Slightly different ordering, but same data:

#! perl -slw
use strict;

my %ref;
open REF, '<', 'ref.txt' or die $!;
while( <REF> ) {
    chomp;
    my @cols = split ' ';
    push @{ $ref{ $cols[0] } }, [ @cols[ 1, 2 ] ];
}
close REF;

open QUERY, '<', 'query.txt' or die $!;
while( <QUERY> ) {
    chomp;
    my @cols = split ' ';
    my $overlaps = 0;
    for my $ref ( @{ $ref{ $cols[ 0 ] } } ) {
        my( $sRef, $eRef ) = @$ref;
        next if $cols[ 1 ] > $eRef or $cols[ 2 ] < $sRef;
        ++$overlaps;
    }
    print join "\t", @cols[ 0 .. 2 ], $overlaps, @cols[ 3 .. $#cols ];
}
close QUERY;

__END__
c:\test>819005
c1      100     12000   4       +       AT
c1      19800   20000   1       -       AG
c1      20049   20800   0       -       GC
c9      10078   14008   1       -       AG
c11     10078   14008   0       -       TG
c15     10078   14008   0       -       TC
c9      1078    10008   1       -       TA
c10     10080   10000   0       -       TT
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