This file is indexed.

/usr/bin/wgsim_eval.pl is in samtools 1.3.1-3.

This file is owned by root:root, with mode 0o755.

The actual contents of the file can be viewed below.

  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
#!/usr/bin/env perl
#
#    Copyright (C) 2009 Genome Research Ltd.
#    Portions copyright (C) 2009-2011 Broad Institute.
#
#    Author: Heng Li <lh3@sanger.ac.uk>
#
# Permission is hereby granted, free of charge, to any person obtaining a copy
# of this software and associated documentation files (the "Software"), to deal
# in the Software without restriction, including without limitation the rights
# to use, copy, modify, merge, publish, distribute, sublicense, and/or sell
# copies of the Software, and to permit persons to whom the Software is
# furnished to do so, subject to the following conditions:
#
# The above copyright notice and this permission notice shall be included in
# all copies or substantial portions of the Software.
#
# THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR
# IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,
# FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL
# THE AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER
# LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING
# FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER
# DEALINGS IN THE SOFTWARE.

use strict;
use warnings;
use Getopt::Std;

die (qq/
Usage:   wgsim_eval.pl <command> <arguments>

Command: alneval       evaluate alignment in the SAM format
         vareval       evaluate variant calls in the pileup format
         unique        keep the top scoring hit in SAM
         uniqcmp       compare two alignments without multiple hits
\n/) if (@ARGV == 0);
my $command = shift(@ARGV);
if ($command eq 'alneval') {
    &alneval;
} elsif ($command eq 'vareval') {
    &vareval;
} elsif ($command eq 'unique') {
    &unique;
} elsif ($command eq 'uniqcmp') {
    &uniqcmp;
} else {
    die("[wgsim_eval] unrecognized command.\n");
}
exit;

sub alneval {
    my %opts = (g=>5);
    getopts('pcag:', \%opts);
    die(qq/
Usage:   wgsim_eval.pl alneval [options] <in.sam>\n
Options: -p        print wrong alignments
         -g INT    correct if withint INT of the true coordinate
         -a        generate ROC curves

The default output has columns of mapping quality, number of correct
alignments \/ total number of alignments at that mapping quality,
cumulative sum of number of alignments, and the ratio of cumulative
correct alignments over cumulative total alignments.

The -a option outputs columns with mapping quality, number of mapped
reads with mqual >= the mqual in the first column, and the number of
mismapped reads.  Together they can be used to produce ROC curves for
accuracy of aligners.
\n/) if (@ARGV == 0 && -t STDIN);
    my (@c0, @c1, %fnfp);
    my ($max_q, $flag) = (0, 0);
    my $gap = $opts{g};
    $flag |= 1 if (defined $opts{p});
    $flag |= 2 if (defined $opts{c});
    while (<>) {
        next if (/^\@/);
        my @t = split("\t");
        next if (@t < 11);
        my $line = $_;
        my ($q, $is_correct, $chr, $left, $rght) = (int($t[4]/10), 1, $t[2], $t[3], $t[3]);
        $max_q = $q if ($q > $max_q);
        # right coordinate
        $_ = $t[5]; s/(\d+)[MDN=X]/$rght+=$1,'x'/eg;
        --$rght;
        # correct for clipping
        my ($left0, $rght0) = ($left, $rght);
        $left -= $1 if (/^(\d+)[SH]/);
        $rght += $1 if (/(\d+)[SH]$/);
        $left0 -= $1 if (/(\d+)[SH]$/);
        $rght0 += $1 if (/^(\d+)[SH]/);
        # skip unmapped reads
        next if (($t[1]&0x4) || $chr eq '*');
        # parse read name and check
        if ($t[0] =~ /^(\S+)_(\d+)_(\d+)_/) {
            if ($1 ne $chr) { # different chr
                $is_correct = 0;
            } else {
                if ($flag & 2) {
                    if (($t[1]&0x40) && !($t[1]&0x10)) { # F3, forward
                        $is_correct = 0 if (abs($2 - $left) > $gap && abs($2 - $left0) > $gap);
                    } elsif (($t[1]&0x40) && ($t[1]&0x10)) { # F3, reverse
                        $is_correct = 0 if (abs($3 - $rght) > $gap && abs($3 - $rght0) > $gap);
                    } elsif (($t[1]&0x80) && !($t[1]&0x10)) { # R3, forward
                        $is_correct = 0 if (abs($3 - $left) > $gap && abs($3 - $left0) > $gap);
                    } else { # R3, reverse
                        $is_correct = 0 if (abs($2 - $rght) > $gap && abs($3 - $rght0) > $gap);
                    }
                } else {
                    if ($t[1] & 0x10) { # reverse
                        $is_correct = 0 if (abs($3 - $rght) > $gap && abs($3 - $rght0) > $gap); # in case of indels that are close to the end of a reads
                    } else {
                        $is_correct = 0 if (abs($2 - $left) > $gap && abs($2 - $left0) > $gap);
                    }
                }
            }
        } else {
            warn("[wgsim_eval] read '$t[0]' was not generated by wgsim?\n");
            next;
        }
        ++$c0[$q];
        ++$c1[$q] unless ($is_correct);
        @{$fnfp{$t[4]}} = (0, 0) unless (defined $fnfp{$t[4]});
        ++$fnfp{$t[4]}[0];
        ++$fnfp{$t[4]}[1] unless ($is_correct);
        print STDERR $line if (($flag&1) && !$is_correct && $q > 0);
    }
    # print
    my ($cc0, $cc1) = (0, 0);
    if (!defined($opts{a})) {
        for (my $i = $max_q; $i >= 0; --$i) {
            $c0[$i] = 0 unless (defined $c0[$i]);
            $c1[$i] = 0 unless (defined $c1[$i]);
            $cc0 += $c0[$i]; $cc1 += $c1[$i];
            printf("%.2dx %12d / %-12d  %12d  %.3e\n", $i, $c1[$i], $c0[$i], $cc0, $cc1/$cc0) if ($cc0);
        }
    } else {
        for (reverse(sort {$a<=>$b} (keys %fnfp))) {
            next if ($_ == 0);
            $cc0 += $fnfp{$_}[0];
            $cc1 += $fnfp{$_}[1];
            print join("\t", $_, $cc0, $cc1), "\n";
        }
    }
}

