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Commits on Jan 31, 2019

• Remove old meryl file to allow for merge with new version of canu

  AnastasiaMiles

  committed
  19f6802

Commits on Jan 29, 2019

• Add stddevTest to BUILDTESTS.

  brianwalenz

  committed
  6509201

• Fix, maybe, crash in ovlStoreStats. Issue marbl#1223.

  brianwalenz

  committed
  b78b376

Commits on Jan 24, 2019

• Don't save raw mhap output when saveOverlaps=stores.

  brianwalenz

  committed
  23dbfe4

• Be thread safe when printing kmers.

  brianwalenz

  committed
  4fb5e5f

• Merge pull request marbl#1219 from godotgildor/master

  Show description for b071055
  brianwalenz

  authored
  b071055

Commits on Jan 19, 2019

• Merge pull request marbl#4 from godotgildor/dx_retry_upload_ua

  Show description for edc513a
  godotgildor

  authored
  edc513a

• Patching retry upload code

  Show description for 34521d9
  

  Brett T. Hannigan

  committed
  34521d9

Commits on Jan 17, 2019

• Comments on secret options. Shhh!

  brianwalenz

  committed
  9e6834c

• Store read-to-tig alignments in tgStore, fix (but not fully) multialignment output.

  brianwalenz

  committed
  a6871e4

• Set the recomputed min/max positions in the tgTig output, too.

  brianwalenz

  committed
  dc94228

• Fix memory leak: not releasing read bases/quals.

  brianwalenz

  committed
  634b051

• Add an untested copy constructor for stuffedBits.

  brianwalenz

  committed
  598ff79

Commits on Jan 11, 2019

• Add gridEngineResourceOption; replaces gridEngineMemoryOption and gridEngineThreadsOption.

  brianwalenz

  committed
  27ebc98

Commits on Jan 10, 2019

• Allow matches to N (and n) ambiguity bases. Based on Martinsos/edlib@92f6a3f.

  brianwalenz

  committed
  3a3c336

Commits on Jan 9, 2019

• Add limited support for mutating sequences.

  brianwalenz

  committed
  dfacdcb

Commits on Jan 3, 2019

• Update copyright block (and remove a stray whitespace).

  brianwalenz

  committed
  93e66aa

• Split sequence.C into multiple files.

  brianwalenz

  committed
  75d46fc

• Update derived-from text in copyright blurb.

  brianwalenz

  committed
  b838597

• Remove stray whitespace.

  brianwalenz

  committed
  bfd6a09

• Remember all of the files each file is derived from.

  brianwalenz

  committed
  ce2163b

• Keep track of the shift in read position to compute better initial placements during realignment.

  brianwalenz

  committed
  5fcc24b

Commits on Jan 2, 2019

• Trim Ns from the ends of reads.

  brianwalenz

  committed
  7287e8d

• Add 'support' for RNA sequence from FASTQ files. Issue marbl#776.

  brianwalenz

  committed
  4a41db9

• Unset the grid task ID environment variable if it is set so our jobs don't get confused when running outside grid control. Issue marbl#1199.

  brianwalenz

  committed
  84576e1

Commits on Dec 21, 2018

• Link to papers for minimum coverage needed, add motivation to not use Illumina for correction. Issue marbl#1187.

  brianwalenz

  committed
  ec32609

• Allow single-task jobs to run even if the machine allows exactly one copy to run. Issue marbl#1186.

  brianwalenz

  committed
  27d47bc

Commits on Dec 20, 2018

• When converting a counting operation to a pass-thru operation, open the input in thread-aware mode.

  brianwalenz

  committed
  7cb336e

• Just some comments.

  brianwalenz

  committed
  c82d844

• Fix return type of functions that don't return values.

  brianwalenz

  committed
  c979289

• Minor changes to debug logging.

  brianwalenz

  committed
  c7d30cb

Commits on Dec 19, 2018

• Parse brackets before saving copies of the filename.

  brianwalenz

  committed
  a5773f9

Commits on Dec 17, 2018

• Add summarize option -split-n to break sequences at N's, then generate statistics.

  brianwalenz

  committed
  d1dba71

• Add option -norealign to turn off read realignment. Issue marbl#1159.

  brianwalenz

  committed
  f6b8d4e

• Update command line error handling to use vector<char*>. Add -VVVV support.

  brianwalenz

  committed
  598f8b5

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