58e2f5fe1c0d0a135859157e21d12d0d *DESCRIPTION
01114f6951e6e40ce15508e701370f39 *INDEX
56370c56978858ebef67c8bd8c42b932 *Meta/Rd.rds
67d0d5964f3a04d88f780b55cff145de *Meta/features.rds
75f0d947feb65a62f93828f1a2b97c84 *Meta/hsearch.rds
50b120819e414ce1d3bf57c56ab82e12 *Meta/links.rds
1cb1168ca228ca371f4db39edab75dfc *Meta/nsInfo.rds
cae6bfec3fbbc39e5c9c8c1b6a0ddd1b *Meta/package.rds
4d995250f04e009cb2cc79e2e4257c23 *Meta/vignette.rds
7eb4fbbbede837223c7b6cfcb082b010 *NAMESPACE
1516404704604ee42e96331724e79b75 *NEWS
ebf0fc819595d631b8bf280c4b049940 *R/amplican
43173d74bcd2fc42543365cb72a8a212 *R/amplican.rdb
b879451fbbe29bd17dc2323e752aeabb *R/amplican.rdx
b8ccc81f31c0559fa085bd79613e7357 *TODO
a272ac41fce47d6da16060c76dfda77b *doc/amplicanOverview.R
18f35f735b7f1186539479877068a00c *doc/amplicanOverview.Rmd
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6b59d5f4c92230fdecf23eba01c13c7c *doc/example_amplicon_report.R
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f7e09e656e7adeab4d08374f51d5f43f *doc/example_barcode_report.R
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d1fd334a6de242a797224b0f1eea3d48 *doc/example_barcode_report.html
5a439e661cf5ac1dfdef40d9c616813c *doc/example_group_report.R
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f723acd64c52c009eb377b05895d8c39 *doc/example_guide_report.R
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77fe6b9ceee70f11019a28f6b7e10bbe *doc/example_id_report.R
83b812e79ee36e54aea7c4dfd4c4a37c *doc/example_id_report.Rmd
38f62dfe41747622579e6ca3e8f6b7e6 *doc/example_id_report.html
df4641d793b8a0c11a6e8c56907c1048 *doc/example_index.R
e0a23b3217b10e80f997eb0aafa8c5cf *doc/example_index.Rmd
d4b53a99cdd6ae319b8d79eb04d0da7e *doc/example_index.html
7131ab7b643c5b11ea9ba149b4feede7 *doc/index.html
76d9b86f9c262152ff6206ed59d5bfc9 *extdata/R1_001.fastq
e9b23c3d59fbbfde82020662525dc0c6 *extdata/R1_002.fastq
d07236649c07ec61d4eec9914cc11833 *extdata/R2_001.fastq
09c06d090060558414906686147b955d *extdata/R2_002.fastq
ec94d593ef31ec53f37c31481d51b891 *extdata/config.csv
edea2c9bbd0920fac8d68f4866b378f3 *extdata/results/RunParameters.txt
8a126cf151de4db61309faa218482457 *extdata/results/alignments/AlignmentsExperimentSet.rds
829ede2b4ee0eed965d64e4313e815c6 *extdata/results/alignments/alignments.txt
20e60e63971f4271adaba015e8356280 *extdata/results/alignments/events_filtered_shifted.csv
20e60e63971f4271adaba015e8356280 *extdata/results/alignments/events_filtered_shifted_normalized.csv
c475e45313b924748580d9e897710b80 *extdata/results/alignments/raw_events.csv
6658a89f707a57d30aa48a43e724a8e0 *extdata/results/alignments/unassigned_reads.csv
b36361211ef17ac080a35a3de925628a *extdata/results/barcode_reads_filters.csv
202b29d290fc86a48046bdcb079a06d7 *extdata/results/config_summary.csv
