forked from wtsi-npg/npg_qc
-
Notifications
You must be signed in to change notification settings - Fork 0
/
Copy pathMANIFEST
611 lines (611 loc) · 28.2 KB
/
MANIFEST
1
2
3
4
5
6
7
8
9
10
11
12
13
14
15
16
17
18
19
20
21
22
23
24
25
26
27
28
29
30
31
32
33
34
35
36
37
38
39
40
41
42
43
44
45
46
47
48
49
50
51
52
53
54
55
56
57
58
59
60
61
62
63
64
65
66
67
68
69
70
71
72
73
74
75
76
77
78
79
80
81
82
83
84
85
86
87
88
89
90
91
92
93
94
95
96
97
98
99
100
101
102
103
104
105
106
107
108
109
110
111
112
113
114
115
116
117
118
119
120
121
122
123
124
125
126
127
128
129
130
131
132
133
134
135
136
137
138
139
140
141
142
143
144
145
146
147
148
149
150
151
152
153
154
155
156
157
158
159
160
161
162
163
164
165
166
167
168
169
170
171
172
173
174
175
176
177
178
179
180
181
182
183
184
185
186
187
188
189
190
191
192
193
194
195
196
197
198
199
200
201
202
203
204
205
206
207
208
209
210
211
212
213
214
215
216
217
218
219
220
221
222
223
224
225
226
227
228
229
230
231
232
233
234
235
236
237
238
239
240
241
242
243
244
245
246
247
248
249
250
251
252
253
254
255
256
257
258
259
260
261
262
263
264
265
266
267
268
269
270
271
272
273
274
275
276
277
278
279
280
281
282
283
284
285
286
287
288
289
290
291
292
293
294
295
296
297
298
299
300
301
302
303
304
305
306
307
308
309
310
311
312
313
314
315
316
317
318
319
320
321
322
323
324
325
326
327
328
329
330
331
332
333
334
335
336
337
338
339
340
341
342
343
344
345
346
347
348
349
350
351
352
353
354
355
356
357
358
359
360
361
362
363
364
365
366
367
368
369
370
371
372
373
374
375
376
377
378
379
380
381
382
383
384
385
386
387
388
389
390
391
392
393
394
395
396
397
398
399
400
401
402
403
404
405
406
407
408
409
410
411
412
413
414
415
416
417
418
419
420
421
422
423
424
425
426
427
428
429
430
431
432
433
434
435
436
437
438
439
440
441
442
443
444
445
446
447
448
449
450
451
452
453
454
455
456
457
458
459
460
461
462
463
464
465
466
467
468
469
470
471
472
473
474
475
476
477
478
479
480
481
482
483
484
485
486
487
488
489
490
491
492
493
494
495
496
497
498
499
500
501
502
503
504
505
506
507
508
509
510
511
512
513
514
515
516
517
518
519
520
521
522
523
524
525
526
527
528
529
530
531
532
533
534
535
536
537
538
539
540
541
542
543
544
545
546
547
548
549
550
551
552
553
554
555
556
557
558
559
560
561
562
563
564
565
566
567
568
569
570
571
572
573
574
575
576
577
578
579
580
581
582
583
584
585
586
587
588
589
590
591
592
593
594
595
596
597
598
599
600
601
602
603
604
605
606
607
608
609
610
611
bin/gtck_combine_gt_data.sh
bin/gtck_extract_fluidigm_data_from_irods.sh
bin/gtck_genplexlist.sh
bin/gtck_install_to_repos.sh
bin/gtck_refresh_check_data.sh
bin/reformat_fluidigm_snp26_results_irods.pl
bin/qc
bin/qc_db_delete_autoqc
bin/mqc_outcome_reporter
bin/npg_qc_autoqc_data.pl
bin/npg_qc_illumina_analysis_loader
bin/npg_qc_save_files.pl
bin/npg_qc_tag_sniff.pl
bin/call_gtck_composite_rpt.pl
bin/genotype_call_results_reporter
Build.PL
Changes
lib/npg_qc/illumina/loader/Cluster_Density.pm
lib/npg_qc/illumina/loader.pm
lib/npg_qc/autoqc/autoqc.pm
lib/npg_qc/autoqc/constants.pm
lib/npg_qc/autoqc/checks/adapter.pm
lib/npg_qc/autoqc/checks/alignment_filter_metrics.pm
lib/npg_qc/autoqc/checks/bam_flagstats.pm
lib/npg_qc/autoqc/checks/bcfstats.pm
lib/npg_qc/autoqc/checks/check.pm
lib/npg_qc/autoqc/checks/gc_bias.pm
lib/npg_qc/autoqc/checks/gc_fraction.pm
lib/npg_qc/autoqc/checks/genotype.pm
lib/npg_qc/autoqc/checks/genotype_call.pm
lib/npg_qc/autoqc/checks/insert_size.pm
lib/npg_qc/autoqc/checks/pulldown_metrics.pm
lib/npg_qc/autoqc/checks/qX_yield.pm
lib/npg_qc/autoqc/checks/ref_match.pm
lib/npg_qc/autoqc/checks/rna_seqc.pm
lib/npg_qc/autoqc/checks/samtools_stats.pm
lib/npg_qc/autoqc/checks/sequence_error.pm
lib/npg_qc/autoqc/checks/spatial_filter.pm
lib/npg_qc/autoqc/checks/tag_metrics.pm
lib/npg_qc/autoqc/checks/tags_reporters.pm
lib/npg_qc/autoqc/checks/upstream_tags.pm
