ea88e180bd38533cc81e8273e0e2a5b6 *DESCRIPTION
2ea55fbe3522e70c91b70fa25d8f7089 *NAMESPACE
13833988d4d11752a9be4fa341f6fa6e *R/load_bwa_assignment.R
db946f230e8bce36be9ac09fbd346a7b *R/load_bwa_assignments.R
e9fc4215f3da993825f809f3e91c2b68 *R/load_gottcha2_assignment.R
39da3074d074345fa05b8ba2497ab91a *R/load_gottcha2_assignments.R
3d3b8db1f0353425595e1105d62d5bc0 *R/load_gottcha_assignment.R
1b2ae9310053b3713ef0c82091449b90 *R/load_gottcha_assignments.R
728dad533702dfdd4f3baea1d104ab79 *R/load_kraken_assignment.R
4d6ef0697a39f9d383c757de3c17d117 *R/load_kraken_assignments.R
50e8bc7f583940c2376856849b10295a *R/load_metaphlan_assignment.R
663a3344f47e5b76e4600b7a15515487 *R/load_metaphlan_assignments.R
1d6747df27e4b145421442a30277475b *R/merge_bwa_assignments.R
f2eff5227b3a1d12f16c7da20f11cf86 *R/merge_bwa_assignments_counts.R
c0c5f0266d77645ee16a5e1a1a6a488e *R/merge_gottcha_assignments.R
dfc611236816745c64c8de2e42f25ae2 *R/merge_gottcha_assignments_count.R
b1809299d7eb852a2f528866bd860d34 *R/merge_kraken_assignments.R
fd4be93f3e69fe99e8ef9944fd0c7b72 *R/merge_metaphlan_assignments.R
4428a031d827a0c8048470ba5110ff6d *R/plot_bwa_assignment.R
0cb3b531427b1a78d8aa0776076177b9 *R/plot_gottcha_assignment.R
954f39eba22a80e1e93a3e871f9f8d9d *R/plot_kraken_assignment.R
8d7009e6420077cdd645b1acb32b2fd1 *R/plot_merged_assignment.R
3623363581f4743a26f7a0c63660394d *R/plot_metaphlan_assignment.R
6f055ce25e055488b414f974ace77bd1 *README.md
c2644857806405fe7e1dd52fc368232e *man/load_bwa_assignment.Rd
b01f068989b6e5607de49667ea1a4e12 *man/load_bwa_assignments.Rd
2fe3836f03bd19e1661478c63c11ab88 *man/load_gottcha2_assignment.Rd
66e3e6bf77fa6665cf42d066b55569f0 *man/load_gottcha2_assignments.Rd
e494b2f058ebf6bba3de3f71ac96eca8 *man/load_gottcha_assignment.Rd
d1bb860bf7d2ad39caf2c93d00886ad1 *man/load_gottcha_assignments.Rd
dffa54e53b05413857898948407388ab *man/load_kraken_assignment.Rd
ed78d7ad19ee41328027f2745fca1e59 *man/load_kraken_assignments.Rd
cb9ea433925d12b1e59c74c34e52cad2 *man/load_metaphlan_assignment.Rd
174c8f4128cff5039c5ab6a6b11b79a4 *man/load_metaphlan_assignments.Rd
47bf85ef2df47f96254607f01e65df16 *man/merge_bwa_assignments.Rd
6eced69a480ad10f8b62780ab1dea27a *man/merge_bwa_counts.Rd
d9ca738cf8d4a3fbefc854a6b95d1ca9 *man/merge_gottcha_assignments.Rd
b0669681904948770f528ca697d82e08 *man/merge_gottcha_counts.Rd
69812acfa17baab717ec99ada86e5410 *man/merge_kraken_assignments.Rd
bd97bd64ec3874b5557837760b1919af *man/merge_metaphlan_assignments.Rd
b081c5f87adae0575efdd9a92df40ec7 *man/plot_bwa_assignment.Rd
1ba55bd00cb029a013802091727e6a2a *man/plot_gottcha_assignment.Rd
322835c5f27c21ae587b9895a4aca7c5 *man/plot_kraken_assignment.Rd
477d4187c7677a20364a39eabe242769 *man/plot_merged_assignment.Rd
