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brianwalenz

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Commits on Jul 28, 2019

• Remove overly aggressive (read: wrong) assert.

  brianwalenz

  committed
  1c71780

Commits on Jul 27, 2019

• Fix more flaws in optimizePositions(). Issue marbl#1414.

  brianwalenz

  committed
  6f8bafc

Commits on Jul 24, 2019

• Only reset the iteration count if unitigger.sh doesn't exist.

  brianwalenz

  committed
  cd10b3b

• Move code for running unitigger to functions.

  brianwalenz

  committed
  31a04ca

• Add 'true' and 'false' aliases in purgeOverlaps.

  brianwalenz

  committed
  3259e28

• Unlink output files before opening them; seems to resolve weird error when two overlap jobs write to same output.

  brianwalenz

  committed
  be81b1a

• Disable logging when seeking to a specific overlap.

  brianwalenz

  committed
  6521c02

Commits on Jul 19, 2019

• Don't check job_is_first_task, and allow qconf to fail.

  brianwalenz

  committed
  56d8be4

• Explicitly check if there are overlaps to output before writing any output.

  brianwalenz

  committed
  48555da

Commits on Jul 15, 2019

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

  brianwalenz

  committed
  88b5e4e

• Merge in removal of coverage stat and gapped cosnensus.

  brianwalenz

  committed
  80d9095

• Remove support for 'gapped' consensus sequence.

  brianwalenz

  committed
  92f8c95

• Remove coverage stat support.

  brianwalenz

  committed
  48b24d3

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

  brianwalenz

  committed
  eb1c67c

• Merge from master.

  brianwalenz

  committed
  f64beda

• Fix sync between alignment and overlap output.

  brianwalenz

  committed
  e758d6e

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

  brianwalenz

  committed
  730f95e

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

  brianwalenz

  committed
  c8f2c4b

• Handle 3-bit encoded sequence.

  brianwalenz

  committed
  d234021

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

  brianwalenz

  committed
  27bda6e

• Don't preallocate space for the cache.

  brianwalenz

  committed
  262edd9

• Actually decode unencoded reads.

  brianwalenz

  committed
  5614e1d

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

Commits on Jul 8, 2019

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

  brianwalenz

  committed
  94bfaac

Commits on Jul 5, 2019

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

  brianwalenz

  committed
  40763d8

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

  brianwalenz

  committed
  3c35b83

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

  brianwalenz

  committed
  9f10c4a

• Add interface between stuffedBits abd readBuffer/writeBuffer.

  brianwalenz

  committed
  2b06be7

• Add increaseArrayPair().

  brianwalenz

  committed
  2b836b4

Commits on Jun 27, 2019

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

  brianwalenz

  committed
  7733c8c

• Output reverse oriented reads too.

  brianwalenz

  committed
  650fdc2

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

  brianwalenz

  committed
  f40aed4

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

  brianwalenz

  committed
  3c80cef

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

  brianwalenz

  committed
  672fa5d

Commits on Jun 10, 2019

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

  brianwalenz

  committed
  093a51f

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