minimap2 0.2.22.0 → 0.2.24.1

data/ext/minimap2/tex/blasr-mc.eval

@@ -0,0 +1,17 @@
+Q	60	32681	57	0.001744133
+Q	39	3	1	0.001774569
+Q	38	3	1	0.001804999
+Q	35	5	1	0.001835311
+Q	34	31	2	0.001894692
+Q	20	11	2	0.001955154
+Q	19	4	1	0.001985460
+Q	15	29	5	0.002136296
+Q	14	6	1	0.002166417
+Q	10	11	1	0.002196193
+Q	6	11	2	0.002256442
+Q	5	1	1	0.002286864
+Q	4	1	1	0.002317285
+Q	3	36	15	0.002771602
+Q	2	5	2	0.002832085
+Q	1	12	9	0.003105023
+Q	0	220	83	0.005594194

data/ext/minimap2/tex/bowtie2-s3.sam.eval

@@ -0,0 +1,28 @@
+Q	42	16872292	669	0.000039651	16872292
+Q	40	835329	636	0.000073697	17707621
+Q	31	6544	2	0.000073783	17714165
+Q	30	8882	6	0.000074084	17723047
+Q	27	68499	9	0.000074305	17791546
+Q	26	132041	81	0.000078277	17923587
+Q	25	129378	96	0.000083033	18052965
+Q	24	92056	382	0.000103665	18145021
+Q	23	14341	402	0.000125720	18159362
+Q	22	132838	146	0.000132789	18292200
+Q	21	122274	124	0.000138641	18414474
+Q	18	112183	103	0.000143361	18526657
+Q	17	126981	213	0.000153804	18653638
+Q	16	16356	208	0.000164810	18669994
+Q	15	42804	782	0.000206223	18712798
+Q	14	16026	318	0.000223025	18728824
+Q	12	170250	814	0.000264087	18899074
+Q	11	48351	1409	0.000337777	18947425
+Q	8	1843	311	0.000354156	18949268
+Q	7	62266	4435	0.000586276	19011534
+Q	6	413997	50057	0.003150647	19425531
+Q	5	404	58	0.003153568	19425935
+Q	4	704	154	0.003161381	19426639
+Q	3	1473	681	0.003196193	19428112
+Q	2	17541	16462	0.004039875	19445653
+Q	1	534344	354879	0.021693547	19979997
+Q	0	11939	9917	0.022176642	19991936
+U	8064

data/ext/minimap2/tex/bwa-s3.sam.eval

@@ -0,0 +1,52 @@
+Q	60	18784147	3	0.000000160	18784147
+Q	52	19002	1	0.000000213	18803149
+Q	50	7152	2	0.000000319	18810301
+Q	49	6797	1	0.000000372	18817098
+Q	48	52188	2	0.000000477	18869286
+Q	47	48775	3	0.000000634	18918061
+Q	46	19447	2	0.000000739	18937508
+Q	45	25983	3	0.000000896	18963491
+Q	44	13455	1	0.000000949	18976946
+Q	43	14573	2	0.000001053	18991519
+Q	42	8697	4	0.000001263	19000216
+Q	41	8645	2	0.000001368	19008861
+Q	40	176603	75	0.000005264	19185464
+Q	38	2503	2	0.000005368	19187967
+Q	37	4117	3	0.000005523	19192084
+Q	36	2924	16	0.000006356	19195008
+Q	35	2323	8	0.000006772	19197331
+Q	34	2344	10	0.000007292	19199675
+Q	33	4279	6	0.000007603	19203954
+Q	32	2092	4	0.000007810	19206046
+Q	31	2625	11	0.000008382	19208671
+Q	30	2828	13	0.000009057	19211499
+Q	29	1581	1	0.000009108	19213080
+Q	28	1543	6	0.000009420	19214623
+Q	27	70916	223	0.000020948	19285539
+Q	26	1288	16	0.000021777	19286827
+Q	25	25551	122	0.000028065	19312378
+Q	24	14345	84	0.000032390	19326723
+Q	23	7308	87	0.000036878	19334031
+Q	22	8358	125	0.000043325	19342389
+Q	21	4836	71	0.000046983	19347225
+Q	20	5888	123	0.000053325	19353113
+Q	19	4656	83	0.000057600	19357769
+Q	18	3948	87	0.000062081	19361717
+Q	17	4418	114	0.000067954	19366135
+Q	16	4226	131	0.000074702	19370361
+Q	15	5760	164	0.000083144	19376121
+Q	14	4697	257	0.000096384	19380818
+Q	13	5246	313	0.000112503	19386064
+Q	12	4170	241	0.000124908	19390234
+Q	11	4095	304	0.000140557	19394329
+Q	10	3857	360	0.000159087	19398186
+Q	9	5300	438	0.000181617	19403486
+Q	8	4206	572	0.000211050	19407692
+Q	7	4676	787	0.000251541	19412368
+Q	6	3923	688	0.000286924	19416291
+Q	5	3294	708	0.000323333	19419585
+Q	4	2936	693	0.000358965	19422521
+Q	3	3928	816	0.000400897	19426449
+Q	2	2613	810	0.000442533	19429062
+Q	1	3515	1188	0.000503587	19432577
+Q	0	567423	376636	0.019321100	20000000

