Find the Overlap region between in the two file

Overlap.pl

# Author : Shujia Huang
# Date   : 2013-01-10

#!/usr/bin/perl
use strict;
use warnings;
use Getopt::Long;

my ( $posFile, $regionFile ); 

GetOptions (

	"i=s"	=> \$posFile,
	"r=s"	=> \$regionFile,
);

Usage() unless $posFile && $regionFile;

my %region;
my %index;

GetRegion ( $regionFile, \%region, \%index );

open IN, $posFile or die "Cannot open file $posFile: $!\n";
while ( <IN> ){
#chr10   105186  105186  T       C       chr10   105186  T       C    ......
	chomp;
	my @tmp   = split;
	my $refId = $tmp[0];
	next if ( !exists $index{$refId} );

	my $flag      = 1;
	my $isOverlap = 0;
	for( my $i = $index{$refId}; $i < @{$region{$refId}}; ++$i ) {

		next if ( $tmp[1] > $region{$refId}->[$i][1] );
		last if ( $tmp[2] < $region{$refId}->[$i][0] ); 

		if ( $flag ) {
			$flag = 0;
			$index{$refId} = $i;
		}
		$isOverlap = 1;
		last;
		#$length=OverlapLength($tmp[1],$tmp[2],$region{$refId}->[$i][0],$region{$refId}->[$i][1]);
	}

	if ( $isOverlap ) {
		print join "\t", @tmp ; print "\n";
	}

}
close IN;

###################################################################
###################################################################
sub GetRegion {

	my ( $file, $region, $index ) = @_;
	
	open I, $file or die "Cannot open file $file : $!\n";
	while ( <I> ) {
	# chr1    mRNA    65298905        65432187        -       NM_002227       JAK1
		chomp;
		my @tmp = split;
		push ( @{ $$region{$tmp[0]} }, [ @tmp[2,3], $_ ] );
	}
	close I;

	for my $refId ( keys %$region ) {
		@{ $$region{$refId} } = sort {$a->[0] <=> $b->[0]} @{ $$region{$refId} };
		$$index{ $refId }     = 0;
	}
}

sub OverlapLength {
    my ($reg1,$reg2,$tar1,$tar2)= @_;
    my $length = 0;
    if($tar1>=$reg1 && $tar1<=$reg2 && $tar2>=$reg2)
    {
        $length=$reg2-$tar1+1;
    }elsif($tar1>=$reg1 && $tar1<=$reg2 && $tar2<=$reg2)
    {
        $length=$tar2-$tar1+1;
    }elsif($tar2>=$reg1 && $tar2<=$reg2 && $tar1<=$reg1)
    {
        $length=$tar2-$reg1+1;
    }else
    {
        $length=$reg2-$reg1+1;
    }
    return $length;
}

################################################################
sub IsOvlap {
# 
    my ( $start1, $end1, $start2, $end2 ) = @_;
    my $isOvlp = 0;

    $isOvlp = 1 if ( $end1 >= $start2 and $start1 <= $end2 );

    return $isOvlp;
}

sub OvlapReg {
# Reture the overlap region.
    my ( $start1, $end1, $start2, $end2 ) = @_;
    my ( $start, $end ) = ( 0, 0 );

    if ( $end1 >= $start2 and $end1 <= $end2 and $start1 <= $start2 ) {
        $start = $start2;
        $end   = $end1;
    }
    elsif ( $end1 >= $start2 and $end1 <= $end2 and $start1 > $start2 ) {
        die "The end position is bigger than start position : $end1 > $start1\n" if ( $start1 > $end1 );
        $start = $start1;
        $end   = $end1;
    }
    elsif ( $start1 <= $start2 and $end1 > $end2 ) {
        die "The end position is bigger than start position : $end2 > $start2\n" if ( $start2 > $end2 );
        $start = $start2;
        $end   = $end2;
    }
    elsif ( $start1 <= $end2 and $end1 > $end2 ) {
        $start = $start1;
        $end   = $end2;
    }

    return ( $start, $end );
}

sub Usage {
    print STDERR <<U;
Version : 0.0.1 ( 2012-01-10 )
Author  : Shujia Huang
Created : 2013/01/10
Last Modify :

    Usage : perl $0 [Options] -i [cout infile] > output

    Options :

        -i  [str]   Position file. Should be sorted! ( Find the positions which in the Region file "-r". )
        -r  [str]   Region file. Not required sorting.

U
    exit(0);
}