#!/usr/bin/env perl

use strict;

use warnings;

use Getopt::Std;

my %opts;

getopts("2n", \%opts);

die("Usage: ls *.las | xargs -i LAdump -cd reads.db {} | da2paf.pl [-2n] <(DBdump -rh reads.db)\n") if @ARGV < 1;

my $is_dbl = defined($opts{2});

my $with_name = defined($opts{n});

warn("Reading sequence lengths...\n");

my $fn = shift(@ARGV);

open(FH, $fn) || die;

my ($id, $pre, @len, @name);

while (<FH>) {

if (/^R\s(\d+)/) {

$id = $1;

} elsif (/^H\s\S+\s(\S+)/) {

$pre = $1;

} elsif (/^L\s(\S+)\s(\d+)\s(\d+)/) {

$len[$id] = $3 - $2;

$name[$id] = "$pre/$1/$2_$3";

}

}

close(FH);

warn("Converting mappings...\n");

my ($id0, $id1, $strand, $ab, $ae, $bb, $be, $skip);

while (<>) {

if (/^P\s(\S+)\s(\S+)\s([nc])/) {

$id0 = $1; $id1 = $2; $strand = $3 eq 'n'? '+' : '-';

$skip = !$is_dbl && $id0 > $id1? 1 : 0;

} elsif (!$skip && /^C\s(\d+)\s(\d+)\s(\d+)\s(\d+)/) {

$ab = $1, $ae = $2, $bb = $3, $be = $4;

} elsif (!$skip && /^D\s(\d+)/) {

my $bl = $ae - $ab > $be - $bb? $ae - $ab : $be - $bb;

my $ml = $bl - $1;

my ($n0, $n1) = $with_name? ($name[$id0], $name[$id1]) : ($id0, $id1);

if ($strand eq '+') {

print join("\t", $n0, $len[$id0], $ab, $ae, '+', $n1, $len[$id1], $bb, $be, $ml, $bl, 255), "\n";

} else {

my $l = $len[$id1];

print join("\t", $n0, $len[$id0], $ab, $ae, '-', $n1, $l, $l - $be, $l - $bb, $ml, $bl, 255), "\n";

}

}

}