61e4f5ec45479c332fc4285aa247a4f3 *help/AnIndex
f7cab535be93dc8909169d7c06eb94ac *help/aliases.rds
8c500a778330de60f32c4f0c11cd860d *help/amplican.rdb
4caf6db9d09f1d518fa7ba71510018e3 *help/amplican.rdx
7630702ecfb08dcf3829d7af9c617194 *help/paths.rds
c59b454d59b828122e92938dd3103f8b *html/00Index.html
4bcc33a360392c2b6610fff0e71ff7af *html/AlignmentsExperimentSet-class.html
b6763e6916890c631fdc3f2643803b1a *html/R.css
268eda03d29963075cfc88276087d14b *html/alphabetQuality.html
6f6a4a726afc813721fdef7136804bd8 *html/amplican.html
87d8eb500cbd8fd5740d47b8f96be433 *html/amplicanAlign.html
0e1262b27d4b5fba2f171dc9c0519807 *html/amplicanConsensus.html
983a7a03151a6b2006fb18e819724aad *html/amplicanFilter.html
9bf33d2469dd98316691d6c4cd9f9067 *html/amplicanMap.html
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bad1bc98593cbc0cc98e750a1b030c12 *html/amplicanOverlap.html
8d6b45d39486e5cea16ceadb94b978d2 *html/amplicanPipeline.html
580b54a753da7992d82c57827fe29cc0 *html/amplicanReport.html
056ad993e3c356d3c793a38a785b5db1 *html/amplicanSummarize.html
942b255789fb001c742634949816184e *html/amplican_print_reads.html
40aa4733f850e4a2a80dca9b2542a770 *html/assignedCount.html
163a9498f810964475958df72d2d1877 *html/barcodeData-set.html
bb1be3a233f09649c2d6bff0494119e5 *html/barcodeData.html
976662cc72b5e3b10c7c615bd4b65932 *html/checkConfigFile.html
c0700bd50487e423612a626c66dc20d8 *html/checkFileWriteAccess.html
1f63a3f97bb003012f11f725d4054aa7 *html/checkPrimers.html
7aa4905ee52f1de60321f87b824627d1 *html/checkTarget.html
a8def42de4a4a72ea4b99b6aa2aad199 *html/cigarsToEvents.html
3742014dc5356a9015605dcdec91ea0a *html/comb_along.html
8d999c9e451b20b246342d4038be5342 *html/cumsumw.html
1644d4688e8ccb457384fee6c9a909f3 *html/decode.html
31f77408cecb7fc177814c9aed38dc79 *html/defGR.html
d2dfda99424ebe243222dde0fdf6cc68 *html/experimentData-set.html
994e46b3ab0e6e1d4e8376f73f581588 *html/experimentData.html
9136a4b51be0f94e5170b09ba26603d2 *html/extractEvents.html
77752eafe57439eb144b3fc3abde6f3f *html/findEOP.html
6b55d1b5e36eef3161fe64d86a782f2c *html/findLQR.html
65b824b448111691ae7ac98727249e64 *html/findPD.html
1e8236c9b63458736692dc2a9faf0e06 *html/flipRanges.html
0969527a761c941db2748296aa9c3e25 *html/fwdReads-set.html
2799f89a23cbf31578296751fb0a7071 *html/fwdReads.html
180c8f17b186cd38a8ef132ff74f2dda *html/fwdReadsType-set.html
bb4186d8d4d0c6310d82db8a0ea7bafe *html/fwdReadsType.html
76bc36917551d9c8e99a6e6ba48f057f *html/getEventInfo.html
e194e258e7e849cd16f86106a65fd641 *html/getEvents.html
ec94c5d2540cb8f2dc1189c98bbad870 *html/get_amplicon.html
c24d120aa6ba22450c54fdad6343cfdb *html/get_left_primer.html
7ba05ac7137f9fda79b86153c655b150 *html/get_right_primer.html
