#5 srf2fastq.c: Sequentially outputting paired-end data

[Jordan Mendler]

Some aligners, such as Bfast (https://secure.genome.ucla.edu/index.php/BFAST), require fastq input for paired-end data to be in sequential records within a single file. For instance, the fastq should look like:
@read1, end 1
....
@read1, end 2
....
@read2, end 1
...
@read2, end 2

I have attached a patch for srf2fastq to add a -S option to do this. It outputs to stdout as usual, except outputs one region at a time, rather than joining multiple regions.

[Jordan Mendler]

Add support to sequentially output multiple reads.

[James Bonfield]

Applied to the svn repository and so will be in the next release. Thanks.