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added benchmark results

This commit is contained in:
Heng Li 2017-08-01 15:12:49 -04:00
parent 0c563e1868
commit 9306299e4d
8 changed files with 254 additions and 0 deletions
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17
tex/blasr-mc.eval 100644
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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

55
tex/bwa.eval 100644
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@ -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

20
tex/eval2roc.pl 100755
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#!/usr/bin/perl
use strict;
use warnings;
use Getopt::Std;
my %opts = (n=>33088);
getopts('n:', \%opts);
my $pseudo = .5;
my $tot = $pseudo;
my $err = $pseudo;
while (<>) {
chomp;
if (/^Q\t(\d+)\t(\d+)\t(\d+)/) {
$tot += $2;
$err += $3;
print join("\t", $1, $err/$tot, $tot / $opts{n}), "\n";
}
}

49
tex/minialign.eval 100644
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@ -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

30
tex/mm2.approx.eval 100644
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@ -0,0 +1,30 @@
Q 60 32066 0 0.000000000
Q 40 32 1 0.000031155
Q 38 19 1 0.000062272
Q 36 11 1 0.000093376
Q 35 32 1 0.000124378
Q 33 15 1 0.000155400
Q 32 58 1 0.000186145
Q 27 11 1 0.000217095
Q 26 80 1 0.000247494
Q 21 19 2 0.000309186
Q 20 16 1 0.000339936
Q 19 19 1 0.000370622
Q 18 22 2 0.000432099
Q 17 37 5 0.000585751
Q 15 24 2 0.000646930
Q 14 18 3 0.000738939
Q 13 30 6 0.000922821
Q 12 18 1 0.000953054
Q 11 29 2 0.001013638
Q 10 30 1 0.001043393
Q 9 20 5 0.001196099
Q 8 25 8 0.001440348
Q 7 28 6 0.001622830
Q 6 35 12 0.001988132
Q 5 34 12 0.002352725
Q 4 29 8 0.002594865
Q 3 36 14 0.003018937
Q 2 46 15 0.003471482
Q 1 69 36 0.004558162
Q 0 167 94 0.007377173

17
tex/mm2.eval 100644
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@ -0,0 +1,17 @@
Q 60 32072 0 0.000000000
Q 43 206 1 0.000030981
Q 27 201 1 0.000061578
Q 15 59 1 0.000092200
Q 12 25 1 0.000122839
Q 11 16 1 0.000153473
Q 10 24 1 0.000184032
Q 9 17 2 0.000245248
Q 8 27 3 0.000336938
Q 7 23 1 0.000367309
Q 6 20 1 0.000397675
Q 5 18 4 0.000519751
Q 4 17 1 0.000550038
Q 3 29 5 0.000702204
Q 2 32 4 0.000823522
Q 1 54 6 0.001004872
Q 0 234 106 0.004202697

38
tex/ngmlr.eval 100644
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@ -0,0 +1,38 @@
Q 60 23616 0 0.000000000
Q 45 3520 1 0.000036851
Q 41 1840 1 0.000069023
Q 37 328 2 0.000136500
Q 36 276 1 0.000169033
Q 35 480 1 0.000199601
Q 33 375 2 0.000262855
Q 31 178 2 0.000326659
Q 30 153 5 0.000487551
Q 29 200 1 0.000516696
Q 27 100 3 0.000611601
Q 26 93 3 0.000706056
Q 25 75 2 0.000768393
Q 24 82 1 0.000798314
Q 23 80 6 0.000987387
Q 22 71 6 0.001175835
Q 21 76 7 0.001394921
Q 20 63 9 0.001676897
Q 19 55 4 0.001800322
Q 18 62 8 0.002048987
Q 17 55 7 0.002265718
Q 16 60 10 0.002575539
Q 15 82 9 0.002850877
Q 14 67 7 0.003063745
Q 13 62 11 0.003401042
Q 12 64 13 0.003799084
Q 11 56 5 0.003947900
Q 10 58 17 0.004468303
Q 9 70 22 0.005139796
Q 8 23 9 0.005414604
Q 7 41 17 0.005933068
Q 6 42 18 0.006480881
Q 5 33 9 0.006751757
Q 4 29 9 0.007022948
Q 3 27 15 0.007478764
Q 2 23 10 0.007781024
Q 1 9 2 0.007840364
Q 0 13 8 0.008083105

28
tex/roc.gp 100644
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set t po eps enh co so "Helvetica,18"
set style line 1 lt 1 pt 1 lc rgb "#FF0000" lw 2;
set style line 2 lt 1 pt 2 lc rgb "#00C000" lw 2;
set style line 3 lt 1 pt 3 lc rgb "#0080FF" lw 2;
set style line 4 lt 1 pt 4 lc rgb "#C000FF" lw 2;
set style line 5 lt 1 pt 5 lc rgb "#00EEEE" lw 2;
set style line 6 lt 1 pt 6 lc rgb "#C04000" lw 2;
set style line 7 lt 1 lc rgb "#C8C800" lw 2;
set style line 8 lt 1 lc rgb "#FF80FF" lw 2;
set style line 9 lt 1 lc rgb "#4E642E" lw 2;
set style line 10 lt 1 lc rgb "#800000" lw 2;
set style line 11 lt 1 lc rgb "#67B7F7" lw 2;
set style line 12 lt 1 lc rgb "#FFC127" lw 2;
set xlab "False positive rate"
set ylab "Sensitivity"
set yran [0.9:1]
set out "roc-color.eps"
set log x
set format x "10^{%L}"
set key bot right
plot "<./eval2roc.pl blasr-mc.eval" u 2:3 t "blasr-mc" w lp ls 1, \
"<./eval2roc.pl bwa.eval" u 2:3 t "bwa-mem" w lp ls 2, \
"<./eval2roc.pl minialign.eval" u 2:3 t "minialign" w lp ls 3, \
"<./eval2roc.pl mm2.eval" u 2:3 t "minimap2" w lp ls 4, \
"<./eval2roc.pl ngmlr.eval" u 2:3 t "ngm-lr" w lp ls 5