lib/npg_qc/autoqc/checks/verify_bam_id.pm
lib/npg_qc/autoqc/db_loader.pm
lib/npg_qc/autoqc/parse/alignment.pm
lib/npg_qc/autoqc/parse/samtools_stats.pm
lib/npg_qc/autoqc/qc_store/options.pm
lib/npg_qc/autoqc/qc_store.pm
lib/npg_qc/autoqc/qc_store/query.pm
lib/npg_qc/autoqc/qc_store/query_non_tracking.pm
lib/npg_qc/autoqc/results/adapter.pm
lib/npg_qc/autoqc/results/alignment_filter_metrics.pm
lib/npg_qc/autoqc/results/bam_flagstats.pm
lib/npg_qc/autoqc/results/bcfstats.pm
lib/npg_qc/autoqc/results/base.pm
lib/npg_qc/autoqc/results/collection.pm
lib/npg_qc/autoqc/results/contamination.pm
lib/npg_qc/autoqc/results/gc_bias.pm
lib/npg_qc/autoqc/results/gc_fraction.pm
lib/npg_qc/autoqc/results/genotype.pm
lib/npg_qc/autoqc/results/genotype_call.pm
lib/npg_qc/autoqc/results/insert_size.pm
lib/npg_qc/autoqc/results/pulldown_metrics.pm
lib/npg_qc/autoqc/results/qX_yield.pm
lib/npg_qc/autoqc/results/ref_match.pm
lib/npg_qc/autoqc/results/result.pm
lib/npg_qc/autoqc/results/rna_seqc.pm
lib/npg_qc/autoqc/results/samtools_stats.pm
lib/npg_qc/autoqc/results/sequence_error.pm
lib/npg_qc/autoqc/results/sequence_summary.pm
lib/npg_qc/autoqc/results/spatial_filter.pm
lib/npg_qc/autoqc/results/split_stats.pm
lib/npg_qc/autoqc/results/tag_decode_stats.pm
lib/npg_qc/autoqc/results/tag_metrics.pm
lib/npg_qc/autoqc/results/tags_reporters.pm
lib/npg_qc/autoqc/results/upstream_tags.pm
lib/npg_qc/autoqc/results/verify_bam_id.pm
lib/npg_qc/autoqc/role/adapter.pm
lib/npg_qc/autoqc/role/alignment_filter_metrics.pm
lib/npg_qc/autoqc/role/bam_flagstats.pm
lib/npg_qc/autoqc/role/contamination.pm
lib/npg_qc/autoqc/role/gc_fraction.pm
lib/npg_qc/autoqc/role/genotype.pm
lib/npg_qc/autoqc/role/genotype_call.pm
lib/npg_qc/autoqc/role/insert_size.pm
lib/npg_qc/autoqc/role/pulldown_metrics.pm
lib/npg_qc/autoqc/role/qX_yield.pm
lib/npg_qc/autoqc/role/ref_match.pm
lib/npg_qc/autoqc/role/result.pm
lib/npg_qc/autoqc/role/rpt_key.pm
lib/npg_qc/autoqc/role/sequence_error.pm
lib/npg_qc/autoqc/role/tag_decode_stats.pm
lib/npg_qc/autoqc/role/tag_metrics.pm
lib/npg_qc/autoqc/role/tags_reporters.pm
lib/npg_qc/autoqc/role/upstream_tags.pm
lib/npg_qc/autoqc/role/verify_bam_id.pm
lib/npg_qc/autoqc/types.pm
lib/npg_qc/file_store.pm
lib/npg_qc/mqc/reporter.pm
lib/npg_qc/mqc/outcomes.pm
lib/npg_qc/mqc/outcomes/keys.pm
lib/npg_qc/report/genotype_call.pm
lib/npg_qc/report/common.pm
lib/npg_qc/Schema.pm
lib/npg_qc/Schema/Composition.pm
lib/npg_qc/Schema/Flators.pm
lib/npg_qc/Schema/Mqc/OutcomeEntity.pm
lib/npg_qc/Schema/Mqc/OutcomeDict.pm
lib/npg_qc/Schema/Result/Adapter.pm
lib/npg_qc/Schema/Result/AlignmentFilterMetrics.pm
lib/npg_qc/Schema/Result/BamFlagstats.pm
lib/npg_qc/Schema/Result/Bcfstats.pm
lib/npg_qc/Schema/Result/ClusterDensity.pm
lib/npg_qc/Schema/Result/Contamination.pm
lib/npg_qc/Schema/Result/Fastqcheck.pm
lib/npg_qc/Schema/Result/GcBias.pm
lib/npg_qc/Schema/Result/GcFraction.pm
lib/npg_qc/Schema/Result/Genotype.pm
lib/npg_qc/Schema/Result/GenotypeCall.pm
lib/npg_qc/Schema/Result/InsertSize.pm
lib/npg_qc/Schema/Result/MqcLibraryOutcomeDict.pm
lib/npg_qc/Schema/Result/MqcLibraryOutcomeEnt.pm
lib/npg_qc/Schema/Result/MqcLibraryOutcomeHist.pm
lib/npg_qc/Schema/Result/MqcOutcomeDict.pm
lib/npg_qc/Schema/Result/MqcOutcomeEnt.pm
lib/npg_qc/Schema/Result/MqcOutcomeHist.pm
lib/npg_qc/Schema/Result/PulldownMetrics.pm
lib/npg_qc/Schema/Result/QXYield.pm
lib/npg_qc/Schema/Result/RefMatch.pm
lib/npg_qc/Schema/Result/RnaSeqc.pm
lib/npg_qc/Schema/Result/SamtoolsStats.pm
lib/npg_qc/Schema/Result/SeqComponent.pm
lib/npg_qc/Schema/Result/SeqComponentComposition.pm
lib/npg_qc/Schema/Result/SeqComposition.pm
lib/npg_qc/Schema/Result/SequenceError.pm
lib/npg_qc/Schema/Result/SequenceSummary.pm
lib/npg_qc/Schema/Result/SpatialFilter.pm
lib/npg_qc/Schema/Result/SplitStatsCoverage.pm
lib/npg_qc/Schema/Result/SplitStats.pm
lib/npg_qc/Schema/Result/TagDecodeStats.pm
lib/npg_qc/Schema/Result/TagMetrics.pm
lib/npg_qc/Schema/Result/TagsReporters.pm
