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Commits on Feb 24, 2020

• Default max coverage to 50x for hifi datasets

  skoren

  committed
  7c9e9f9

Commits on Feb 14, 2020

• Disallow hifi combinations

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  c6563e6

Commits on Feb 12, 2020

• Disable trimming for hifi data, not needed w/new bogart updates and recent libraries

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  19d80b2

• Pass covgap and lopsided options to bogart

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  f1ae005

Commits on Feb 7, 2020

• Fix position estimates to avoid flipping/shrinking reads to less than 0

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  2804339

Commits on Jan 22, 2020

• Fix settings when mixing pacbio and nanopore data, removed now obsolete data checks in correctreads.pm

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  c25ec85

Commits on Jan 16, 2020

• Fix memory rounding on LSF

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  0ab4228

Commits on Jan 7, 2020

• Parameter updates for hifi

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  ec93693

• Fix read staging

  skoren

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  2520b74

Commits on Dec 27, 2019

• Move layout conversion to uncompressed space to a function, clean it up, and use compressed/uncompressed translation to compute positions within reads

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  5b94050

• Update to always dump trimmed uncompressed reads

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  3ae7c5f

• Fix trim conversion error on 5' end

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  94397cb

Commits on Dec 26, 2019

• Update parameters for hifi data

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  3460ffd

• Narrower band for alignments, with previous commit the large band isn't needed

  skoren

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  998b964

• Update consensus read positions when we move from compresed to uncompressed reads

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  e341aae

• Add quantile error rate when median fails

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  36e4876

Commits on Dec 20, 2019

• Fix support for old options (-pacbio-raw and the like) in trios and flush output on error

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  55bb984

• Clean up logging a bit more

  skoren

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  8e72f9a

• Use runtime determined bin path, not hardcoded one at shell script output time

  Show description for 4142326
  skoren

  committed
  4142326

• Fix overzealous removal of parameters from last commit, some of those are still used

  skoren

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  9803c42

Commits on Dec 19, 2019

• Removed unused cnsPartitioning parameters, update partitioning for consensus to limit reads per partition too

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  b667053

Commits on Dec 12, 2019

• Add -layout-verbose and disable the full layout dump by default which was big and almost never used

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  bf94b57

• Report bubbles in the report too

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  37addcf

Commits on Nov 27, 2019

• Update store version for error rate bit change

  skoren

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  afcfa3e

• Remove unused high-precision mode and increase bits used always

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  a8709d6

Commits on Nov 20, 2019

• Allow negative positions while optimizing, they get adjusted to start at 0 at the end, update prints to use signed values

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  3a35672

Commits on Nov 19, 2019

• Update to python3

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  ed32e61

• Fix to avoid updating a read in the middle of a set of changes

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  126b9c8

• Add more logging to optimize positions, including expand/contract

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  3689546

• Properly check if contig sequence exists

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  792e5fb

Commits on Nov 15, 2019

• Some fixes to previous commit, don't stop when we hit the end of A since we'd never relax the error rate criteria that way. Increase tolerance for erate and length as well.

  skoren

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  d35232d

• Clean up bed alignment, use only the contigs size change for the ratio, and ensure we try all attempts to expand region until we run out of sequence

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  ca4243f

Commits on Nov 14, 2019

• Use ratio when computing the unitig positions within contigs too

  skoren

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  39afb6d

• Try trimming sequence when aligning to see if we can find a shorter match, use updated length for error rate tolerance

  skoren

  committed
  43ddb77

• Pass error rate to gfa alignment rather than hard-coding, use ratio of original to post-consensus length to adjust alignment positions

  skoren

  committed
  26ed56f

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