Draft: Fix memory problem with alt hla

[vinjana]

Looks like a lot, but most changes are only refactorings (mostly groovification, layout, and some other small things).

• minor: Added bwaPostAltJsK8Options to allow setting opt K8 options for bwa-postalt.js
• minor: Added SAMPESORT_MEMSIZE to allow reducing memory for SAM sorting. Default: ~2 GiB.
• minor: Upgrade from COWorkflows 1.2.76 to COWorkflowsBasePlugin 1.4.2.
  • minor: Old FLAG_USE_EXISTING_PAIRED_BAMS was renamed to FLAG_USE_ONLY_EXISTING_PAIRED_BAMS
  • minor: Removed FLAG_RUN_SLIM_WORKFLOW. Corresponding code is unused for years.
• patch: Little refactorings and groovification of old Java code

[vinjana]

Sorry, the COWorkflowsBasePlugin 1.4.2 bump has to be rolled back. I somehow get compilation problems now, and have no clue why, because the original changes are actually really old.

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