lib/npg_qc/Schema/Result/UpstreamTags.pm
lib/npg_qc/Schema/Result/UqcOutcomeDict.pm
lib/npg_qc/Schema/Result/UqcOutcomeEnt.pm
lib/npg_qc/Schema/Result/UqcOutcomeHist.pm
lib/npg_qc/Schema/Result/VerifyBamId.pm
lib/npg_qc/Schema/ResultSet.pm
lib/npg_qc/Schema/ResultSet/MqcOutcomeEnt.pm
lib/npg_qc/utils/bam_genotype.pm
lib/npg_qc/utils/genotype_calling.pm
MANIFEST
README
scripts/npgqc_dbix_schema_loader.pl
t/00-critic.t
t/00-distribution.t
t/00-podcoverage.t
t/00-pod.t
t/00-scripts_compile.t
t/10-file_store.t
t/10-autoqc-parse-samtools_stats.t
t/30-illumina-loader-Cluster_Density.t
t/30-illumina-loader.t
t/50-npg_qc-Schema.t
t/50-schema-result-Contamination.t
t/50-schema-result-Fastqcheck.t
t/50-schema-result-InsertSize.t
t/50-schema-result-Adapter.t
t/50-schema-result-Genotype.t
t/50-schema-result-GenotypeCall.t
t/50-schema-result-BamFlagstats.t
t/50-schema-result-Bcfstats.t
t/50-schema-result-SequenceError.t
t/50-schema-result-RefMatch.t
t/50-schema-result-SpatialFilter.t
t/50-schema-result-GcFraction.t
t/50-schema-result-TagsReporters.t
t/50-schema-result-UpstreamTags.t
t/50-schema-result-GcBias.t
t/50-schema-result-TagDecodeStats.t
t/50-schema-result-QXYield.t
t/50-schema-result-TagMetrics.t
t/50-schema-result-AlignmentFilterMetrics.t
t/50-schema-result-PulldownMetrics.t
t/50-schema-result-SplitStats.t
t/50-schema-result-MqcLibraryOutcomeDict.t
t/50-schema-result-MqcLibraryOutcomeEnt.t
t/50-schema-result-MqcLibraryOutcomeHist.t
t/50-schema-result-MqcOutcomeDict.t
t/50-schema-result-MqcOutcomeEnt.t
t/50-schema-result-MqcOutcomeHist.t
t/50-schema-result-VerifyBamId.t
t/50-schema-result-SamtoolsStats.t
t/50-schema-result-SeqComposition.t
t/50-schema-result-SequenceSummary.t
t/50-schema-result-UqcOutcomeDict.t
t/50-schema-result-UqcOutcomeEnt.t
t/50-schema-result-UqcOutcomeHist.t
t/50-schema-resultset.t
t/50-schema-resultset-MqcOutcomeEnt.t
t/60-autoqc-autoqc.t
t/60-autoqc-checks-adapter.t
t/60-autoqc-checks-af_metrics.t
t/60-autoqc-checks-bam_flagstats.t
t/60-autoqc-checks-bcfstats.t
t/60-autoqc-checks-check.t
t/60-autoqc-checks-gc_bias.t
t/60-autoqc-checks-gc_fraction.t
t/60-autoqc-checks-genotype.t
t/60-autoqc-checks-genotype_call.t
t/60-autoqc-checks-insert_size.t
t/60-autoqc-checks-pulldown_metrics.t
t/60-autoqc-checks-qX_yield.t
t/60-autoqc-checks-ref_match.t
t/60-autoqc-checks-rna_seqc.t
t/60-autoqc-checks-sequence_error.t
t/60-autoqc-checks-spatial_filter.t
t/60-autoqc-checks-tag_metrics.t
t/60-autoqc-checks-tags_reporters.t
t/60-autoqc-checks-upstream_tags.t
t/60-autoqc-results-upstream_tags.t
t/60-autoqc-checks-verify_bam_id.t
t/60-autoqc-db_loader.t
t/60-autoqc-parse-alignment.t
t/60-autoqc-qc_store-query.t
t/60-autoqc-qc_store.t
t/60-autoqc-role-result.t
t/60-autoqc-role-rpt_key.t
t/60-autoqc-results-adapter.t
t/60-autoqc-results-af_metrics.t
t/60-autoqc-results-bam_flagstats.t
t/60-autoqc-results-bcfstats.t
t/60-autoqc-results-collection.t
t/60-autoqc-results-contamination.t
t/60-autoqc-results-gc_bias.t
t/60-autoqc-results-gc_fraction.t
t/60-autoqc-results-genotype.t
t/60-autoqc-results-genotype_call.t
t/60-autoqc-results-insert_size.t
t/60-autoqc-results-pulldown_metrics.t
t/60-autoqc-results-qX_yield.t
t/60-autoqc-results-ref_match.t
t/60-autoqc-results-result.t
t/60-autoqc-results-rna_seqc.t
t/60-autoqc-results-samtools_stats.t
t/60-autoqc-results-sequence_error.t
t/60-autoqc-results-sequence_summary.t
t/60-autoqc-results-spatial_filter.t
t/60-autoqc-results-split_stats.t
t/60-autoqc-results-tag_decode_stats.t
t/60-autoqc-results-tag_metrics.t
t/60-autoqc-results-verify_bam_id.t
t/70-mqc-reporter.t
t/70-mqc-outcomes.t
t/70-report-genotype_call.t
t/80-autoqc-qc-script.t
t/data/autoqc/bam_flagstats/16960_1_0.tar.gz
t/data/autoqc/bam_flagstats/17448_1_9.tar.gz
t/data/autoqc/bam_flagstats/24135_1#1.bam_flagstats.json
t/data/autoqc/bam_flagstats/24135_1#1.flagstat
t/data/autoqc/bam_flagstats/4783_5_bam_flagstats.json
