bwa mem -K hidden option reference?

[ryanrichholt]

Regarding this line:

Use -K 100000000 to achieve deterministic alignment results (Note: this is a hidden option)

Can you explain which randomness this hidden option eliminates? As far as I know, the alignments are deterministic given identical inputs, but batching or reordering of the reads would cause changes in output. Here is a description of the randomness: https://www.biostars.org/p/238628/#238817

[liuxf09]

bwa processes reads by chunks, while the default chunk size is threads * 10M bases. This chunk size may affect the bwa results: in bwa, it needs compute the insert size distribution per chunk after initial alignment, which is used in the later algorithm to choose the best alignment. Unless this chunk size is fixed using -K option, it may change with the number of threads, hence not deterministic result.