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#!/usr/bin/env perl
use strict;
use warnings;
use Getopt::Std;
my %opts = ();
getopts("2f:l:", \%opts);
die("Usage: mhap2paf.pl [-2] [-f name_list] [-l min_len] <in.mhap>\n") if (@ARGV == 0 && -t STDIN);
my $is_dbl = defined($opts{2});
my $min_blen = defined($opts{l})? $opts{l} : 0;
my @a = ();
if (defined $opts{f}) {
open(FH, $opts{f} =~ /\.gz$/? "gzip -dc $opts{f} |" : $opts{f}) || die;
while (<FH>) {
chomp;
my @t = split;
push(@a, $t[0]);
}
close(FH);
}
while (<>) {
chomp;
my @t = split;
my $bl = $t[6] - $t[5] > $t[10] - $t[9]? $t[6] - $t[5] : $t[10] - $t[9];
my $r = $t[2];
my $ml = int($bl * ($r <= 1.? $r : .01 * $r) + .499);
my $cm = "cm:i:" . int($t[3] + .499);
my $rev = $t[4] == $t[8]? '+' : '-';
next if $bl < $min_blen;
if (@a) {
$t[0] = $a[$t[0]-1];
$t[1] = $a[$t[1]-1];
}
print(join("\t", @t[0,7,5,6], $rev, @t[1,11,9,10], $ml, $bl, 255, $cm), "\n");
print(join("\t", @t[1,11,9,10], $rev, @t[0,7,5,6], $ml, $bl, 255, $cm), "\n") if ($is_dbl);
}
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