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Commits on Sep 8, 2017

• Rearrange methods.

  brianwalenz

  committed
  f8f55b0

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• Engineering; move global score computation outside main function.

  brianwalenz

  committed
  8e2acad

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• Use ovl.correctionScore(), NOT the legacy score (incorrectly added when falcon_sense merged).

  brianwalenz

  committed
  6bdfc82

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• Add a_len(), b_len() and correctionScore().

  brianwalenz

  committed
  1d5b188

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• Fix parameter links. Update contigFilter text.

  brianwalenz

  committed
  bc1ca42

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Commits on Sep 1, 2017

• Parse # bases as long not int

  skoren

  committed
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Commits on Aug 24, 2017

• Use correct path to asm.readsToCorrect when estimating memory requirement.

  brianwalenz

  committed
  e234bb3

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• Set corMemory based on generateCorrectionLayouts estimate.

  brianwalenz

  committed
  b2e67e1

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• Add simple estimate of memory needed for read consenuss.

  brianwalenz

  committed
  b01e557

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• Slightly optimize memory, cleanup code a bit.

  brianwalenz

  committed
  e5fce2e

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• Use single-process read correction; corConsensus=falcon replaces 'falconpipe'.

  brianwalenz

  committed
  32ef2c8

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• Remove reference to obsolete 'unitigger' unitigging algorithm.

  brianwalenz

  committed
  86d4a1b

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• Reuse consensus data structure for all reads processed.

  brianwalenz

  committed
  43a6c2d

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• Use expected position when aligning evidence to template.

  brianwalenz

  committed
  58d4242

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• Swap number of tigs and number of reads in log message.

  brianwalenz

  committed
  246f889

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• Use new falconConsensus to output corrected reads directly.

  brianwalenz

  committed
  4d84589

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• Include fasta.H, not fasta.C.

  brianwalenz

  committed
  b1bb636

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• Add refactored falcon consensus.

  brianwalenz

  committed
  e2044db

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Commits on Aug 18, 2017

• Fix parameters for early Nanopore data.

  brianwalenz

  committed
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Commits on Aug 14, 2017

• Bump version to 1.6.

  brianwalenz

  committed
  78d0188

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• Update for the last copyright update.

  brianwalenz

  committed
  54b4bec

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• Update copyright info.

  brianwalenz

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  9e9bd67

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• Remove whitespace on blank line.

  brianwalenz

  committed
  b2c2c91

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• Remove whitespace at end of lines.

  brianwalenz

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  ddf4768

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• Remove whitespace on blank line.

  brianwalenz

  committed
  8578316

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• Remove whitespace on blank line.

  brianwalenz

  committed
  229187a

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• Remove whitespace on blank line.

  brianwalenz

  committed
  4b75dde

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• Remove whitespace at end of lines.

  brianwalenz

  committed
  aed7b50

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Commits on Aug 11, 2017

• Fix paths to remove .cns files and ctgcns/utgcns directories.

  brianwalenz

  committed
  8f83b2f

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• Disable logging of subreads, very big and not useful.

  brianwalenz

  committed
  1710d6d

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Commits on Aug 10, 2017

• Switch to pre-allocated array instead of vector, and use inplace sort, to prevent memory spikes during errorProfile computation.

  brianwalenz

  committed
  3392d75

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• Reserve 25% of memory for computing.

  brianwalenz

  committed
  d80d001

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• Add reportErrorProfiles() for repeats.

  brianwalenz

  committed
  b2ef408

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• Add functions to return wall and cpu time.

  brianwalenz

  committed
  1ab6f3c

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Commits on Aug 9, 2017

• Suggest random sampling for plasmids. Issue marbl#583.

  brianwalenz

  committed
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