Try something like this (UNTESTED): 

#!/usr/bin/perl
# perl.ID.match.pl
use strict;
use warnings;

open my $KEY, '<', 'chr1.coverage.txt' or die "error reading 'chr1.cov
+erage.txt' because: $!";
my $pattern = join '|', map /^([^\t]+)/ ? "\Q$1\E" : (), <$KEY>;
close $KEY;

open my $FULL, '<', 'chr1.txt' or die "error reading 'chr1.txt' becaus
+e: $!";
open my $OUT, '>', 'chr1.match.txt' or die "error reading 'chr1.match.
+txt' because: $!";

while ( <$FULL> ) {
    print $OUT $_ if /^(?:$pattern)\t/;
    }

close $FULL;
close $OUT;

exit 0;

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In reply to Re: help speeding up my perl code by jwkrahn
in thread help speeding up my perl code by a217

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