data/ext/minimap2/tex/bwa.eval

@@ -0,0 +1,55 @@
+Q	60	31721	27	0.000851171
+Q	59	54	4	0.000975610
+Q	58	29	5	0.001131933
+Q	57	21	2	0.001194030
+Q	56	14	4	0.001319137
+Q	55	22	6	0.001506544
+Q	54	12	4	0.001631475
+Q	53	16	3	0.001724733
+Q	51	10	1	0.001755541
+Q	50	10	1	0.001786330
+Q	49	11	3	0.001879699
+Q	47	8	2	0.001941869
+Q	46	17	1	0.001972140
+Q	44	8	3	0.002065534
+Q	43	10	1	0.002096174
+Q	42	13	1	0.002126595
+Q	41	14	3	0.002219444
+Q	40	13	2	0.002281036
+Q	38	17	4	0.002404747
+Q	37	15	4	0.002528484
+Q	36	12	1	0.002558742
+Q	35	19	3	0.002650783
+Q	34	12	3	0.002743313
+Q	33	7	1	0.002773882
+Q	32	21	3	0.002865508
+Q	31	11	2	0.002926799
+Q	30	14	3	0.003018891
+Q	29	17	1	0.003048401
+Q	28	11	2	0.003109549
+Q	27	20	5	0.003262998
+Q	26	11	1	0.003292948
+Q	25	14	4	0.003415725
+Q	24	16	5	0.003569212
+Q	23	43	6	0.003750426
+Q	21	15	1	0.003779664
+Q	20	29	7	0.003992943
+Q	19	22	2	0.004052089
+Q	18	28	4	0.004172204
+Q	16	25	5	0.004323390
+Q	15	24	5	0.004474480
+Q	14	25	5	0.004625204
+Q	13	23	3	0.004714365
+Q	12	22	1	0.004741963
+Q	11	32	11	0.005075674
+Q	10	35	7	0.005285315
+Q	9	32	12	0.005648503
+Q	8	33	8	0.005888126
+Q	7	39	7	0.006095506
+Q	6	42	14	0.006515953
+Q	5	38	15	0.006966725
+Q	4	37	12	0.007325113
+Q	3	49	18	0.007862737
+Q	2	63	21	0.008486434
+Q	1	55	27	0.009292156
+Q	0	153	77	0.011576593

data/ext/minimap2/tex/eval2roc.pl

@@ -0,0 +1,33 @@
+#!/usr/bin/perl
+
+use strict;
+use warnings;
+use Getopt::Std;
+
+my %opts = (n=>33088, s=>100);
+getopts('n:', \%opts);
+
+my $pseudo = .5;
+my $tot = $pseudo;
+my $err = $pseudo;
+my $tot_last_out = -$opts{s};
+my $state = 0;
+my $mapq = 0;
+while (<>) {
+	chomp;
+	if (/^Q\t(\d+)\t(\d+)\t(\d+)/) {
+		$tot += $2;
+		$err += $3;
+		if ($tot - $tot_last_out >= $opts{s}) {
+			print join("\t", $1, $err/$tot, $tot / $opts{n}), "\n";
+			$tot_last_out = $tot;
+			$state = 0;
+		} else {
+			$state = 1;
+			$mapq = $1;
+		}
+	}
+}
+if ($state) {
+	print join("\t", $mapq, $err/$tot, $tot / $opts{n}), "\n";
+}

