bio-vcf 0.8.2 → 0.9.0
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- checksums.yaml +4 -4
- data/.travis.yml +8 -2
- data/Gemfile +4 -6
- data/README.md +92 -57
- data/Rakefile +3 -41
- data/TAGS +115 -0
- data/VERSION +1 -1
- data/bin/bio-vcf +58 -70
- data/bio-vcf.gemspec +23 -75
- data/features/cli.feature +6 -1
- data/features/multisample.feature +12 -0
- data/features/step_definitions/cli-feature.rb +2 -2
- data/features/step_definitions/multisample.rb +19 -0
- data/features/step_definitions/vcf_header.rb +1 -1
- data/features/support/env.rb +0 -9
- data/lib/bio-vcf/pcows.rb +210 -0
- data/lib/bio-vcf/vcfheader.rb +28 -9
- data/lib/bio-vcf/vcfheader_line.rb +455 -160
- data/lib/bio-vcf/vcfrecord.rb +30 -15
- data/ragel/gen_vcfheaderline_parser.rl +68 -25
- data/ragel/generate.sh +4 -1
- data/template/vcf2json.erb +16 -16
- data/template/vcf2json_full_header.erb +16 -17
- data/template/vcf2json_use_meta.erb +35 -35
- data/test/data/input/gatk_exome.vcf +237 -0
- data/test/data/input/gatk_wgs.vcf +1000 -0
- data/test/data/input/test.bed +632 -0
- data/test/data/regression/eval_once-stderr.new +1 -0
- data/test/data/regression/eval_once.new +1 -0
- data/test/data/regression/eval_once.ref +1 -0
- data/test/data/regression/eval_r.info.dp-stderr.new +4 -0
- data/test/data/regression/eval_r.info.dp.new +150 -0
- data/test/data/regression/ifilter_s.dp-stderr.new +28 -0
- data/test/data/regression/ifilter_s.dp.new +31 -0
- data/test/data/regression/r.info.dp-stderr.new +4 -0
- data/test/data/regression/r.info.dp.new +147 -0
- data/test/data/regression/rewrite.info.sample-stderr.new +4 -0
- data/test/data/regression/rewrite.info.sample.new +150 -0
- data/test/data/regression/s.dp-stderr.new +12 -0
- data/test/data/regression/s.dp.new +145 -0
- data/test/data/regression/seval_s.dp-stderr.new +4 -0
- data/test/data/regression/seval_s.dp.new +36 -0
- data/test/data/regression/sfilter_seval_s.dp-stderr.new +12 -0
- data/test/data/regression/sfilter_seval_s.dp.new +31 -0
- data/test/data/regression/thread4-stderr.new +4 -0
- data/test/data/regression/thread4.new +150 -0
- data/test/data/regression/thread4_4-stderr.new +15 -0
- data/test/data/regression/thread4_4.new +150 -0
- data/test/data/regression/thread4_4_failed_filter-stderr.new +5 -0
- data/test/data/regression/thread4_4_failed_filter-stderr.ref +5 -2
- data/test/data/regression/thread4_4_failed_filter.new +110 -0
- data/test/data/regression/vcf2json_full_header-stderr.new +4 -0
- data/test/data/regression/vcf2json_full_header.new +225 -0
- data/test/data/regression/vcf2json_full_header.ref +222 -258
- data/test/data/regression/vcf2json_use_meta-stderr.new +4 -0
- data/test/data/regression/vcf2json_use_meta.new +4697 -0
- data/test/data/regression/vcf2json_use_meta.ref +4697 -0
- data/test/performance/metrics.md +18 -1
- data/test/tmp/test.vcf +12469 -0
- metadata +38 -62
- data/Gemfile.lock +0 -81
- data/ragel/gen_vcfheaderline_parser.rb +0 -483
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|
+
17 80051440 80051680 FASN
|
|
538
|
+
17 80053121 80053391 FASN
|
|
539
|
+
17 80054193 80054321 FASN
|
|
540
|
+
19 1206877 1207237 STK11
|
|
541
|
+
19 1218395 1218517 STK11
|
|
542
|
+
19 1219305 1219427 STK11
|
|
543
|
+
19 1220370 1220504 STK11
|
|
544
|
+
19 1220527 1220767 STK11
|
|
545
|
+
19 1221210 1221338 STK11
|
|
546
|
+
