take input from STDIN

[Matthew MacManes]

Hello, 

It looks like SolexaQA cannot currently take files from STDIN-- is this something that could be added?  Specifically, I want to use 'gzip -c' to avoid having to decompress fastq files. 

Thanks, Matt  

[MPC]

Hi Matt,

This is something we can look at adding in the future, but given the
way the code is currently written, it would not be an easy addition.

DynamicTrim could potentially be changed with relatively little
effort. However, LengthSort accepts multiple file I/O and therefore
cannot handle data from just a single stream (STDIN). Conversely,
SolexaQA reads part of its input data multiple times (e.g., to
determine the file format). Therefore, SolexaQA must pull data from a
file rather than a transient I/O stream like STDIN.

It might technically be possible to modify the underlying algorithms
to accommodate data from STDIN, but I would be reluctant to make such
major changes without evidence of significant user demand.

Best
-Murray