On Thu, Jul 28, 2011 at 9:43 PM, Assaf Gordon gordon@cshl.edu wrote:

Hi,

The attached patch enables the BWA wrapper to work with Illumina-1.3+ FASTQ files without Grooming (which goes well with the name of the tool: "Map with BWA for Illumina" ).

Actually, Changing the XML and the python code, testing the tool and mapping to the mouse genome all together took less time than grooming one 4.2GB FASTQ file :)

Comments are welcomed,  -gordon

Hi Gordon,

You asked for comments, so:

It concerns me that you're doing this for both "fastqillumina" format (good) and "fastqsolexa" (bad). Treating the later as fastqillumina would give negative scores and probably cause trouble. Unless BWA copes but if so it is a poor choice of argument name?

In the XML wrapper you've not updated the help text for the FASTQ parameters to indicate it would now accept Illumina FASTQ as well as Sanger FASTQ.

Peter

P.S. It is a patch file, but it has extension xml??

Hi Assaf,

I placed the patch into a ticket for us to be able to track status more easily: https://bitbucket.org/galaxy/galaxy-central/issue/635/patch-bwa-wrapper-with...

Thank you!

Jen Galaxy team

On 7/28/11 2:26 PM, Assaf Gordon wrote:

Hello Peter and all,

Peter Cock wrote, On 07/28/2011 05:08 PM:

...

It concerns me that you're doing this for both "fastqillumina" format (good) and "fastqsolexa" (bad). Treating the later as fastqillumina would give negative scores and probably cause trouble. Unless BWA copes but if so it is a poor choice of argument name?

In the XML wrapper you've not updated the help text for the FASTQ parameters to indicate it would now accept Illumina FASTQ as well as Sanger FASTQ.

Peter

P.S. It is a patch file, but it has extension xml??

These are all valid comments, here's an updated patch (with a ".patch" extension :) ).

Thanks! -gordon

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