Hi Monks
I'm enjoying you wisdom for quite some time now
and first of all I wanted to thank you for making my life easier and me a better perl user!

Now I ran into a problem I just can't figure out and hope you can again share your wisdom with me.

In my current script I am building an IntervalTree with the
package Set::IntervalTree of a file containing genomic
coordinates together with some other info I want to retrieve for coordinate ranges.

This works just perfect and does what I need, but now I
would like to store the built tree to disk and retrieve
it later on so that I do not have to rebuild it every
time I search for coordinates.
I used Storable already in several scripts and thought it
would be a great idea to do so again, from what I have
read in your great Object Serialization Basics this looked very promising.

So I create a hash of trees for each chromosome that is
found in my input file like this 

 while (<FILE>){
    my @line = split (/\t/,$_); ## tab separated file
    my @tmp = split(/\./,$line[1]); ## chromosome name in field 2, as 
+part of a dot separated string
    $chr{"$tmp[1]"} =  new Set::IntervalTree() unless (defined $chr{"$
+tmp[1]"});
    $chr{"$tmp[1]"} -> insert($count,$line[2]-1,$line[3]+1); ## fields
+ 3 and 4 contain the coordinates, -1 and +1 to allow search for direc
+t overlaps at start and end
}

[download]

which works fine, then I store this hash using Storable 
store (\%chr, "$file.coordinates") or die "Can't store %chr in file.co
+ordinates!\n";

[download]

In a second run I check for the presence of this file and
if it exists I try to retrieve it via 
    my $hashref;
    %chr = %{$hashref = retrieve("$file.coordinates")};

[download]

But when I later on try to access coordinates in this
deserialized hash I get a segmentation fault.
I guess the problem is that I would to somehow create a
new IntervalTree object first and just fill it with the
contents from disk but I just can't figure out how.

I hope you can understand the problem from the bit of code I post.
Your help is much appreciated, thank you for your time!

In reply to Storing and retrieving a hash of objects by Frnak

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