15 getopts('pcag:', \%opts);
16 die("Usage: wgsim_eval.pl [-pca] [-g $opts{g}] <in.sam>\n") if (@ARGV == 0 && -t STDIN);
18 my ($max_q, $flag) = (0, 0);
20 $flag |= 1 if (defined $opts{p});
21 $flag |= 2 if (defined $opts{c});
27 my ($q, $is_correct, $chr, $left, $rght) = (int($t[4]/10), 1, $t[2], $t[3], $t[3]);
28 $max_q = $q if ($q > $max_q);
30 $_ = $t[5]; s/(\d+)[MDN]/$rght+=$1,'x'/eg;
32 # correct for soft clipping
33 my ($left0, $rght0) = ($left, $rght);
34 $left -= $1 if (/^(\d+)[SH]/);
35 $rght += $1 if (/(\d+)[SH]$/);
36 $left0 -= $1 if (/(\d+)[SH]$/);
37 $rght0 += $1 if (/^(\d+)[SH]/);
39 next if (($t[1]&0x4) || $chr eq '*');
40 # parse read name and check
41 if ($t[0] =~ /^(\S+)_(\d+)_(\d+)_/) {
42 if ($1 ne $chr) { # different chr
46 if (($t[1]&0x40) && !($t[1]&0x10)) { # F3, forward
47 $is_correct = 0 if (abs($2 - $left) > $gap && abs($2 - $left0) > $gap);
48 } elsif (($t[1]&0x40) && ($t[1]&0x10)) { # F3, reverse
49 $is_correct = 0 if (abs($3 - $rght) > $gap && abs($3 - $rght0) > $gap);
50 } elsif (($t[1]&0x80) && !($t[1]&0x10)) { # R3, forward
51 $is_correct = 0 if (abs($3 - $left) > $gap && abs($3 - $left0) > $gap);
52 } else { # R3, reverse
53 $is_correct = 0 if (abs($2 - $rght) > $gap && abs($3 - $rght0) > $gap);
56 if ($t[1] & 0x10) { # reverse
57 $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
59 $is_correct = 0 if (abs($2 - $left) > $gap && abs($2 - $left0) > $gap);
64 warn("[wgsim_eval] read '$t[0]' was not generated by wgsim?\n");
68 ++$c1[$q] unless ($is_correct);
69 @{$fnfp{$t[4]}} = (0, 0) unless (defined $fnfp{$t[4]});
71 ++$fnfp{$t[4]}[1] unless ($is_correct);
72 print STDERR $line if (($flag&1) && !$is_correct && $q > 0);
75 my ($cc0, $cc1) = (0, 0);
76 if (!defined($opts{a})) {
77 for (my $i = $max_q; $i >= 0; --$i) {
78 $c0[$i] = 0 unless (defined $c0[$i]);
79 $c1[$i] = 0 unless (defined $c1[$i]);
80 $cc0 += $c0[$i]; $cc1 += $c1[$i];
81 printf("%.2dx %12d / %-12d %12d %.3e\n", $i, $c1[$i], $c0[$i], $cc0, $cc1/$cc0) if ($cc0);
84 for (reverse(sort {$a<=>$b} (keys %fnfp))) {
88 print join("\t", $_, $cc0, $cc1), "\n";