f7fa218d46c6dcf3c5e7480b82edeb26 *html/goodAvgQuality.html
f6812f2c5cb567827af776318c2edb30 *html/goodBaseQuality.html
cef5c1c8b85adf24a0659e4a3966aafb *html/lookupAlignment.html
227bc8e9426762cd3f62c94fbe264c08 *html/makeAlignment.html
b9090baf00e7fd5f173cababf2782ccb *html/metaplot_deletions.html
e3e0b4554ae119d4f26ebdc59079f0dd *html/metaplot_insertions.html
3b867f4635c577ada67383bc6c5bbc06 *html/metaplot_mismatches.html
1eb85242211e5a34e2ccf2011a08cd9f *html/pairToEvents.html
c326f055e499275b45704c31a4cc77eb *html/plot_amplicon.html
04141b9bae9a0d45edd40ac457435dd1 *html/plot_cuts.html
fed5110e331d9b6ac6d55133530f3a23 *html/plot_deletions.html
f376f7316bc2a43ebc2eaf2eeaba9ce7 *html/plot_height.html
238fb2f0fde63f06954dc106c5135b3b *html/plot_heterogeneity.html
952862572cf08097147608dc3a8bef37 *html/plot_insertions.html
e17873769b0dab0c74ea2d6fa2b08971 *html/plot_mismatches.html
156e15261c8d78f347985f35d23d6339 *html/plot_variants.html
d7996c3a673e599a8fe0a2cbac9a8e47 *html/readCounts-set.html
8eb22126132976929fcda72bab8ccad2 *html/readCounts.html
747a417d58c8363e81911b7204915262 *html/revComp.html
664b38d3391ef3066ccad8165139f940 *html/rveReads-set.html
1c21b476c152649ce9e2823ade8099e1 *html/rveReads.html
fa31f55fad9db54c6f377fa0a8d4dd44 *html/rveReadsType-set.html
f77b79012a5bbdcf0800c382280da9cd *html/rveReadsType.html
0cdff72ff061a241650f23b39371c33a *html/unassignedCount.html
fbf8400f064c2c8f5d970fbd91784f1d *html/unassignedData-set.html
28b50010fef4c6bec05a8f63df0fb512 *html/unassignedData.html
7511430b0687fe50d248fbaf92305a40 *html/upperGroups.html
5d8285a054f7a59b86e8b14ad87827d5 *html/writeAlignments.html
4fa77711108e61f3e8a486add8060a2a *rmarkdown/templates/amplicon_report/skeleton/skeleton.Rmd
655218255ebe76ff75d364fa460699ff *rmarkdown/templates/amplicon_report/template.yaml
6d75664702668085b30adfc79ae9f7f7 *rmarkdown/templates/barcode_report/skeleton/skeleton.Rmd
91dcd8aab8a92b0b874855a7fef5c4d8 *rmarkdown/templates/barcode_report/template.yaml
736a7f171c983e68bf7db7c4cb77155a *rmarkdown/templates/group_report/skeleton/skeleton.Rmd
d09ec79227254463515c1460602e23ea *rmarkdown/templates/group_report/template.yaml
44ebe0ec3bb4143e35d51deb680c912f *rmarkdown/templates/guide_report/skeleton/skeleton.Rmd
4f2ab0b3739252a8431f9d2ef5d04276 *rmarkdown/templates/guide_report/template.yaml
8d929479f71c8e6ce1762710a2e941cf *rmarkdown/templates/id_report/skeleton/skeleton.Rmd
d0f78fe1028bf29d03ad956315e83e92 *rmarkdown/templates/id_report/template.yaml
39d964dedd1f521737941d05509d8235 *rmarkdown/templates/index_report/skeleton/skeleton.Rmd
08df645e81995db2d228de09f69a0cea *rmarkdown/templates/index_report/template.yaml
60b0f0e1f1870a8c9e5ca15743d862ed *test_data/test_aln.csv
08c09237fc07e51e8e66072379825ace *test_data/test_cfg.csv