sub vareval {
    my %opts = (g=>10, Q=>200);
    getopts('g:p', \%opts);
    my $skip = $opts{g};
    die("Usage: wgsim_eval.pl vareval [-g $opts{g}] <wgsim.snp> <pileup.flt>\n") if (@ARGV < 1);

    my $is_print = defined($opts{p})? 1 : 0;

    my ($fh, %snp, %indel);
    # read simulated variants
    open($fh, $ARGV[0]) || die;
    while (<$fh>) {
        my @t = split;
        if (@t != 5 || $t[2] eq '-' || $t[3] eq '-') {
            $indel{$t[0]}{$t[1]} = 1;
        } else {
            $snp{$t[0]}{$t[1]} = $t[3];
        }
    }
    close($fh);

    shift(@ARGV);
    my (@cnt);
    for my $i (0 .. 3) {
        for my $j (0 .. $opts{Q}) {
            $cnt[$i][$j] = 0;
        }
    }
    while (<>) {
        my @t = split;
        my $q = $t[5];
        next if ($t[2] eq $t[3]);
        $q = $opts{Q} if ($q > $opts{Q});
        if ($t[2] eq '*') {
            my $hit = 0;
            ++$cnt[2][$q];
            for my $i ($t[1] - $skip .. $t[1] + $skip) {
                if (defined $indel{$t[0]}{$i}) {
                    $hit = 1; last;
                }
            }
            ++$cnt[3][$q] if ($hit == 0);
            print STDERR $_ if ($hit == 0 && $is_print);
        } else {
            ++$cnt[0][$q];
            ++$cnt[1][$q] unless (defined $snp{$t[0]}{$t[1]});
            print STDERR $_ if (!defined($snp{$t[0]}{$t[1]}) && $is_print);
        }
    }

    for (my $i = $opts{Q} - 1; $i >= 0; --$i) {
        $cnt[$_][$i] += $cnt[$_][$i+1] for (0 .. 3);
    }

    for (my $i = $opts{Q}; $i >= 0; --$i) {
        print join("\t", $i, $cnt[0][$i], $cnt[1][$i], $cnt[2][$i], $cnt[3][$i]), "\n";
    }
}

sub unique {
    # -f: parameter to recalute mapping quality
    # -Q: do not recalculate mapping quality
    # -a, -b, -q, -r: scoring system
    my %opts = (f=>250.0, q=>5, r=>2, a=>1, b=>3);
    getopts('Qf:q:r:a:b:m', \%opts);
    die(qq/
Usage:   wgsim_eval.pl unique [options] <in.sam>\n
Options: -Q         recompuate mapping quality from multiple hits
         -f FLOAT   mapQ=FLOAT*(best1-best2)\/best1 [opts{f}]
         -a INT     matching score (when AS tag is absent) [$opts{a}]
         -q INT     gap open penalty [$opts{q}]
         -r INT     gap extension penalty [$opts{r}]
\n/) if (@ARGV == 0 && -t STDIN);
    my $last = '';
    my $recal_Q = defined($opts{Q});
    my $multi_only = defined($opts{m});
    my @a;
    while (<>) {
        my $score = -1;
        print $_ if (/^\@/);
        $score = $1 if (/AS:i:(\d+)/);
        my @t = split("\t");
        next if (@t < 11);
        if ($score < 0) { # AS tag is unavailable
            my $cigar = $t[5];
            my ($mm, $go, $ge) = (0, 0, 0);
            $cigar =~ s/(\d+)[ID]/++$go,$ge+=$1/eg;
            $cigar = $t[5];
            $cigar =~ s/(\d+)M/$mm+=$1/eg;
            $score = $mm * $opts{a} - $go * $opts{q} - $ge * $opts{r}; # no mismatches...
        }
        $score = 1 if ($score < 1);
        if ($t[0] ne $last) {
            &unique_aux(\@a, $opts{f}, $recal_Q, $multi_only) if (@a);
            $last = $t[0];
        }
        push(@a, [$score, \@t]);
    }
    &unique_aux(\@a, $opts{f}, $recal_Q, $multi_only) if (@a);
}