t/data/autoqc/bam_flagstats/4783_5_metrics_optical.txt
t/data/autoqc/bam_flagstats/4783_5.flagstat
t/data/autoqc/bam_flagstats/4921_3_bam_flagstats.json
t/data/autoqc/bcfstats/data/21835_5.bcfstats.json
t/data/autoqc/bcfstats/samplesheet_21835.csv
t/data/autoqc/dbix_loader/run/12233_1.upstream_tags.json
t/data/autoqc/dbix_loader/run/12233_1.adapter.json
t/data/autoqc/dbix_loader/run/12233_1.gc_fraction.json
t/data/autoqc/dbix_loader/run/12233_1.insert_size.json
t/data/autoqc/dbix_loader/run/12233_1.qX_yield.json
t/data/autoqc/dbix_loader/run/12233_1.ref_match.json
t/data/autoqc/dbix_loader/run/12233_1.sequence_error.json
t/data/autoqc/dbix_loader/run/12233_1.tag_metrics.json
t/data/autoqc/dbix_loader/run/12166_1.spatial_filter.json
t/data/autoqc/dbix_loader/is/more/12187_1.insert_size.json
t/data/autoqc/dbix_loader/is/update/12187_2.insert_size.json
t/data/autoqc/dbix_loader/is/update/12187_2.insert_size.json
t/data/autoqc/dbix_loader/run/lane/12233_1#0.adapter.json
t/data/autoqc/dbix_loader/run/lane/12233_1#0_bam_flagstats.json
t/data/autoqc/dbix_loader/run/lane/12233_1#0.gc_bias.json
t/data/autoqc/dbix_loader/run/lane/12233_1#0.gc_fraction.json
t/data/autoqc/dbix_loader/run/lane/12233_1#0.insert_size.json
t/data/autoqc/dbix_loader/run/lane/12233_1#0.qX_yield.json
t/data/autoqc/dbix_loader/run/lane/12233_1#0.ref_match.json
t/data/autoqc/dbix_loader/run/lane/12233_1#0.sequence_error.json
t/data/autoqc/dbix_loader/run/lane/12166_2#1.adapter.json
t/data/autoqc/dbix_loader/run/lane/12166_2#1.alignment_filter_metrics.json
t/data/autoqc/dbix_loader/run/lane/12166_2#1_bam_flagstats.json
t/data/autoqc/dbix_loader/run/lane/12166_2#1.gc_bias.json
t/data/autoqc/dbix_loader/run/lane/12166_2#1.gc_fraction.json
t/data/autoqc/dbix_loader/run/lane/12166_2#1.insert_size.json
t/data/autoqc/dbix_loader/run/lane/12166_2#1_phix_bam_flagstats.json
t/data/autoqc/dbix_loader/run/lane/12166_2#1.qX_yield.json
t/data/autoqc/dbix_loader/run/lane/12166_2#1.ref_match.json
t/data/autoqc/dbix_loader/run/lane/12166_2#1.sequence_error.json
t/data/autoqc/dbix_loader/run/lane/12240_1#14.pulldown_metrics.json
t/data/autoqc/dbix_loader/run/lane/12220_1#16_bam_flagstats.json
t/data/autoqc/dbix_loader/run/lane/12220_1#21_bam_flagstats.json
t/data/autoqc/dbix_loader/run/lane/12240_1#9.pulldown_metrics.json
t/data/autoqc/dbix_loader/run/lane/12220_1#16.alignment_filter_metrics.json
t/data/autoqc/dbix_loader/run/lane/12220_1#16_human_bam_flagstats.json
t/data/autoqc/dbix_loader/run/lane/12220_1#21.alignment_filter_metrics.json
t/data/autoqc/dbix_loader/run/lane/12220_1#21_human_bam_flagstats.json
t/data/autoqc/dbix_loader/run/lane/12233_1#56.adapter.json
t/data/autoqc/dbix_loader/run/lane/12233_1#56_bam_flagstats.json
t/data/autoqc/dbix_loader/run/lane/12233_1#56.gc_bias.json
t/data/autoqc/dbix_loader/run/lane/12233_1#56.gc_fraction.json
t/data/autoqc/dbix_loader/run/lane/12233_1#56.genotype.json
t/data/autoqc/dbix_loader/run/lane/12233_1#56.insert_size.json
t/data/autoqc/dbix_loader/run/lane/12233_1#56.qX_yield.json
t/data/autoqc/dbix_loader/run/lane/12233_1#56.ref_match.json
t/data/autoqc/dbix_loader/run/lane/12233_1#56.sequence_error.json
t/data/autoqc/dbix_loader/run/lane/12233_1#72.adapter.json
t/data/autoqc/dbix_loader/run/lane/12233_1#72_bam_flagstats.json
t/data/autoqc/dbix_loader/run/lane/12233_1#72.gc_bias.json
t/data/autoqc/dbix_loader/run/lane/12233_1#72.gc_fraction.json
t/data/autoqc/dbix_loader/run/lane/12233_1#72.genotype.json
t/data/autoqc/dbix_loader/run/lane/12233_1#72.insert_size.json
t/data/autoqc/dbix_loader/run/lane/12233_1#72.qX_yield.json
t/data/autoqc/dbix_loader/run/lane/12233_1#72.ref_match.json
t/data/autoqc/dbix_loader/run/lane/12233_1#72.sequence_error.json
t/data/autoqc/dbix_loader/run/12166_2.spatial_filter.json
t/data/autoqc/dbix_loader/run/11180_1.tags_reporters.json
t/data/autoqc/upstream_tags/9669_1.upstream_tags.json
t/data/autoqc/upstream_tags/lane1/12920_1#0.bam