02f84fa2b3d53d036adb5da51251b150 *man/plot_metaphlan_assignment.Rd
8cc3abe3ef42f275abaae30c45c28f57 *tests/test_data/100187/gottcha-genDB-b/allReads-gottcha-genDB-b.list.txt
f3705b0eaa9995986ee864143b305a72 *tests/test_data/100187/gottcha-speDB-b/allReads-gottcha-speDB-b.list.txt
d8d417122f7d1e4bd244afe4a7bc4dbc *tests/test_data/100187/gottcha-strDB-b/allReads-gottcha-strDB-b.list.txt
6de8b6d01fa488c9bd97a053ce08b76d *tests/test_data/100197/gottcha-genDB-b/allReads-gottcha-genDB-b.list.txt
34b2b92bed4456701370c11f6a4f40e1 *tests/test_data/100197/gottcha-speDB-b/allReads-gottcha-speDB-b.list.txt
d709d2cc0b58c3e90491ab40c5e29447 *tests/test_data/100197/gottcha-strDB-b/allReads-gottcha-strDB-b.list.txt
4e0e15cffb4c3bf81991a2f85c59c6a6 *tests/test_data/100198/gottcha-genDB-b/allReads-gottcha-genDB-b.list.txt
978987e55e2dd3856a8449b2f0cdcd9c *tests/test_data/100198/gottcha-speDB-b/allReads-gottcha-speDB-b.list.txt
6f19f8bde773935894c6402f46fa29d1 *tests/test_data/100198/gottcha-strDB-b/allReads-gottcha-strDB-b.list.txt
6958ba552204eb3f1a708bdc93d86106 *tests/test_data/100204/gottcha-genDB-b/allReads-gottcha-genDB-b.list.txt
71239f57abffa8f1eb9d0af3fc2780a1 *tests/test_data/100218/gottcha-genDB-b/allReads-gottcha-genDB-b.list.txt
d3374d360a82f6301fd3c4f58e54cb9a *tests/test_data/100218/gottcha-speDB-b/allReads-gottcha-speDB-b.list.txt
7b9602c33a4bc93125b8f41fdb40cc16 *tests/test_data/100218/gottcha-strDB-b/allReads-gottcha-strDB-b.list.txt
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7b864e370a57cbd1b2a78bf362a8d67d *tests/test_data/100236/gottcha-speDB-b/allReads-gottcha-speDB-b.list.txt
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1d6b7961129f83b85836a89deb2dd0c7 *tests/test_data/100237/gottcha-genDB-b/allReads-gottcha-genDB-b.list.txt
313e987ff729efec87acb03bb81c622e *tests/test_data/100237/gottcha-speDB-b/allReads-gottcha-speDB-b.list.txt
a0dcc57c78fa6a191ce073ea35f3a671 *tests/test_data/100237/gottcha-strDB-b/allReads-gottcha-strDB-b.list.txt
2afcff5d8a3358aeebf187893aaf54d5 *tests/test_data/100301/gottcha-genDB-b/allReads-gottcha-genDB-b.list.txt
92832b4731d29aa6144e08ed3a593192 *tests/test_data/100301/gottcha-speDB-b/allReads-gottcha-speDB-b.list.txt
77eecb1c00679768b0d1adcda0d56de3 *tests/test_data/100301/gottcha-strDB-b/allReads-gottcha-strDB-b.list.txt
8139db5682ff7be70b2fbadba68c0277 *tests/test_data/100400/gottcha-genDB-b/allReads-gottcha-genDB-b.list.txt
3f0ea8b20ac7dc21ba80d6f1b544d8ca *tests/test_data/100400/gottcha-speDB-b/allReads-gottcha-speDB-b.list.txt
8b5e1b07d826fc436fa829c62afeea6c *tests/test_data/100400/gottcha-strDB-b/allReads-gottcha-strDB-b.list.txt
1d343a320a47dca749271abe80cbcccb *tests/test_data/100404/gottcha-genDB-b/allReads-gottcha-genDB-b.list.txt
