Illumina's changing file formats

[MPC]

Hi everyone,

Just a quick announcement that I have just uploaded version 1.9 of the
SolexaQA package. You can download it here:

http://solexaqa.sourceforge.net/

Note that Illumina (and others) have made a number of substantial (and
largely unjustified) changes to the read header lines. I am now aware
of at least eleven different variants:

http://solexaqa.sourceforge.net/questions.htm#headers

It is now at the point where it is logically impossible to extract the
tile number from the header line without knowing what version the data
is, and there is no way to figure this out from the header line
alone. There are also large numbers of file variants with
substantially different numbers of tiles. I have seen variants with
32, 48, 100, 120 and 320 tiles.

In combination, it is increasingly difficult to maintain a single
version of the SolexaQA code that can accommodate all of Illumina's
whimsical file variants.

If you run into any problems with the SolexaQA package, please send me
an email and bear with me as I attempt to update the code.

Best
-Murray