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Commits on Jul 17, 2019

• Add check for array size on LSF clusters

  skoren

  committed
  6db7ff8

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• Stop of quality issues but not on too many short reads

  skoren

  committed
  a446548

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• Fix uninitialized check for overflow QV

  skoren

  committed
  6e61f02

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Commits on Jul 15, 2019

• Minor fixes (that got lost in the merge) for removal of gapped consensus.

  brianwalenz

  committed
  88b5e4e

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• Merge in removal of coverage stat and gapped cosnensus.

  brianwalenz

  committed
  80d9095

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• Remove support for 'gapped' consensus sequence.

  brianwalenz

  committed
  92f8c95

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• Remove coverage stat support.

  brianwalenz

  committed
  48b24d3

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• Remove very old code that attempted to add mated reads to unitigs.

  brianwalenz

  committed
  eb1c67c

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• Merge from master.

  brianwalenz

  committed
  f64beda

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• Fix sync between alignment and overlap output.

  brianwalenz

  committed
  e758d6e

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• Add read length histograms to sqStoreDumpMetaData; support reporting metadata for only specific read types.

  brianwalenz

  committed
  730f95e

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• Allow stdin inputs (for summarize). Note that not every mode supports stdin.

  brianwalenz

  committed
  c8f2c4b

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• Handle 3-bit encoded sequence.

  brianwalenz

  committed
  d234021

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• Write output overlaps to a file (not a store); ensure alignment and overlap outputs are sync'd.

  brianwalenz

  committed
  27bda6e

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• Don't preallocate space for the cache.

  brianwalenz

  committed
  262edd9

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• Actually decode unencoded reads.

  brianwalenz

  committed
  5614e1d

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Commits on Jul 11, 2019

• Update parameter-reference.rst

  skoren

  authored
  a95437e

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• Update quick-start.rst

  skoren

  authored
  7cfe598

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• Add option to control when unassigned reads are included for trio binning, set default to 5%

  skoren

  committed
  b681534

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Commits on Jul 10, 2019

• Don't preallocate dataBlocks, don't allow more reads to be loaded after the initial batch, and load the correct subset when a subset load is requested.

  brianwalenz

  committed
  417d4d5

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Commits on Jul 8, 2019

• Fix error positioning the file when searching for EOL and the buffer is exhausted.

  brianwalenz

  committed
  94bfaac

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Commits on Jul 5, 2019

• Implement version 8 of seqStore. Working, but not complete and not well tested.

  brianwalenz

  committed
  40763d8

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• Add homopoly-compression support; add 2-bit ACGT and 3-bases-in-8-bit ACGTN encodings.

  brianwalenz

  committed
  3c35b83

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• Add support for IFF files; remove memory-mapped file support; fix error with seek() where the buffer would always be reloaded.

  brianwalenz

  committed
  9f10c4a

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• Add interface between stuffedBits abd readBuffer/writeBuffer.

  brianwalenz

  committed
  2b06be7

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• Add increaseArrayPair().

  brianwalenz

  committed
  2b836b4

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Commits on Jun 28, 2019

• Comment removal of fofn files since those are sentinels and removing them too early breaks ovlstore cleanup

  skoren

  committed
  b00a9c2

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• Add import of paf format, fix paf dump which was missing () for proper operation order, add identity to paf dump

  skoren

  committed
  360a37d

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Commits on Jun 27, 2019

• Don't return a value before the first valid data point.

  brianwalenz

  committed
  7733c8c

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• Output reverse oriented reads too.

  brianwalenz

  committed
  650fdc2

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• Correctly decide if 'simulate' mode has a genome supplied.

  brianwalenz

  committed
  f40aed4

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• Fix numerous problems detecting the state of precompute computation and overlap store construction when using object storage.

  brianwalenz

  committed
  3c80cef

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• Don't destroy our config object before we're done using it.

  brianwalenz

  committed
  672fa5d

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Commits on Jun 10, 2019

• Remove unused bits of C++11. Issue 1383.

  brianwalenz

  committed
  093a51f

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• Remove (ancient) utilities for working with Illumina reads.

  brianwalenz

  committed
  890f679

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