69405bc29aea0c42a9e03b43809d63a2 *tests/test_data/100404/gottcha-speDB-b/allReads-gottcha-speDB-b.list.txt
33e996417dc2bf2e2dff2f1ddda42087 *tests/test_data/100404/gottcha-strDB-b/allReads-gottcha-strDB-b.list.txt
833a09df2fd6c69d02855ba5b48d0ab9 *tests/test_data/100455/gottcha-genDB-b/allReads-gottcha-genDB-b.list.txt
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eea03d75560dbf417d41f6774e3c4f1d *tests/test_data/100455/gottcha-strDB-b/allReads-gottcha-strDB-b.list.txt
262f908ce3c1cd3d3a9346e4703a1615 *tests/test_data/100456/gottcha-genDB-b/allReads-gottcha-genDB-b.list.txt
f313b1698956650e31ea4e3a602a605e *tests/test_data/100456/gottcha-speDB-b/allReads-gottcha-speDB-b.list.txt
f951ef776d68616ebea927b154d41e15 *tests/test_data/100456/gottcha-strDB-b/allReads-gottcha-strDB-b.list.txt
7275b743cf019608c481d69010ac1cbb *tests/test_data/100477/gottcha-genDB-b/allReads-gottcha-genDB-b.list.txt
a8ccf1100fa3cd5d48e2f377eeb07cb2 *tests/test_data/248/allReads-bwa.list.txt
a295e85545b6956be1a4ba14ce1688b4 *tests/test_data/248/allReads-gottcha-genDB-b.list.txt
e04a4d1255cd1200868867d1bee08910 *tests/test_data/248/allReads-gottcha-genDB-v.list.txt
122c3ab49393d1aa68eaa2e4799e5c18 *tests/test_data/248/allReads-gottcha-speDB-b.list.txt
0fbb21f924b8b417ef4ad27942264aa9 *tests/test_data/248/allReads-gottcha-speDB-v.list.txt
3ed7b2f100aa38c0da063f4c5c769fc2 *tests/test_data/248/allReads-gottcha-strDB-b.list.txt
c0a358c6272a59de8ee3b9db50b490d8 *tests/test_data/248/allReads-gottcha-strDB-v.list.txt
6c4e85b73e95cf4c36fe31116afa90ed *tests/test_data/248/allReads-kraken_mini.list.txt
0a664e1598f3408d6514b6230d016590 *tests/test_data/248/allReads-metaphlan.list.txt
8cf1d5964242aa701bddce9d803c5b8b *tests/test_data/248/retrieve.sh
fab85bbdc29442178d1bac7d63be43e7 *tests/test_data/SRR059928/SRR059928_gottcha2-speDB-refseq/allReads.summary.tsv
a0e82c7d75468184853f760af9f8c3f5 *tests/test_data/SRR061287/SRR061287_gottcha2-speDB-refseq/allReads.summary.tsv
e0dd4c430182774054ce23fafa5749e0 *tests/test_data/SRR062284/SRR062284_gottcha2-speDB-refseq/allReads.summary.tsv
6568ce60da399d374ee14718809fad58 *tests/test_data/SRR062419/SRR062419_gottcha2-speDB-refseq/allReads.summary.tsv
6b1df4c1ef99153dbf4a4f7ef3fc2130 *tests/test_data/SRR353621/SRR353621_gottcha2-speDB-refseq/allReads.summary.tsv
4b30d68dd376b4dead738ab66ad1dbdc *tests/test_data/SSputum-DNase-RAB/bwa/allReads-bwa.list.txt
96cae67de4b741b995f0aa7effe2c708 *tests/test_data/SSputum-DNase-RAB/gottcha-genDB-b/allReads-gottcha-genDB-b.list.txt
1487c8fa6f031a6656b55db2207d67c2 *tests/test_data/SSputum-DNase-RAB/gottcha-genDB-v/allReads-gottcha-genDB-v.list.txt
d41d8cd98f00b204e9800998ecf8427e *tests/test_data/SSputum-DNase-RAB/gottcha-speDB-b/allReads-gottcha-speDB-b.list.txt
