File: sam2fastq.pl

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#!/usr/bin/perl

#-------------------------------------------------------------------------------
# Convert from SAM to FASTQ
#
# 																Pablo Cingolani
#-------------------------------------------------------------------------------

while( $l = <STDIN> ) {
	chomp $l;
	@t = split /\t/, $l;
	print "\@$t[0]\n$t[9]\n+\n$t[10]\n";
}