Re^4: suffix array efficiency

[oiskuu]

in reply to Re^3: suffix array efficiency
in thread suffix array efficiency

The degenerate (1-letter) case:

     20000  1 -5
kennethk     0.154/s
RobertCraven  7.55/s
xxx           23.0/s
hdb           28.5/s

The 4-letter case packs only 8 bits of data into 32-bit values and therefore performs poorly. With genomic data one would of course pack differently.

Much more importantly: is there no XS module for constructing suffix arrays? Seems like a very worthy problem.

[kennethk]

I'm not a bioinformatics guy, but if massive runs are actually a significant concern in this system, it's pretty easy to fix the worst-case behavior by adaptively boosting the window, so that worst case regresses to hdb's solution:

sub kennethk {
    my $string = shift;
    my $off = 0;
    my $step = 10;
    my @indices = sort {$off = 0;
                        until (substr($string, $a+$off, $step) cmp sub
+str($string, $b+$off, $step)){
                            $off += $step;
                            $step *= 2;
                        }                                             
+                          } 0 .. length($string) - 1;
    $_++ for @indices;
    return @indices;
}

which gives a degenerate-case comparison of

RobertCraven 2.90/s
kennethk     12.8/s
xxx          13.1/s
hdb          14.2/s

and comparable behavior in the rest of the benchmarks.

I also note your computer is twice as fast as mine. Wanna trade?