f2679e6e5490cddd119e03b257f80dd6 *tests/test_data/SSputum-DNase-RAB/gottcha-speDB-v/allReads-gottcha-speDB-v.list.txt
e11dc9454bf7ed5904100785a3475431 *tests/test_data/SSputum-DNase-RAB/gottcha-strDB-b/allReads-gottcha-strDB-b.list.txt
0cf583f6a71a47d79a4052896a83c62c *tests/test_data/SSputum-DNase-RAB/gottcha-strDB-v/allReads-gottcha-strDB-v.list.txt
9fdea34b35bd45c8a2de42f4b5bf0862 *tests/test_data/SSputum-DNase-RAB/kraken_mini/allReads-kraken_mini.list.txt
01c1d24de338c47c672b96d9e59c170e *tests/test_data/SSputum-DNase-RAB/metaphlan/allReads-metaphlan.list.txt
e3d00fcb5104b02b1bc93744a6aa4085 *tests/test_data/SSputum-DNase-cDNA/bwa/allReads-bwa.list.txt
d41d8cd98f00b204e9800998ecf8427e *tests/test_data/SSputum-DNase-cDNA/gottcha-genDB-b/allReads-gottcha-genDB-b.list.txt
1dfef8495a992be297f974383078fc00 *tests/test_data/SSputum-DNase-cDNA/gottcha-genDB-v/allReads-gottcha-genDB-v.list.txt
1e8e06b69e11593bc6b733057adbdf2e *tests/test_data/SSputum-DNase-cDNA/gottcha-speDB-b/allReads-gottcha-speDB-b.list.txt
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bb046973d5f7e6b112b5cc5c723a841c *tests/test_data/SSputum-DNase-cDNA/gottcha-strDB-b/allReads-gottcha-strDB-b.list.txt
3eacb9f3b7e4525119ec208c22dc5b21 *tests/test_data/SSputum-DNase-cDNA/gottcha-strDB-v/allReads-gottcha-strDB-v.list.txt
0e398a50eb7a7dc23753bb1e47341fa2 *tests/test_data/SSputum-DNase-cDNA/kraken_mini/allReads-kraken_mini.list.txt
a6c4e12d086819898fa6b526fec81898 *tests/test_data/SSputum-DNase-cDNA/metaphlan/allReads-metaphlan.list.txt
f77fdb985ad4b031e6ef8c0f29653239 *tests/test_data/SSputum-dil-DNase-RAB/bwa/allReads-bwa.list.txt
96983eae31d0a8698238d4b835445ad2 *tests/test_data/SSputum-dil-DNase-RAB/gottcha-genDB-b/allReads-gottcha-genDB-b.list.txt
7e5c31fc6f3e871aab4ea761d0f27b70 *tests/test_data/SSputum-dil-DNase-RAB/gottcha-genDB-v/allReads-gottcha-genDB-v.list.txt
65ca10a0b2d9e35ecd392028cbf5fec0 *tests/test_data/SSputum-dil-DNase-RAB/gottcha-speDB-b/allReads-gottcha-speDB-b.list.txt
9d9ac2dfa04bffce0aaf5a978899ec14 *tests/test_data/SSputum-dil-DNase-RAB/gottcha-speDB-v/allReads-gottcha-speDB-v.list.txt
cb220f2323191d68ebc7949f9245ccf9 *tests/test_data/SSputum-dil-DNase-RAB/gottcha-strDB-b/allReads-gottcha-strDB-b.list.txt
6aa93c2cbbf0c939ad34db70498eec12 *tests/test_data/SSputum-dil-DNase-RAB/gottcha-strDB-v/allReads-gottcha-strDB-v.list.txt
3eb86fa15788d86ac118926d3f74793d *tests/test_data/SSputum-dil-DNase-RAB/kraken_mini/allReads-kraken_mini.list.txt
01c1d24de338c47c672b96d9e59c170e *tests/test_data/SSputum-dil-DNase-RAB/metaphlan/allReads-metaphlan.list.txt
c6e945599eab3f93f309f9a1a7216376 *tests/test_data/SSputum-dil-DNase-cDNA/bwa/allReads-bwa.list.txt
