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  • UCSC Bin indexing system

    Does anyone know how exactly works the Bin indexing system used in the UCSC genome browser?
    I found just few words in this webpage http://genomewiki.ucsc.edu/index.php...ndexing_system
    but i'm not familiar with java and I'm not able to translate this code in perl.
    Any suggestion?
    Thanks in advance

  • #2
    See http://plindenbaum.blogspot.it/2010/...ng-genome.html (via http://www.biostars.org/post/show/95...d-by-sam-ucsc/ )

    Perl Implementation: No guarantees ...

    sub binFromRangeStandard
    {
    my $zstart;
    my $zend;
    my $i;
    my $startBin;
    my $endBin;
    my $retval;
    my @binOffsets = (512+64+8+1, 64+8+1, 8+1, 1, 0);

    $zstart = $_[0];
    $zend = $_[1];
    $startBin = $zstart;
    $endBin = $zend-1;
    $startBin = $startBin >> 17;
    $endBin = $endBin >> 17;
    for ($i=0; $i<5; $i = $i + 1){
    if ($startBin == $endBin){
    $retval = $binOffsets[$i] + $startBin ;
    return $retval;
    }

    $startBin = $startBin >> 3;
    $endBin = $endBin >> 3;
    }
    $retval = 0;
    return $retval;
    }

    Comment


    • #3
      Thanks for your help.
      I'll test it as soon as possible. Thanks again

      Comment

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