#!/usr/bin/env perl
use strict;

# chain line
my ($ch_score, $ch_name, $ch_size, $ch_target_strand, $ch_target_start, $ch_target_end,
   $ch_query_name, $ch_query_size, $ch_query_strand, $ch_query_start, $ch_query_end, $ch_id);

# track positions
my $current_pos;
my $current_end;

while(<>) {
    chomp;

    if( /chain/ ) {
        my @arr = split ' ';
        ($ch_score, $ch_name, $ch_size, $ch_target_strand, $ch_target_start, $ch_target_end, $ch_query_name, $ch_query_size, $ch_query_strand, $ch_query_start, $ch_query_end, $ch_id) = ($arr[1],$arr[2],$arr[3],$arr[4],$arr[5],$arr[6],$arr[7],$arr[8],$arr[9],$arr[10],$arr[11],$arr[12]);
        print "$ch_name\tname\tmatch\t$ch_query_start\t$ch_query_end\t.\t.\t.\tID=$ch_id;target=$ch_query_name\n";
        $current_pos=$ch_query_start;
        $current_end=$ch_query_start;
    }
    else {
        my @match = split '\t';
        if($match[0]) {
            $current_end = $current_pos+$match[0];
            print "$ch_query_name\tname\tmatch_part\t$current_pos\t$current_end\t.\t.\t.\tParent=$ch_id;target=$ch_name\n";
            $current_pos = $current_end;
        }
        if($match[1]) {
            $current_end = $current_pos+$match[1];
            print "$ch_query_name\tname\tgap\t$current_pos\t$current_end\t.\t.\t.\tParent=$ch_id;target=$ch_name\n";
            $current_pos = $current_end;
        }
        if($match[2]) {
            print "$ch_query_name\tname\tinsertion\t$current_pos\t$current_pos\t.\t.\t.\tParent=$ch_id;target=$ch_name;len=$ch_size;len2=$match[2]\n";
        }
    }
}