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

open my $fh1, '<', \<<EOF or die $!; 
1 19002930  0.74
1 19002931 -0.12
EOF

my %data;
while (<$fh1>) {
	next if /CHR/;
	my ($chr, $bp, $min) = split;
	$data{$chr,$bp} = $min;
}

open my $fh2, '<', \<<EOF or die $!;
1 19002930 0.84 0.12 0.94
1 19002931 0 -.20 .12
EOF

while (<$fh2>) {
	my ($chr, $bp, @rest) = split;
	if (defined(my $min = $data{$chr,$bp})) {
		print join(" ", $chr, $bp, grep $_ >= $min, @rest), "\n";	
	}
}