t/data/autoqc/upstream_tags/lane1/13362_1#0.bam
t/data/autoqc/upstream_tags/lane1/6954_1#0.bam
t/data/autoqc/090721_IL29_2549/data/2549_2_1.fastq
t/data/autoqc/090721_IL29_2549/data/2549_2.bam
t/data/autoqc/090721_IL29_2549/data/2549_3.fastq
t/data/autoqc/090721_IL29_2549/data/2549_6#1_1.fastq
t/data/autoqc/090721_IL29_2549/data/2549_6#1.bam
t/data/autoqc/090721_IL29_2549/data/2549_6#2.bam
t/data/autoqc/090908_IL11_3715/qc/3715_5.adapter.json
t/data/autoqc/090908_IL11_3715/qc/3715_6.adapter.json
t/data/autoqc/090908_IL11_3715/qc/3715_7.adapter.json
t/data/autoqc/090908_IL11_3715/qc/3715_8.adapter.json
t/data/autoqc/1937_1_1.fastq
t/data/autoqc/1937_1_1.fastq.gz
t/data/autoqc/1937_1_2.fastq
t/data/autoqc/1937_2_1.fastq
t/data/autoqc/1937_3_1.fastq
t/data/autoqc/1937_3_2.fastq
t/data/autoqc/4056_1.contamination.json
t/data/autoqc/4068_3.sequence_error.json
t/data/autoqc/4078_1.sequence_error.json
t/data/autoqc/4360_8_tag_decode_stats.json
t/data/autoqc/4453_2#0.gc_fraction.json
t/data/autoqc/4453_2#0.qX_yield.json
t/data/autoqc/26659_1.qX_yield.json
t/data/autoqc/5374_2_1-5374_2_2_human_split_stats.json
t/data/autoqc/5428_2.ref_match.json
t/data/autoqc/9999_1.blat
t/data/autoqc/9999_1.fastq
t/data/autoqc/9999_1.sequence_error.json
t/data/autoqc/adapter.fasta
t/data/autoqc/af_metrics/7880_1#0.alignment_filter_metrics.json
t/data/autoqc/af_metrics/7880_1#0.bam_alignment_filter_metrics.json
t/data/autoqc/af_metrics/7908_1#1.alignment_filter_metrics.json
t/data/autoqc/alignment_empty.sam
t/data/autoqc/alignment_few.sam
t/data/autoqc/alignment_one.sam
t/data/autoqc/alignment_refmatch.sam
t/data/autoqc/alignment.bam
t/data/autoqc/alignment.sam
t/data/autoqc/alignment_small.sam
t/data/autoqc/fixtures/Adapter.yml
t/data/autoqc/gbs_plex_repository/Hs_MajorQC/default/all/bcftools/Hs_MajorQC.annotation.vcf
t/data/autoqc/gbs_plex_repository/Hs_MajorQC/default/all/bcftools/Hs_MajorQC.info.json
t/data/autoqc/gbs_plex_repository/Hs_MajorQC/default/all/bcftools/Hs_MajorQC.ploidy
t/data/autoqc/gbs_plex_repository/Hs_MajorQC/default/all/fasta/Hs_MajorQC.fa
t/data/autoqc/gc_bias/sam-3lines
t/data/autoqc/gc_bias/sam_aligned_header
t/data/autoqc/gc_bias/sam_unaligned_header
t/data/autoqc/geno_refset_repository/study3705/GRCh38_full_analysis_set_plus_decoy_hla/bcfdb/study3705.bcf
t/data/autoqc/geno_refset_repository/study3705/GRCh38_full_analysis_set_plus_decoy_hla/bcfdb/study3705.bcf.csi
t/data/autoqc/geno_refset_repository/study3705/GRCh38_full_analysis_set_plus_decoy_hla/bcftools/study3705.annotation.vcf
t/data/autoqc/geno_refset_repository/study3705/GRCh38_full_analysis_set_plus_decoy_hla/bcftools/study3705.info.json
t/data/autoqc/geno_refset_repository/study3705/GRCh38_full_analysis_set_plus_decoy_hla/bcftools/study3705.ploidy
t/data/autoqc/genotype/6812_1.genotype.json
t/data/autoqc/genotype/6812_2.genotype.json
t/data/autoqc/genotype/6812_3.genotype.json
t/data/autoqc/genotype/6812_4.genotype.json
t/data/autoqc/genotype/6812_5.genotype.json
t/data/autoqc/genotype/6812_6.genotype.json
t/data/autoqc/genotype/6812_7.genotype.json
t/data/autoqc/genotype/6812_8.genotype.json
t/data/autoqc/genotype_call/samplesheet_24135.csv
t/data/autoqc/genotype_call/samplesheet_24135_test.csv
t/data/autoqc/genotype_call/data/24135_1#1.genotype_call.json
t/data/autoqc/gc_fraction/Homo_sapiens.NCBI36.48.dna.all.fa.json
t/data/autoqc/gc_fraction/samplesheet_27138.csv
t/data/autoqc/gc_fraction/27138_1#1_F0xB00.stats
t/data/autoqc/insert_size/6062_8#1.insert_size.json
t/data/autoqc/insert_size/6062_8#2.insert_size.json
t/data/autoqc/insert_size_expected_mean.json
t/data/autoqc/insert_size_expected_size.json
t/data/autoqc/insert_size/15155_8.insert_size.json
t/data/autoqc/insert_size/alignment_isize_normfit.sam
t/data/autoqc/insert_size/npg/run/1937.xml
t/data/autoqc/insert_size/npg/run/1938.xml
t/data/autoqc/insert_size/npg/run/2549.xml
t/data/autoqc/insert_size/npg/run/3871.xml
