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Commits on Mar 12, 2019

• Report the number of reads filtered (too short) by splitHaplotype. Issue marbl#1276.

  brianwalenz

  committed
  6337e00

Commits on Oct 26, 2018

• Add kmerIterator(), update splitHaplotypes and meryl to use it to generate kmers.

  brianwalenz

  committed
  9944342

Commits on Oct 22, 2018

• Update copyright info.

  brianwalenz

  committed
  fcc3fe1

Commits on Oct 19, 2018

• Add a comment about loading sequences.

  brianwalenz

  committed
  77c964d

Commits on Oct 18, 2018

• Fix error in computing thresholds at small frequencies; remove dead code from unused high-end threshold.

  brianwalenz

  committed
  752d129

• Accept a haplotype noise threshold directly on the command line, or compute it from the reads histogram.

  brianwalenz

  committed
  54db050

Commits on Oct 17, 2018

• Write a log (to stdout) of the number of reads/bases assigned to each haplotype.

  brianwalenz

  committed
  622b673

Commits on Oct 5, 2018

• Make haplotyping (mostly) work in cloud mode. It still requires input files to be on a network disk.

  brianwalenz

  committed
  8cb8c1a

Commits on Sep 27, 2018

• Fix race conditions when counting the number of kmers loaded; reduce memory needed to construct lookup table; fix reporting of said memory; generally disable logging.

  brianwalenz

  committed
  fbd9082

• Cleanup logging.

  brianwalenz

  committed
  edf1e5a

• Use a 5-frequency window average (down from 9), and handle the start correctly, when computing the min/max frequencies to use.

  brianwalenz

  committed
  e084d3a

• Allow wildcard in -R: '-R *fasta'.

  brianwalenz

  committed
  5e08ded

• Fix bad indenting.

  brianwalenz

  committed
  810a7e5

Commits on Sep 17, 2018

• Add support for trio-binning to canu.

  brianwalenz

  committed
  75bc966

Commits on Jul 21, 2018

• Fold reverse-complementing into 'sequence' library.

  brianwalenz

  committed
  1674b22

• Collect all string processing classes/functions into strings.H.

  brianwalenz

  committed
  8076733

Commits on Jul 20, 2018

• Make utility/files.H and utility/strings.H.

  brianwalenz

  committed
  ce12198

• Rename 'AS_UTL/' to 'utility/'.

  brianwalenz

  committed
  fb95293

Commits on Apr 18, 2018

• Rename gatekeeper/gkpStore to sequence store/seqStore. Existing assemblies should be upgradable by just renaming *.gkpStore to *.seqStore.

  brianwalenz

  committed
  01d1823

Commits on Apr 2, 2018

• Slightly change interface to getting read length; needed to support 'ignore' in next commit.

  brianwalenz

  committed
  0289dc3

• printf() formats.

  brianwalenz

  committed
  b39d5dc

Commits on Feb 27, 2018

• Update copyright info.

  brianwalenz

  committed
  0fff8a5

Commits on Feb 8, 2018

• Merge in trioCanu.

  brianwalenz

  committed
  91f5a49

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