#!/usr/bin/perl 
#===============================================================================
#
#         FILE:  tranMappedJuncReads.pl
#
#        USAGE:  ./tranMappedJuncReads.pl  <read len>
#
#  DESCRIPTION:  Translate the mapped short reads to the reference genome using
#                bowtie to the mapping format needed by IsoInfer
#
#      OPTIONS:  ---
# REQUIREMENTS:  ---
#         BUGS:  ---
#        NOTES:  ---
#       AUTHOR:  Jianxing Feng (feeldead), feeldead@gmail.com
#      COMPANY:  THU
#      VERSION:  1.0
#      CREATED:  05/29/2010 10:39:52 PM
#     REVISION:  ---
#===============================================================================
if( @ARGV < 1 ){
  die("Usage: ./tranMappedJuncReads.pl <read len> \n");
}

$read_len = $ARGV[0];

while (<STDIN>)
{
	chomp;
	@tmp = split(/\t/);
	@junc = split(/\|/, $tmp[2]);

	$cross_len = $junc[3];
	$cross_strengh = $read_len - $cross_len;

	$junc_first_end = $junc[1] + $cross_len;
	$junc_second_start = $junc[2];

	$chr = $junc[0];
	$strand = $tmp[1];

	$first_start = $tmp[3] + $junc[1];
	$second_end = $junc_second_start + $tmp[3] + $cross_strengh;

	print "$chr\t$strand\t$first_start,$junc_second_start\t$junc_first_end,$second_end\n";
}