t/data/autoqc/insert_size/npg/run/3938.xml
t/data/autoqc/insert_size/npg/run/4174.xml
t/data/autoqc/insert_size/npg/run/4261.xml
t/data/autoqc/insert_size/npg/run/4748.xml
t/data/autoqc/insert_size/npg/run/4799.xml
t/data/autoqc/insert_size/st/batches/2797.xml
t/data/autoqc/insert_size/st/batches/3432.xml
t/data/autoqc/insert_size/st/batches/4837.xml
t/data/autoqc/insert_size/st/batches/5230.xml
t/data/autoqc/insert_size/st/batches/5364.xml
t/data/autoqc/insert_size/st/batches/2809.xml
t/data/autoqc/insert_size/st/batches/4793.xml
t/data/autoqc/insert_size/st/batches/6637.xml
t/data/autoqc/insert_size/st/batches/6669.xml
t/data/autoqc/insert_size/st/samples/1898.xml
t/data/autoqc/insert_size/st/studies/186.xml
t/data/autoqc/load/3510_1.insert_size.json
t/data/autoqc/load/3510_1_1_human_split_stats.json
t/data/autoqc/load/3510_5.qX_yield.json
t/data/autoqc/load/do_not_add_files_to_this_dir
t/data/autoqc/load/some.json
t/data/autoqc/npg/instrument/15.xml
t/data/autoqc/npg/instrument/42.xml
t/data/autoqc/npg/run/1937.xml
t/data/autoqc/npg/run/2222.xml
t/data/autoqc/npg/run/2549.xml
t/data/autoqc/npg/run/3612.xml
t/data/autoqc/pulldown_metrics/pdm.out
t/data/autoqc/qc/1937_3.map
t/data/autoqc/qX_yield/npg/instrument/15.xml
t/data/autoqc/qX_yield/npg/run/2549.xml
t/data/autoqc/reference.bwt
t/data/autoqc/references/Homo_sapiens/GRCh38_full_analysis_set_plus_decoy_hla/all/fasta/GRCh38_full_analysis_set_plus_decoy_hla.fasta
t/data/autoqc/references/Homo_sapiens/NCBI36/all/bwa/someref.fa.bwt
t/data/autoqc/references/Homo_sapiens/NCBI36/all/fasta/someref.fa
t/data/autoqc/references/No_bowtie/Sanger/all/fasta/Sanger.fa
t/data/autoqc/references/NPD_Chimera/default/all/bowtie/Composite_20100310.fasta.1.ebwt
t/data/autoqc/references/NPD_Chimera/default/all/fasta/Composite_20100310.fasta
t/data/autoqc/references/NPD_Chimera/default/README
t/data/autoqc/references/Vibrio_cholerae/M66-2/all/fasta/V_chol.fasta
t/data/autoqc/ref_match/narrow.fastq
t/data/autoqc/rendered/json_paired_run/3565_1.insert_size.json
t/data/autoqc/rendered/json_paired_run/3565_1.qX_yield.json
t/data/autoqc/rendered/json_paired_run/3565_2.insert_size.json
t/data/autoqc/rendered/json_paired_run/3565_2.qX_yield.json
t/data/autoqc/rendered/json_paired_run/3565_3.insert_size.json
t/data/autoqc/rendered/json_paired_run/3565_3.qX_yield.json
t/data/autoqc/rendered/json_paired_run/3565_4.insert_size.json
t/data/autoqc/rendered/json_paired_run/3565_4.qX_yield.json
t/data/autoqc/rendered/json_paired_run/3565_5.insert_size.json
t/data/autoqc/rendered/json_paired_run/3565_5.qX_yield.json
t/data/autoqc/rendered/json_paired_run/3565_6.insert_size.json
t/data/autoqc/rendered/json_paired_run/3565_6.qX_yield.json
t/data/autoqc/rendered/json_paired_run/3565_7.insert_size.json
t/data/autoqc/rendered/json_paired_run/3565_7.qX_yield.json
t/data/autoqc/rendered/json_paired_run/3565_8.insert_size.json
t/data/autoqc/rendered/json_paired_run/3565_8.qX_yield.json
t/data/autoqc/rendered/json_single_run/3612_1.insert_size.json
t/data/autoqc/rendered/json_single_run/3612_1.qX_yield.json
t/data/autoqc/rendered/json_single_run/3612_2.insert_size.json
t/data/autoqc/rendered/json_single_run/3612_2.qX_yield.json
t/data/autoqc/rendered/json_single_run/3612_3.insert_size.json
t/data/autoqc/rendered/json_single_run/3612_3.qX_yield.json
t/data/autoqc/rendered/json_single_run/3612_4.insert_size.json
t/data/autoqc/rendered/json_single_run/3612_4.qX_yield.json
t/data/autoqc/rendered/json_single_run/3612_5.insert_size.json
t/data/autoqc/rendered/json_single_run/3612_5.qX_yield.json
t/data/autoqc/rendered/json_single_run/3612_6.insert_size.json
t/data/autoqc/rendered/json_single_run/3612_6.qX_yield.json
t/data/autoqc/rendered/json_single_run/3612_7.insert_size.json
t/data/autoqc/rendered/json_single_run/3612_7.qX_yield.json
t/data/autoqc/rendered/json_single_run/3612_8.insert_size.json
t/data/autoqc/rendered/json_single_run/3612_8.qX_yield.json
