Update DALIGNER; bug-fixes

• Sync dazzler repos from upstream (thegenemyers).
  • This might change the merge tasks, impacting restarts. Not sure.
• Several bug-fixes and simplifications.
  • Warnings for old-style config.

Prefer `-` to `_` in flags

-foo-bar is more posixy than --foo_bar. But we continue to support the old style, with a warning.

New, simpler configuration for job-submission (via pypeflow)

• https://github.com/PacificBiosciences/FALCON/wiki/Configuration
  • The legacy configuration should still work, but you will see warnings.
• Also, a change to job-submission options should be reflected in each task upon restart.
  • We still need to make other options dynamic like that (the tricky part involves options that affect the number of parallel jobs), but at least you can change how jobs are submitted when you resume a workflow.

Minor fixes

Nothing noticeable.

Updates for sge option strings

• Fix for PacificBiosciences/FALCON_unzip#103
• Simplification in job distribution
  • For now, pwatcher=fs_based (the default) still works. (And you can use ${NPROC} in those string. And you can provide simply sge_option to cover all tasks. This matters mostly for Falcon_unzip.)
  • But pwatcher=blocking is much simpler.
  • This page will eventually be updated with details: https://github.com/PacificBiosciences/pypeFLOW/wiki/configuration

Backward-incompatible release

Lots of bug-fixes. Unfortunately, if you have a partial run, you will have to start-over to use this version of Falcon.

(And backwards-incompatible with 2.0.0, as far as restarting with directories from a previous partial run.)

Many improvements

• PacificBiosciences/DAZZ_DB@925dd76...f29d27d
• pb-cdunn/FALCON-examples@9026fd8...b3b0917
• PacificBiosciences/pypeFLOW@f928267...f23a1b2
• PacificBiosciences/DALIGNER@7c09c81...0fe5240
• PacificBiosciences/FALCON@080378c...86cec61

Remove assertion on las_fn

• Updates to submodules.
  • FALCON: Drop assertion; no longer needed, and sometimes problematic.
  • Other minor changes.
• Expect user to run git submodule update --init theirself.

Tested with FALCON_unzip 0.4.0

• Fix job-concurrency setting
• If skip_checks = true, actually skip any bad .las files and continue.
  • This can skip important data, but at least you can complete your run.
  • Probably, it is better to set use_tmpdir = /tmp, since file-system latency is the likely cause of bad .las files.
• Drop FALCON_unzip from this integration package.

More bug-fixes

• PacificBiosciences/FALCON_unzip@c936cb9...38de578
• PacificBiosciences/FALCON@87b6262...b052cae
• PacificBiosciences/pypeFLOW@bdd41db...5cfa45b
• pb-cdunn/FALCON-make@02ed9de...ac46547