19 1221915 1222036 STK11
|
|
547
|
+
19 1222957 1223197 STK11
|
|
548
|
+
19 1226429 1226669 STK11
|
|
549
|
+
19 1452950 1453190 APC2
|
|
550
|
+
19 1453229 1453351 APC2
|
|
551
|
+
19 1453399 1453639 APC2
|
|
552
|
+
19 1455136 1455262 APC2
|
|
553
|
+
19 1455320 1455560 APC2
|
|
554
|
+
19 1456052 1456173 APC2
|
|
555
|
+
19 1456292 1456414 APC2
|
|
556
|
+
19 1456809 1457008 APC2
|
|
557
|
+
19 1457055 1457269 APC2
|
|
558
|
+
19 1457950 1458071 APC2
|
|
559
|
+
19 1460129 1460369 APC2
|
|
560
|
+
19 1460727 1460877 APC2
|
|
561
|
+
19 1460943 1461213 APC2
|
|
562
|
+
19 1461918 1462188 APC2
|
|
563
|
+
19 1465099 1467207 APC2
|
|
564
|
+
19 1467237 1469148 APC2
|
|
565
|
+
19 1469208 1469356 APC2
|
|
566
|
+
19 1469580 1469826 APC2
|
|
567
|
+
19 1469964 1470269 APC2
|
|
568
|
+
19 18170360 18170480 IL12RB1
|
|
569
|
+
19 18170699 18170894 IL12RB1
|
|
570
|
+
19 18171908 18172029 IL12RB1
|
|
571
|
+
19 18172977 18173099 IL12RB1
|
|
572
|
+
19 18174632 18174872 IL12RB1
|
|
573
|
+
19 18177350 18177506 IL12RB1
|
|
574
|
+
19 18179197 18179335 IL12RB1
|
|
575
|
+
19 18180319 18180559 IL12RB1
|
|
576
|
+
19 18182920 18183157 IL12RB1
|
|
577
|
+
19 18184306 18184428 IL12RB1
|
|
578
|
+
19 18186505 18186734 IL12RB1
|
|
579
|
+
19 18187061 18187181 IL12RB1
|
|
580
|
+
19 18188324 18188464 IL12RB1
|
|
581
|
+
19 18191640 18191810 IL12RB1
|
|
582
|
+
19 18192955 18193077 IL12RB1
|
|
583
|
+
19 18194210 18194331 IL12RB1
|
|
584
|
+
19 18197540 18197661 IL12RB1
|
|
585
|
+
20 39766269 39766509 PLCG1
|
|
586
|
+
20 39788244 39788398 PLCG1
|
|
587
|
+
20 39788495 39788616 PLCG1
|
|
588
|
+
20 39788708 39788829 PLCG1
|
|
589
|
+
20 39791072 39791194 PLCG1
|
|
590
|
+
20 39791233 39791383 PLCG1
|
|
591
|
+
20 39791524 39791674 PLCG1
|
|
592
|
+
20 39791817 39791939 PLCG1
|
|
593
|
+
20 39791978 39792128 PLCG1
|
|
594
|
+
20 39792352 39792474 PLCG1
|
|
595
|
+
20 39792542 39792663 PLCG1
|
|
596
|
+
20 39792719 39792841 PLCG1
|
|
597
|
+
20 39793571 39793741 PLCG1
|
|
598
|
+
20 39793883 39794007 PLCG1
|
|
599
|
+
20 39794079 39794200 PLCG1
|
|
600
|
+
20 39794277 39794466 PLCG1
|
|
601
|
+
20 39794832 39795033 PLCG1
|
|
602
|
+
20 39795114 39795235 PLCG1
|
|
603
|
+
20 39795317 39795497 PLCG1
|
|
604
|
+
20 39796469 39796590 PLCG1
|
|
605
|
+
20 39797397 39797518 PLCG1
|
|
606
|
+
20 39797705 39797827 PLCG1
|
|
607
|
+
20 39798070 39798191 PLCG1
|
|
608
|
+
20 39798710 39798950 PLCG1
|
|
609
|
+
20 39800819 39800941 PLCG1
|
|
610
|
+
20 39801059 39801284 PLCG1
|
|
611
|
+
20 39801367 39801517 PLCG1
|
|
612
|
+
20 39802055 39802177 PLCG1
|
|
613
|
+
20 39802290 39802452 PLCG1
|
|
614
|
+
20 39802545 39802667 PLCG1
|
|
615
|
+
20 39802762 39802951 PLCG1
|
|
616
|
+
20 39803066 39803188 PLCG1
|
|
617
|
+
20 45315390 45315886 TP53RK
|
|
618
|
+
20 45317731 45318091 TP53RK
|
|
619
|
+
22 29083868 29083989 CHEK2
|
|
620
|
+
22 29085101 29085312 CHEK2
|
|
621
|
+
22 29090001 29090122 CHEK2
|
|
622
|
+
22 29091094 29091232 CHEK2
|
|
623
|
+
22 29091677 29091860 CHEK2
|
|
624
|
+
22 29092869 29092992 CHEK2
|
|
625
|
+
22 29095814 29095935 CHEK2
|
|
626
|
+
22 29099462 29099583 CHEK2
|
|
627
|
+
22 29105959 29106080 CHEK2
|
|
628
|
+
22 29107858 29108010 CHEK2
|
|
629
|
+
22 29115366 29115488 CHEK2
|
|
630
|
+
22 29120963 29121149 CHEK2
|
|
631
|
+
22 29121229 29121389 CHEK2
|
|
632
|
+
22 29130389 29130714 CHEK2
|