/usr/bin/zoom2sam.pl is in samtools 1.7-1.
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 | #!/usr/bin/env perl
#
# Copyright (C) 2009 Genome Research Ltd.
#
# 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;
&zoom2sam;
exit;
sub mating {
my ($s1, $s2) = @_;
my $isize = 0;
if ($s1->[2] ne '*' && $s1->[2] eq $s2->[2]) { # then calculate $isize
my $x1 = ($s1->[1] & 0x10)? $s1->[3] + length($s1->[9]) : $s1->[3];
my $x2 = ($s2->[1] & 0x10)? $s2->[3] + length($s2->[9]) : $s2->[3];
$isize = $x2 - $x1;
}
# update mate coordinate
if ($s2->[2] ne '*') {
@$s1[6..8] = (($s2->[2] eq $s1->[2])? "=" : $s2->[2], $s2->[3], $isize);
$s1->[1] |= 0x20 if ($s2->[1] & 0x10);
} else {
$s1->[1] |= 0x8;
}
if ($s1->[2] ne '*') {
@$s2[6..8] = (($s1->[2] eq $s2->[2])? "=" : $s1->[2], $s1->[3], -$isize);
$s2->[1] |= 0x20 if ($s1->[1] & 0x10);
} else {
$s2->[1] |= 0x8;
}
}
sub zoom2sam {
my %opts = ();
getopts("p", \%opts);
die("Usage: zoom2sam.pl [-p] <readLen> <aln.zoom>
Warnings: This script only supports the default Illumina outputs.\n") if (@ARGV < 2);
my $is_paired = defined($opts{p});
my $len = shift(@ARGV);
# core loop
my @s1 = ();
my @s2 = ();
my ($s_last, $s_curr) = (\@s1, \@s2);
while (<>) {
&zoom2sam_aux($_, $s_curr, $is_paired, $len);
if (@$s_last != 0 && $s_last->[0] eq $s_curr->[0]) {
&mating($s_last, $s_curr);
print join("\t", @$s_last), "\n";
print join("\t", @$s_curr), "\n";
@$s_last = (); @$s_curr = ();
} else {
print join("\t", @$s_last), "\n" if (@$s_last != 0);
my $s = $s_last; $s_last = $s_curr; $s_curr = $s;
}
}
print join("\t", @$s_last), "\n" if (@$s_last != 0);
}
sub zoom2sam_aux {
my ($line, $s, $is_paired, $len) = @_;
chomp($line);
my @t = split("\t", $line);
@$s = ();
# read name
$s->[0] = $t[0];
# initial flag (will be updated later)
$s->[1] = 0;
$s->[1] |= 1 | 1<<6 if ($s->[0] =~ /_F$/);
$s->[1] |= 1 | 1<<7 if ($s->[0] =~ /_R$/);
$s->[1] |= 2 if ($is_paired);
# read & quality
$s->[9] = "*"; $s->[10] = "*";
# cigar
$s->[5] = $len . "M";
# coor
my @s = split(/\s+/, $t[1]);
$s->[2] = $s[0];
$t[1] =~ /:(\d+)$/;
$s->[3] = $1 + 1;
if ($s->[0] =~ /_[FR]$/) {
my $u = ($s->[0] =~ /_F$/)? 1 : 0;
my $w = ($t[2] eq '+')? 1 : 0;
$s->[1] |= 0x10 if ($u ^ $w);
$s->[0] =~ s/_[FR]$//;
} else {
$s->[1] |= 0x10 if ($t[2] eq '-');
}
# mapQ
$s->[4] = 30;
# mate coordinate
$s->[6] = '*'; $s->[7] = $s->[8] = 0;
# aux
push(@$s, "NM:i:$t[3]");
}
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