Hm. This is what I get from your latest code:

C:\test>junk95 .
Use of uninitialized value $start in exists at C:\test\junk95.pl line 
+95, <IN2> line 8.
Use of uninitialized value $_ in concatenation (.) or string at C:\tes
+t\junk95.pl line 108, <IN2> line 8.
Use of uninitialized value $_ in concatenation (.) or string at C:\tes
+t\junk95.pl line 108, <IN2> line 8.
c1    100    12000    +    AT                   0
Use of uninitialized value $start in exists at C:\test\junk95.pl line 
+95, <IN2> line 8.
Use of uninitialized value $_ in concatenation (.) or string at C:\tes
+t\junk95.pl line 108, <IN2> line 8.
Use of uninitialized value $_ in concatenation (.) or string at C:\tes
+t\junk95.pl line 108, <IN2> line 8.
c1    19800    20000    -    AG                 0
Use of uninitialized value $start in exists at C:\test\junk95.pl line 
+95, <IN2> line 8.
Use of uninitialized value $_ in concatenation (.) or string at C:\tes
+t\junk95.pl line 108, <IN2> line 8.
Use of uninitialized value $_ in concatenation (.) or string at C:\tes
+t\junk95.pl line 108, <IN2> line 8.
c1    20049    20800    -    GC                 0
Use of uninitialized value $start in exists at C:\test\junk95.pl line 
+95, <IN2> line 8.
Use of uninitialized value $_ in concatenation (.) or string at C:\tes
+t\junk95.pl line 108, <IN2> line 8.
Use of uninitialized value $_ in concatenation (.) or string at C:\tes
+t\junk95.pl line 108, <IN2> line 8.
c10    10080    10000    -    TT                        0
Use of uninitialized value $start in exists at C:\test\junk95.pl line 
+95, <IN2> line 8.
Use of uninitialized value $_ in concatenation (.) or string at C:\tes
+t\junk95.pl line 108, <IN2> line 8.
Use of uninitialized value $_ in concatenation (.) or string at C:\tes
+t\junk95.pl line 108, <IN2> line 8.
c11    10078    14008    -    TG                        0
Use of uninitialized value $start in exists at C:\test\junk95.pl line 
+95, <IN2> line 8.
Use of uninitialized value $_ in concatenation (.) or string at C:\tes
+t\junk95.pl line 108, <IN2> line 8.
Use of uninitialized value $_ in concatenation (.) or string at C:\tes
+t\junk95.pl line 108, <IN2> line 8.
c15    10078    14008    -    TC                        0
Use of uninitialized value $start in exists at C:\test\junk95.pl line 
+95, <IN2> line 8.
Use of uninitialized value $_ in concatenation (.) or string at C:\tes
+t\junk95.pl line 108, <IN2> line 8.
Use of uninitialized value $_ in concatenation (.) or string at C:\tes
+t\junk95.pl line 108, <IN2> line 8.
c9    10078    14008    -    AG                 0
Use of uninitialized value $start in exists at C:\test\junk95.pl line 
+95, <IN2> line 8.
Use of uninitialized value $_ in concatenation (.) or string at C:\tes
+t\junk95.pl line 108, <IN2> line 8.
Use of uninitialized value $_ in concatenation (.) or string at C:\tes
+t\junk95.pl line 108, <IN2> line 8.
c9    1078    10008    -    TA                  0
[download]

Since I've already written it:

#! 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 ' ';
    if( exists $ref{ $cols[ 0 ] } ) {
        for my $ref ( @{ $ref{ $cols[ 0 ] } } ) {
            my( $sRef, $eRef ) = @$ref;
            next if $cols[ 1 ] > $eRef or $cols[ 2 ] < $sRef;
            my $so = $sRef > $cols[ 1 ] ? $sRef : $cols[ 1 ];
            my $eo = $eRef < $cols[ 2 ] ? $eRef : $cols[ 2 ];
            print join "\t", @cols[ 0 .. 2 ], ( $eo - $so + 1 ), @cols
+[ 3 .. $#cols ];
        }
    }
}
close QUERY;
__END__
C:\test>819005
c1      100     12000   15      +       AT
c1      100     12000   171     +       AT
c1      100     12000   11901   +       AT
c1      100     12000   1       +       AT
c1      19800   20000   9       -       AG
c9      10078   14008   9       -       AG
c9      1078    10008   123     -       TA
[download]