Parallelize breseq execution

[jeffreybarrick]

Motivation: There are many steps within breseq that could be easily parallelized to speed up execution.

Implementation: Use a thread pool that relies only on C++11 std:thread to maximize portability. This header can help implement the thread pool: https://github.com/vit-vit/ctpl

• Step 1: Parallelize HTML alignment and coverage graph creation
• Step 2: Parallelize Reference and FASTQ file analysis and conversion.
• Step 3: Parallelize scanning the genome to predict mutations; needs new methods to stitch together RA and MC evidence from different chunks of a large genome. Most challenging, but also highest impact on speed.

[jeffreybarrick]

@ShreyasKudari I'm going to start working on this. Let me know if that conflicts with any of your plans.

[ghfzvc]

Hello, is there a status update on Step 3? Wondering if there are any plans for when work on this might happen. Thanks.

[jeffreybarrick]

No one is working on it at present since we do not have any funding specifically for breseq development.