t/data/autoqc/rna_seqc/data/17550_1#1.bam
t/data/autoqc/rna_seqc/data/17550_3#8.bam
t/data/autoqc/rna_seqc/samplesheet_17550.csv
t/data/autoqc/sequence_error/6376_1_1.fastq.10000
t/data/autoqc/tag_decode_output_no_found_tags.txt
t/data/autoqc/tag_decode_output.txt
t/data/autoqc/tag_decode_stats/6624_3_tag_decode_stats.json
t/data/autoqc/tag_metrics/25152_1.bam.tag_decode.metrics
t/data/autoqc/tag_metrics/25152_1.bam.tag_decode.metrics.hops
t/data/autoqc/tag_metrics/6551_1.bam.tag_decode.metrics
t/data/autoqc/tag_metrics/6551_1.tag_metrics.json
t/data/autoqc/tag_metrics/6552_1.bam.tag_decode.metrics
t/data/autoqc/tag_metrics/6552_1.bam.tag_decode.metrics.hops
t/data/autoqc/tag_metrics/6553_1.bam.tag_decode.metrics
t/data/autoqc/tag_metrics/6553_1.bam.tag_decode.metrics.hops
t/data/autoqc/tag_metrics/6954_1.tag_metrics.json
t/data/autoqc/tag_metrics/samplesheet_25152.csv
t/data/autoqc/tag_metrics/samplesheet_6552.csv
t/data/autoqc/tag_metrics/samplesheet_6553.csv
t/data/autoqc/dbix_loader/is/12187_2.insert_size.json
t/data/autoqc/population_snv_with_vcf/Anopheles_gambiae/default/Standard/PEST/test.vcf.gz
t/data/autoqc/population_snv_with_vcf/Homo_sapiens/default/Standard/1000Genomes_hs37d5/test.vcf.gz
t/data/autoqc/samtools_stats/27178_1#1_F0x900.stats
t/data/autoqc/samtools_stats/27178_1_F0x000.altstats
t/data/autoqc/samtools_stats/27178_1_F0x000.stats
t/data/autoqc/st/samples/1898.xml
t/data/autoqc/st/batches/2797.xml
t/data/autoqc/st/batches/3432.xml
t/data/autoqc/st/batches/30621.xml
t/data/autoqc/st/batches/30804.xml
t/data/autoqc/st/samples/3057.xml
t/data/autoqc/st/samples/3056.xml
t/data/autoqc/st/samples/9832.xml
t/data/autoqc/st/studies/186.xml
t/data/autoqc/st/studies/544.xml
t/data/autoqc/tag_sets/sanger168.tags
t/data/autoqc/tag_sets/sanger168_6.tags
t/data/autoqc/tag_sets/sanger168_7.tags
t/data/autoqc/verify_bam_id/19999_2#1.verify_bam_id.json
t/data/autoqc/verify_bam_id/20000_1#2.verify_bam_id.json
t/data/fixtures/000-mqc_outcome_dict.yml
t/data/fixtures/000-mqc_library_outcome_dict.yml
t/data/fixtures/000-uqc_outcome_dict.yml
t/data/fixtures/autoqc_json.tar.gz
t/data/nfs/sf44/IL2/analysis/123456_IL2_1234/Data/Intensities/Bustard_RTA/PB_cal/archive/qc/1234_1.insert_size.json
t/data/nfs/sf44/IL2/analysis/123456_IL2_1234/Data/Intensities/Bustard_RTA/PB_cal/archive/qc/1234_1.qX_yield.json
t/data/nfs/sf44/IL2/analysis/123456_IL2_1234/Data/Intensities/Bustard_RTA/PB_cal/archive/qc/1234_2.insert_size.json
t/data/nfs/sf44/IL2/analysis/123456_IL2_1234/Data/Intensities/Bustard_RTA/PB_cal/archive/qc/1234_2.qX_yield.json
t/data/nfs/sf44/IL2/analysis/123456_IL2_1234/Data/Intensities/Bustard_RTA/PB_cal/archive/qc/1234_3.insert_size.json
t/data/nfs/sf44/IL2/analysis/123456_IL2_1234/Data/Intensities/Bustard_RTA/PB_cal/archive/qc/1234_3.qX_yield.json
t/data/nfs/sf44/IL2/analysis/123456_IL2_1234/Data/Intensities/Bustard_RTA/PB_cal/archive/qc/1234_4.insert_size.json
t/data/nfs/sf44/IL2/analysis/123456_IL2_1234/Data/Intensities/Bustard_RTA/PB_cal/archive/qc/1234_4.qX_yield.json
t/data/nfs/sf44/IL2/analysis/123456_IL2_1234/Data/Intensities/Bustard_RTA/PB_cal/archive/qc/1234_5.insert_size.json
t/data/nfs/sf44/IL2/analysis/123456_IL2_1234/Data/Intensities/Bustard_RTA/PB_cal/archive/qc/1234_5.qX_yield.json
t/data/nfs/sf44/IL2/analysis/123456_IL2_1234/Data/Intensities/Bustard_RTA/PB_cal/archive/qc/1234_6.insert_size.json
t/data/nfs/sf44/IL2/analysis/123456_IL2_1234/Data/Intensities/Bustard_RTA/PB_cal/archive/qc/1234_6.qX_yield.json
t/data/nfs/sf44/IL2/analysis/123456_IL2_1234/Data/Intensities/Bustard_RTA/PB_cal/archive/qc/1234_7.insert_size.json
t/data/nfs/sf44/IL2/analysis/123456_IL2_1234/Data/Intensities/Bustard_RTA/PB_cal/archive/qc/1234_7.qX_yield.json
t/data/nfs/sf44/IL2/analysis/123456_IL2_1234/Data/Intensities/Bustard_RTA/PB_cal/archive/qc/1234_8.insert_size.json
t/data/nfs/sf44/IL2/analysis/123456_IL2_1234/Data/Intensities/Bustard_RTA/PB_cal/archive/qc/1234_8.qX_yield.json