sub unique_aux {
    my ($a, $fac, $is_recal, $multi_only) = @_;
    my ($max, $max2, $max_i) = (0, 0, -1);
    for (my $i = 0; $i < @$a; ++$i) {
        if ($a->[$i][0] > $max) {
            $max2 = $max; $max = $a->[$i][0]; $max_i = $i;
        } elsif ($a->[$i][0] > $max2) {
            $max2 = $a->[$i][0];
        }
    }
    if ($is_recal) {
        if (!$multi_only || @$a > 1) {
            my $q = int($fac * ($max - $max2) / $max + .499);
            $q = 250 if ($q > 250);
            $a->[$max_i][1][4] = $q < 250? $q : 250;
        }
    }
    print join("\t", @{$a->[$max_i][1]});
    @$a = ();
}

sub uniqcmp {
    my %opts = (q=>20, s=>100, b=>4);
    getopts('pq:s:b:', \%opts);
    die(qq/
Usage:   wgsim_eval.pl uniqcmp [options] <in1.sam> <in2.sam>\n
Options: -q INT     confident mapping if mapping quality above INT [$opts{q}]
         -s INT     same mapping if the distance below INT [$opts{s}]
         -b INT     penalty for a difference [$opts{b}]
\n/) if (@ARGV < 2);
    my ($fh, %a);
    warn("[uniqcmp] read the first file...\n");
    &uniqcmp_aux($ARGV[0], \%a, 0, $opts{b});
    warn("[uniqcmp] read the second file...\n");
    &uniqcmp_aux($ARGV[1], \%a, 1, $opts{b});
    warn("[uniqcmp] stats...\n");
    my @cnt;
    $cnt[$_] = 0 for (0..9);
    for my $x (keys %a) {
        my $p = $a{$x};
        my $z;
        if (defined($p->[0]) && defined($p->[1])) {
            $z = ($p->[0][0] == $p->[1][0] && $p->[0][1] eq $p->[1][1] && abs($p->[0][2] - $p->[1][2]) < $opts{s})? 0 : 1;
            if ($p->[0][3] >= $opts{q} && $p->[1][3] >= $opts{q}) {
                ++$cnt[$z*3+0];
            } elsif ($p->[0][3] >= $opts{q}) {
                ++$cnt[$z*3+1];
            } elsif ($p->[1][3] >= $opts{q}) {
                ++$cnt[$z*3+2];
            }
            print STDERR "$x\t$p->[0][1]:$p->[0][2]\t$p->[0][3]\t$p->[0][4]\t$p->[1][1]:$p->[1][2]\t$p->[1][3]\t$p->[1][4]\t",
            $p->[0][5]-$p->[1][5], "\n" if ($z && defined($opts{p}) && ($p->[0][3] >= $opts{q} || $p->[1][3] >= $opts{q}));
        } elsif (defined($p->[0])) {
            ++$cnt[$p->[0][3]>=$opts{q}? 6 : 7];
            print STDERR "$x\t$p->[0][1]:$p->[0][2]\t$p->[0][3]\t$p->[0][4]\t*\t0\t*\t",
            $p->[0][5], "\n" if (defined($opts{p}) && $p->[0][3] >= $opts{q});
        } else {
            print STDERR "$x\t*\t0\t*\t$p->[1][1]:$p->[1][2]\t$p->[1][3]\t$p->[1][4]\t",
            -$p->[1][5], "\n" if (defined($opts{p}) && $p->[1][3] >= $opts{q});
            ++$cnt[$p->[1][3]>=$opts{q}? 8 : 9];
        }
    }
    print "Consistent (high, high):   $cnt[0]\n";
    print "Consistent (high, low ):   $cnt[1]\n";
    print "Consistent (low , high):   $cnt[2]\n";
    print "Inconsistent (high, high): $cnt[3]\n";
    print "Inconsistent (high, low ): $cnt[4]\n";
    print "Inconsistent (low , high): $cnt[5]\n";
    print "Second missing (high):     $cnt[6]\n";
    print "Second missing (low ):     $cnt[7]\n";
    print "First  missing (high):     $cnt[8]\n";
    print "First  missing (low ):     $cnt[9]\n";
}

sub uniqcmp_aux {
    my ($fn, $a, $which, $b) = @_;
    my $fh;
    $fn = "samtools view $fn |" if ($fn =~ /\.bam/);
    open($fh, $fn) || die;
    while (<$fh>) {
        my @t = split;
        next if (@t < 11);
#       my $l = ($t[5] =~ /^(\d+)S/)? $1 : 0;
        my $l = 0;
        my ($x, $nm) = (0, 0);
        $nm = $1 if (/NM:i:(\d+)/);
        $_ = $t[5];
        s/(\d+)[M=XI]/$x+=$1/eg;
        @{$a->{$t[0]}[$which]} = (($t[1]&0x10)? 1 : 0, $t[2], $t[3]-$l, $t[4], "$x:$nm", $x - $b * $nm);
    }
    close($fh);
}