[emboss-dev] FASTQ parsing speed in EMBOSS

Peter biopython at maubp.freeserve.co.uk
Fri Jul 31 12:01:27 UTC 2009

On Tue, Jul 28, 2009 at 1:51 PM, Peter<biopython at maubp.freeserve.co.uk> wrote:
> I've retitled this and CC'ed it to the EMBOSS dev list - which is
> probably a better place for this now!

Another random thought for speeding up parsing/writing the Solexa/Illumina
FASTQ formats: At some point you need to convert from an integer score to
an ASCII character using an offset of 64. Would clearing/setting the bit be
faster than using integer subtraction/addition?

Sadly this trick won't work for the Sanger FASTQ format as the offset is 33,
not 32.

Peter C.

Credit where due: This idea was based on a discussion with Leighton
Pritchard, where he suggested this could be why Solexa opted for a
64 bit offset in particular.

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