t/data/qcoutcomes/fixtures/000-mqc_library_outcome_dict.yml
t/data/qcoutcomes/fixtures/000-mqc_outcome_dict.yml
t/data/qcoutcomes/fixtures/000-uqc_outcome_dict.yml
t/data/report/genotype_call/mlwarehouse/200-Sample.yml
t/data/report/genotype_call/mlwarehouse/300-IseqFlowcell.yml
t/data/report/genotype_call/mlwarehouse/300-IseqProductMetric.yml
t/data/report/genotype_call/npg_qc/genotype_call.yml
t/data/report/genotype_call/npg_qc/seq_component_composition.yml
t/data/report/genotype_call/npg_qc/seq_component.yml
t/data/report/genotype_call/npg_qc/seq_composition.yml
t/data/reporter/npg_qc/mqc_outcome_dict.yml
t/data/reporter/npg_qc/mqc_outcome_ent.yml
t/data/reporter/npg_qc/seq_component.yml
t/data/reporter/npg_qc/seq_component_composition.yml
t/data/reporter/npg_qc/seq_composition.yml
t/data/reporter/mlwarehouse/300-IseqProductMetric.yml
t/data/reporter/mlwarehouse/400-IseqFlowcell.yml
t/perlcriticrc
t/data/nfs/sf44/ILorHSany_sf25/incoming/140601_HS2_13108_A_C37W5ACXX/InterOp/TileMetricsOut.bin
t/data/nfs/sf44/ILorHSany_sf25/incoming/140605_HS36_13169_B_H9FP5ADXX/InterOp/TileMetricsOut.bin
t/data/fastqcheck/4308_1_2.fastqcheck
t/data/fixtures/npg_tracking/000-designation.yml
t/data/fixtures/npg_tracking/000-entity_type.yml
t/data/fixtures/npg_tracking/000-instrument_mod_dict.yml
t/data/fixtures/npg_tracking/000-instrument_status_dict.yml
t/data/fixtures/npg_tracking/000-manufacturer.yml
t/data/fixtures/npg_tracking/000-run_status_dict.yml
t/data/fixtures/npg_tracking/000-tag.yml
t/data/fixtures/npg_tracking/000-usergroup.yml
t/data/fixtures/npg_tracking/000-user.yml
t/data/fixtures/npg_tracking/100-annotation.yml
t/data/fixtures/npg_tracking/100-event_type.yml
t/data/fixtures/npg_tracking/100-instrument_format.yml
t/data/fixtures/npg_tracking/100-tag_frequency.yml
t/data/fixtures/npg_tracking/100-user2usergroup.yml
t/data/fixtures/npg_tracking/200-event.yml
t/data/fixtures/npg_tracking/200-instrument.yml
t/data/fixtures/npg_tracking/300-instrument_designation.yml
t/data/fixtures/npg_tracking/300-run_lane.yml
t/data/fixtures/npg_tracking/300-run.yml
t/data/qc_store/26291#3_phix_F0x900.samtools_stats.json
t/data/qc_store/26294/26294_1.insert_size.json
t/data/qc_store/26294/26294_1.qX_yield.json
t/data/qc_store/26294/26294_2.insert_size.json
t/data/qc_store/26294/26294_2.qX_yield.json
t/data/qc_store/26294/26294_3.insert_size.json
t/data/qc_store/26294/26294_3.qX_yield.json
t/data/qc_store/26294/26294_4.insert_size.json
t/data/qc_store/26294/26294_4.qX_yield.json
t/data/qc_store/26294/26294_5.insert_size.json
t/data/qc_store/26294/26294_5.qX_yield.json
t/data/qc_store/26294/26294_6.insert_size.json
t/data/qc_store/26294/26294_6.qX_yield.json
t/data/qc_store/26294/26294_7.insert_size.json
t/data/qc_store/26294/26294_7.qX_yield.json
t/data/qc_store/26294/26294_8.insert_size.json
t/data/qc_store/26294/26294_8.qX_yield.json
t/data/qc_store/26291/plex0/qc/26291#0.alignment_filter_metrics.json
t/data/qc_store/26291/plex0/qc/26291#0.bam_flagstats.json
t/data/qc_store/26291/plex0/qc/26291#0_phix.bam_flagstats.json
t/data/qc_store/26291/plex11/qc/26291#11.alignment_filter_metrics.json
t/data/qc_store/26291/plex11/qc/26291#11.bam_flagstats.json
t/data/qc_store/26291/plex11/qc/26291#11_phix.bam_flagstats.json
t/data/qc_store/26291/plex3/qc/26291#3.alignment_filter_metrics.json
t/data/qc_store/26291/plex3/qc/26291#3.bam_flagstats.json
t/data/qc_store/26291/plex3/qc/26291#3_phix.bam_flagstats.json
t/data/qc_store/26291/lane1/qc/26291_1.tag_metrics.json
t/data/qc_store/26291/lane2/qc/26291_2.tag_metrics.json
t/data/samtools_stats/26597_1_F0xB00.stats
t/data/samtools_stats/26607_1#20_F0xB00.stats
t/data/samtools_stats/26607_1#20_F0xB00.samtools_stats.json
t/data/samtools_stats/27138_1#2_F0xB00.stats
t/data/samtools_stats/27258_1#1.empty.stats
t/data/samtools_stats/27053_1#1.single.stats
t/data/26601_qc_archive.tar.gz