Hi,
bpiterate() has been added to BiocParallel 0.99.11. The current
implementation is based on sclapply() from HTSeqGeni and is supported
for the multi-core environment only. Support for other back-ends are in
progress.
For the current implementation, iterating over multiple files can be
Hi,
I have been using FastqStreamer() and yield() to process a large fastq file in
chunks, modifying both the read and name and then appending the output to a new
fastq file as each chunk is processed. This works great, but would benefit
greatly from being parallelized.
As far as I can tell,
Hi Jeff,
See my replies below inline.
On 8/6/14, 7:16 AM, Johnston, Jeffrey wrote:
Hi,
I have been using FastqStreamer() and yield() to process a large fastq file in
chunks, modifying both the read and name and then appending the output to a new
fastq file as each chunk is processed. This
Hi Jeff,
Thanks for the prompt. It looks like bpiterate or bpstream was intended
but didn't quite make it into BiocParallel. I'll discuss with Martin to
see if I'm missing other history / past discussions and then add it in.
Ryan had some ideas for parallel streaming we discussed at Bioc2014