data/ext/minimap2/tex/graphmap.eval

@@ -0,0 +1,4 @@
+Q	40	31897	63	0.001975107
+Q	3	423	267	0.010210396
+Q	2	162	120	0.013853827
+Q	1	188	172	0.019038874

data/ext/minimap2/tex/hs38-simu.sh

@@ -0,0 +1,10 @@
+./pbsim --prefix pb-1 --depth 0.1 --sample-fastq m131017_060208_42213_c100579642550000001823095604021496_s1_p0.1.subreads.fastq --length-min 1000 --length-max 30000 --seed 11 hs38.fa
+
+bin/mason_variator -ir hs38.fa -s 1 -ov hs38-s1.vcf --snp-rate 1e-3 --small-indel-rate 2e-4 --sv-indel-rate 0 --sv-inversion-rate 0 --sv-translocation-rate 0 --sv-duplication-rate 0 --max-small-indel-size 10
+bin/mason_simulator -ir hs38.fa -iv hs38-s1.vcf -n 1000000 --seed 1 -o s1_1.fq -or s1_2.fq -oa s1.sam --illumina-prob-mismatch-scale 2.5
+
+bin/mason_variator -ir hs38.fa -s 2 -ov hs38-s2.vcf --snp-rate 1e-3 --small-indel-rate 2e-4 --sv-indel-rate 0 --sv-inversion-rate 0 --sv-translocation-rate 0 --sv-duplication-rate 0 --max-small-indel-size 10
+bin/mason_simulator -ir hs38.fa -iv hs38-s2.vcf -n 1000000 --seed 2 -o mason-s2_1.fq -or mason-s2_2.fq -oa mason-s2.sam --illumina-prob-mismatch-scale 2.5 --illumina-read-length 150
+
+bin/mason_variator -ir hs38.fa -s 3 -ov hs38-s3.vcf --snp-rate 1e-3 --small-indel-rate 2e-4 --sv-indel-rate 0 --sv-inversion-rate 0 --sv-translocation-rate 0 --sv-duplication-rate 0 --max-small-indel-size 10
+bin/mason_simulator -ir hs38.fa -iv hs38-s3.vcf -n 10000000 --seed 3 -o mason-s3_1.fq -or mason-s3_2.fq -oa mason-s3.sam --illumina-prob-mismatch-scale 2.5 --illumina-read-length 150

data/ext/minimap2/tex/minialign.eval

@@ -0,0 +1,49 @@
+Q	60	32070	190	0.005924540
+Q	59	62	2	0.005975352
+Q	58	37	5	0.006123908
+Q	57	40	7	0.006333633
+Q	56	39	6	0.006512032
+Q	55	32	2	0.006567534
+Q	54	54	2	0.006618420
+Q	53	33	4	0.006735255
+Q	52	39	2	0.006788866
+Q	51	48	3	0.006871264
+Q	50	34	2	0.006925634
+Q	49	32	3	0.007011070
+Q	48	35	2	0.007064967
+Q	47	36	4	0.007179896
+Q	46	23	1	0.007205495
+Q	45	25	1	0.007230614
+Q	44	17	3	0.007318716
+Q	43	17	2	0.007376121
+Q	42	31	5	0.007522016
+Q	41	25	4	0.007638486
+Q	40	26	4	0.007754541
+Q	39	35	2	0.007807258
+Q	37	18	4	0.007924896
+Q	36	13	3	0.008013162
+Q	35	15	2	0.008070411
+Q	34	20	3	0.008156805
+Q	33	11	1	0.008184501
+Q	32	15	3	0.008272003
+Q	31	25	1	0.008296107
+Q	29	8	1	0.008324472
+Q	28	7	2	0.008383452
+Q	27	9	2	0.008441894
+Q	26	30	2	0.008494888
+Q	23	2	1	0.008524710
+Q	22	11	3	0.008612846
+Q	20	23	3	0.008697760
+Q	19	6	1	0.008726479
+Q	18	8	1	0.008754658
+Q	16	6	1	0.008783354
+Q	13	2	1	0.008813108
+Q	12	4	2	0.008872604
+Q	11	7	2	0.008931275
+Q	10	4	3	0.009021009
+Q	9	6	4	0.009140436
+Q	8	6	3	0.009229559
+Q	7	5	1	0.009258419
+Q	6	8	3	0.009346925
+Q	4	8	5	0.009495872
+Q	3	17	8	0.009732801