cushaw2: to work with SOLiD XSQ files directly?

[BioCyberman]

Hi,
I am very interested in testing out cushaw2-gpu. But converting xsq file to csfasta and .qual is not convenient. It takes much more space and I don't want to store both xsq and csfasta/qual files. So it would be a big plus if cushaw2-* programs can work with xsq files directly. XSQ is based on HDF format, so I think there should be enough documentation that talented developers of CUSHAW can make use of XSQ format. Here is HDF homepage: http://www.hdfgroup.org/downloads/index.html
In addition, Lifetech seems to be open to help developers to make other software work with XSQ.
I can provide test data, do testing and give feedback if neccessary.

Thanks.

[Yongchao Liu]

Thanks for you interest in CUSHAW2-GPU. However, CUSHAW2-GPU is designed based on CUSHAW2 version 2.1.8 (i.e. 2.1.x), which does not support color-space alignment. The color-space alignment is supported only from version 2.4.x.

I will spare some time to look into the XSQ format and will try to support this format in the next release of CUSHAW2. At the moment, I am busy with other research stuffs. Hence, the integration of the new format may have to be delayed for some time.

[BioCyberman]

It's good to hear from you. To save you some seconds, here is the link to XSQ file specifications: http://www.lifetechnologies.com/dk/en/home/technical-resources/software-downloads/xsq-software.html

Look forward to new versions of CUSHAW2.

Thanks again.