0874365fa1 *inst/extdata/Strelka-SBS-GRCh37/Strelka.SBS.GRCh37.s1.vcf
933ac0a2815c91fd08c1b07a768a56e2 *inst/reijns_cell_data/reijns_cell_AKO1_4.vcf
08b92c5cf8fd403fc8a29615016ca560 *inst/reijns_cell_data/reijns_cell_BKO1_4.vcf
adc67ba32362c6dc96730af91eb12d2f *inst/reijns_cell_data/reijns_cell_WT1_1.vcf
7c99724824c68384db796f5e6efbc63a *inst/reijns_cell_data/reijns_cell_WT1_2.vcf
132ef1b37e979d0ff7992185512d1d17 *inst/reijns_cell_data/reijns_cell_WT2_4.vcf
88d518b6a2e7e863b31afcf7dd2630ec *man/add_seq_context.Rd
ec05c5da91764bfae7f89459d0801f70 *man/add_transcript_strand.Rd
ed739269eb4ed4d35613b33407431965 *man/all.abundance.Rd
3bb9dc0b40d04ec898fdce5137bb75ef *man/annot_vcf_to_476_catalog.Rd
3c44b939f5185301250f700f468d5455 *man/annot_vcf_to_83_catalog.Rd
47c5a85874eadf7bad6bf8f2a57dcbdc *man/annot_vcf_to_89_catalog.Rd
0300e25c1803f984b4a638195c4dddf9 *man/annotate_id_vcf.Rd
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6023a2f32b0daeed4e7f73b65e2a87e1 *man/as_catalog.Rd
9ec9f2d936ecc039ece49911f7ad4a0e *man/catalog_attrs.Rd
58e30d84a2bc1c8e1127ae9e097ed319 *man/catalog_row_order.Rd
08d75488053b7c72cb121d34f6793211 *man/categorize_1_justified_indel.Rd
65c3e95e3593f3694b48163638fec3ee *man/cbind_catalogs.Rd
354505d2c53f5f8ae48c4e864417d81c *man/change_476_type_ids_to_open_intervals.Rd
3f50fc3bc40a3cf26902f17f02e1a248 *man/change_89_type_ids_to_open_intervals.Rd
dbf2b01d06a6bf40bccdb8ebede41ed3 *man/check_and_fix_chrom_names.Rd
00a5f32433de054f5ade488d956f38b2 *man/check_and_fix_chrom_names_for_trans_ranges.Rd
63c549e2c1880e271b6d2fd89fbb134c *man/check_and_remove_discarded_variants.Rd
fa0c4f91d7c0fdd17948c407558470e6 *man/check_and_reorder_rownames.Rd
8e563527bb229a71120f849479adf239 *man/collapse_catalog.Rd
3afd7d6c4966d9667484b35397378de5 *man/infer_abundance.Rd
391d392ae6a27e486cccf2b252714933 *man/infer_catalog_type.Rd
ee0733eb614850bf6c00a5b662579d82 *man/infer_ref_genome_name.Rd
8b44f646455f9567a519872b37fbf0b5 *man/infer_trans_ranges.Rd
3c30216b379ddc7193b02846e280f441 *man/is_catalog.Rd
f1783a09f86687044f6968caf9b71b71 *man/is_grch37.Rd
551994b2e34d493a49b37b54495ee9b1 *man/is_grch38.Rd
0ddc8ef3ca5a9cd67e9e2ed233f98a5b *man/is_grcm38.Rd
9c90521539b8cf73460719d9f0f9d467 *man/justify_id_vcf.Rd
ea533a08d40c3c56c3c49b7ca22b7bf3 *man/justify_indel.Rd
731fc6b6e71c7004e923c7fff888b831 *man/justify_indels_in_id_vcf_with_contexts.Rd
5ef7de39de4beefb60af42a8c6218921 *man/lcprefix_fast.Rd
14a1e8807459a5e573943297eb128f2b *man/mSigSpectra-package.Rd
32dfd95c3b665ba87f3d3ddda6357784 *man/normalize_genome_arg.Rd
e5bc7be6e9e5b01f464f23f87ed80342 *man/pyr_penta.Rd
9c6f94d0abedfad886cde4024b3e62e8 *man/quick_check_vcf.Rd
e97f71318f64f3e6bbd94462aa8423ce *man/read_catalog.Rd
512b2604baf93b50c7123c4854c03baa *man/read_transcript_ranges.Rd
32aac5bc7eafe93c98752000af52f5e4 *man/read_vcf.Rd
d24972b3c0f0d006e4f287c9d18dd74c *man/read_vcfs.Rd
cd2ed5e75d126235874d688a628c6873 *man/remove_rows_with_duplicated_chrom_and_pos.Rd
9dbec1a8730cd93df3a60929d8b53715 *man/remove_rows_with_pound_sign.Rd
a74d4ac5608d28e6397ee2119574d351 *man/revc_dbs144.Rd
39834f44188dc8aa71ad91f1ffa255d4 *man/revc_sbs96.Rd
c0ea109211802d8a523c8a766d23834c *man/seg_simple.Rd
33dc745b0a52b683222b6f78a2e400ee *man/segment_simple_cpp.Rd
057955b61c83bc207a3ceba7d3172afe *man/select_variants_by_chrom_name.Rd
6b3e762f74614008a53464a3c91b1cac *man/split_vcf.Rd
928ca8cae3f8986ecbfd18cc5d3a7965 *man/standard_chrom_name.Rd
31dea6fe9bda26c5abce829bf0331425 *man/standard_chrom_name_new.Rd
f3e844f9bc495bdb234d08f67691816e *man/stop_if_counts_or_density_illegal.Rd
208a80375d6a43486d369f635e1d5bb1 *man/stop_if_region_illegal.Rd
b1fb2c8261a3cdd168c5c180da600d96 *man/stop_if_transcribed_region_illegal.Rd
8e642dc5f97f0eddad3aed37a7ac4b8f *man/subset_catalog.Rd
23ee899d841f9d802fa76571f41b2b15 *man/trans.ranges.Rd
c6072a6d2372c345b5bb7e4d658a0635 *man/transform_catalog.Rd
8d3390ff5771d15a365899d08edc87d4 *man/vcf_to_dbs_catalog.Rd
a4809ce3f3216db3bfee51c63d9f68a8 *man/vcf_to_id_catalog.Rd
6f75f04c4682470fd25cef56f8168d2b *man/vcf_to_sbs_catalog.Rd
962d0aca04ee164d5a1b1971a1c7d1a4 *man/write_catalog.Rd
2443f4d81a533f65328bbf995fdcec0e *src/RcppExports.cpp
a33142c3e298c870d7c09f29b901f1c2 *src/segment_simple.cpp
05938a389276598bcb5c51f3cae8ae0a *tests/testthat.R
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50375c6433eb367440ebc9afa7ed7140 *tests/testthat/test_end_to_end_id_and_dbs.R
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e7297028dda134caab9494bd2e42c66b *tests/testthat/test_transcript_strand.R
7ad8d989a5f047508d5db5c3ef61f287 *vignettes/mSigSpectra.Rmd
