use strict;
use warnings;
use PDL;
use Inline with => 'PDL';
use PDL::GSL::RNG;

my $genome = '';
my @id_lines;
my @runs;

########################## 
# Read 
########################## 

while ( <DATA> ) { 
    chomp;
    if ( /^>/ ) {
        push @id_lines, $_
    }
    else {
        push @runs, length;
        $genome .= $_
    }
}

########################## 
# Shuffle
########################## 

my $rng = PDL::GSL::RNG-> new( 'taus' );
$rng-> set_seed( time );

my $start  = 0;
my $stop   = length( $genome ) - 1;
my $window = 3;

while ( $start < $stop ) {
    my $len = $start + $window > $stop
        ? $stop - $start
        : $window;
    my $p = mkpiddle( $genome, $start, $len );
    $rng-> ran_shuffle( $p );
    $start += $window
}

########################## 
# Output
########################## 

$start = 0;
for ( 0 .. $#runs ) {
    print $id_lines[ $_ ], "\n",
          substr( $genome, $start, $runs[ $_ ]), "\n";
    $start += $runs[ $_ ]
}

########################## 
# Guts
########################## 
    
use Inline C => <<'END_OF_C';

static void default_magic( pdl *p, int pa ) { p-> data = 0; }

pdl* mkpiddle( char* data, int ofs, int len ) {
    PDL_Indx dims[] = { len };

    pdl* npdl = PDL-> pdlnew();
    
    PDL-> setdims( npdl, dims, 1 );
    npdl-> datatype = PDL_B;
    npdl-> data     = data + ofs;
    npdl-> state   |= PDL_DONTTOUCHDATA | PDL_ALLOCATED;
    PDL-> add_deletedata_magic( npdl, default_magic, 0 );
    return npdl;
}

END_OF_C

__DATA__
>Chr1
CCCTAAACCCTAAACCCTAAACCCTAAACCTCTGAATCCTTAATCCCTAAATCCCTAAAT
>Chr2
TATGACGTTTAGGGACGATCTTAATGACGTTTAGGGTTTTATCGATCAGCGACGTAGGGA
>Chr3
GTTTAGGGTTTAGGGTTTAGGGTTTAGGGTTTAGGGTTTAGGGTTTAGGGTTTAGGGTTT
>Chr4
AACAAGGTACTCTCATCTCTTTACTGGGTAAATAACATATCAACTTGGACCTCATTCATA
>Chr5
AACATGATTCACACCTTGATGATGTTTTTAGAGAGTTCTCGTGTGAGGCGATTCTTGAGG