Reads mapping of ends of chromosomes

[ETHANol]

First, does anybody have a script that will trim reads that map off the ends of chromosomes in SAM files?

Second, in case anyone needs a perl script that will 'take care' of reads that map off the ends of chromosomes in BED files I wrote one. Seems like it works. Maybe trivial to some but not bad for a salty old bench scientist. I think it works but I am no scripting expert. If anyone has reason to believe otherwise I'd like to know.

#/usr/bin/perl
use strict; use warnings;

#bedEndRepair.pl by Ethan Ford.  Use at own risk!!!!!


#bedEndRepair.pl:  Takes reads that map off the end of chromosomes in a bed file and repositions them as a two nucleotide read at
#					end of the chromosome.

#Usage: 1) make a fasta index file with samtools with the following command: 'samtools faidx <ref.fasta>' or
#			make a 2 column tab deliminted text file. The first column contains the chromosome name written as it is in column 1 of your bed file, e.g. chr1,
#			and the second column has the length of the corresponding chromosome (and integer)

#		2) type: "perl bedEndRepair.pl path/to/your/indexfile.fai path/to/your/bedfile.bed" into the command line.
#		3) Output is saved in your current working dirctory with the name yourbedfile.repaired.bed

my $outfile = $ARGV[1];
$outfile =~ s/\.bed$/\.repaired.bed/;
open(BEDOUT, ">$outfile") or die("Failed to open output file");

open(INDEXFILE, $ARGV[0]) or die "Failed to open bed file";
open(BEDFILE, $ARGV[1]) or die "Failed to open index file";


# turns indexfile.fai into a hash
my %indexhash;

while (<INDEXFILE>) {	
	chomp;
	my ($indexchr, $indexlength) = split("\t", $_);
	$indexhash{$indexchr} = $indexlength;
};

while (<BEDFILE>) {
	chomp;
	(my ($chr), my ($start), my ($stop), my ($c4), my ($c5), my ($strand)) = split("\t");
		
	if ($start < 1) 
			{print BEDOUT $chr, "\t", '1', "\t", '2', "\t", $c4, "\t", $c5, "\t", $strand, "\n";}
			
	elsif ($stop > $indexhash{"$chr"})
			{print BEDOUT $chr, "\t", $indexhash{"$chr"}-1, "\t", $indexhash{"$chr"}, "\t", $c4, "\t", $c5, "\t", $strand, "\n";}
						
	else
			{print BEDOUT $chr, "\t", $start, "\t", $stop, "\t", $c4, "\t", $c5, "\t", $strand, "\n";}
							
						
};	
	
close (BEDFILE); close (INDEXFILE); close (BEDOUT);
exit;