Difference: JaysJournal (36 vs. 37)

Revision 372010-06-10 - jayzhang

Line: 1 to 1

May 2010 archive

06/01/10

Line: 135 to 135

I also benchmarked my changes from yesterday (swapping out the Fastq read function). It seems saligner is now faster than readaligner (at least in exact matching). Anyways, here are the times:

Aligner	Exact time (s)	1-mismatch time (s)	Mismatch:Exact ratio

Changed:

<
<

saligner max_results=10

64.461

94.434

1.465

>
>

saligner, max_results=1

64.461

94.434

1.465

The mismatch:exact ratio is still a bit off from bowtie's and readaligner's, but that might also be because mismatches still unecessarily go through the CIGAR generator (which I should fix sometime).

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