ce8f38049440be43dcae8c8b7f53598b *tests/test_data/SSputum-dil-DNase-cDNA/gottcha-genDB-b/allReads-gottcha-genDB-b.list.txt
6927f278a68a2b4f25263e600aed3661 *tests/test_data/SSputum-dil-DNase-cDNA/gottcha-genDB-v/allReads-gottcha-genDB-v.list.txt
0d7faee5f73ea3f5e21f8f3d64ebab52 *tests/test_data/SSputum-dil-DNase-cDNA/gottcha-speDB-b/allReads-gottcha-speDB-b.list.txt
754087bdc1094711bff18799666c3c10 *tests/test_data/SSputum-dil-DNase-cDNA/gottcha-speDB-v/allReads-gottcha-speDB-v.list.txt
b2cdb94b19d2a015153b7093550627ce *tests/test_data/SSputum-dil-DNase-cDNA/gottcha-strDB-b/allReads-gottcha-strDB-b.list.txt
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15613e8e444b051d0c702f1d4b50add7 *tests/test_data/SSputum-dil-DNase-cDNA/kraken_mini/allReads-kraken_mini.list.txt
f322153aea21e74efe393448c33686c9 *tests/test_data/SSputum-dil-DNase-cDNA/metaphlan/allReads-metaphlan.list.txt
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1d4bc7cba1ac3d3db8eaa61e1c571927 *tests/test_data/SSputum-dil-no-RAB/gottcha-speDB-b/allReads-gottcha-speDB-b.list.txt
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11c1d874f44f8cb7d2626e5750830d1d *tests/test_data/SSputum-dil-no-RAB/kraken_mini/allReads-kraken_mini.list.txt
8859d232d24af965aec96ea19b9a44e2 *tests/test_data/SSputum-dil-no-RAB/metaphlan/allReads-metaphlan.list.txt
30e3c669d6d762b5a28e1247097c103d *tests/test_data/SSputum-dil-no-cDNA/bwa/allReads-bwa.list.txt
d41d8cd98f00b204e9800998ecf8427e *tests/test_data/SSputum-dil-no-cDNA/gottcha-genDB-b/allReads-gottcha-genDB-b.list.txt
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e8196418c9e0c680c923fb4d98ad0316 *tests/test_data/SSputum-dil-no-cDNA/kraken_mini/allReads-kraken_mini.list.txt
50261c67f1f657802caceda50158df64 *tests/test_data/SSputum-dil-no-cDNA/metaphlan/allReads-metaphlan.list.txt
ef9605243c77c8418ae34c5cd6bf790c *tests/test_data/SSputum-no-RAB/bwa/allReads-bwa.list.txt
d41d8cd98f00b204e9800998ecf8427e *tests/test_data/SSputum-no-RAB/gottcha-genDB-b/allReads-gottcha-genDB-b.list.txt
f07db79b9900286ac6771e1ebfaa0d7b *tests/test_data/SSputum-no-RAB/gottcha-genDB-v/allReads-gottcha-genDB-v.list.txt
85e5ffe8312bbbacfd12550af6281e6c *tests/test_data/SSputum-no-RAB/gottcha-speDB-b/allReads-gottcha-speDB-b.list.txt
ec522055dba35ec3f6f58f0bb79543cb *tests/test_data/SSputum-no-RAB/gottcha-speDB-v/allReads-gottcha-speDB-v.list.txt
d41d8cd98f00b204e9800998ecf8427e *tests/test_data/SSputum-no-RAB/gottcha-strDB-b/allReads-gottcha-strDB-b.list.txt
da22e636ba268e60f3e3b70619d8d34e *tests/test_data/SSputum-no-RAB/gottcha-strDB-v/allReads-gottcha-strDB-v.list.txt
04ea37b9b205d22348a7d684fb4f16e4 *tests/test_data/SSputum-no-RAB/kraken_mini/allReads-kraken_mini.list.txt
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