How to make bwa short read alignment deterministic for testing

[tnguyensanger]

@gbggrant requested ways to make bwa short read alignment deterministic for testing.

Trawling through the internet indicates that we can make bwa deterministic if we follow all of these steps:

1. Always use the same fastq with the reads in the same order

2. Always use the same machine and bwa settings. Alternatively, if we need to change the machine and threads given to bwa, we can explicitly set the hidden bwa mem option -K to set the chunk size. If -K is not set, then the chunksize is determined by the number threads. This makes a difference to the end bam because the insert size is determined by the chunk.

See past comments from Heng Li:
lh3/bwa#192
lh3/bwa#272
lh3/bwa#121

Also see this centre for common disease genomics repo issue:
CCDG/Pipeline-Standardization#2

[tnguyensanger]

Addressed by #63