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Commits on Apr 13, 2017

• add info that compute nodes must be submit nodes

  skoren

  authored
  723df7c

• Update conf.py

  skoren

  authored
  07e15ea

• Update quick-start.rst

  skoren

  authored
  1cb9106

• Unoffset all adjusted error values by one.

  brianwalenz

  committed
  4f7d819

Commits on Apr 12, 2017

• Actually configure GFA alignment resources.

  brianwalenz

  committed
  4fda1cf

Commits on Apr 11, 2017

• Run './alignGFA.sh' for small jobs, not just 'alignGFA.sh'.

  brianwalenz

  committed
  c54b7af

• Don't recreate scripts - and thus reset iteration count - if they exist.

  brianwalenz

  committed
  15d868c

• Another attempt at fixing non-git-based version numbers.

  brianwalenz

  committed
  3d7b71a

Commits on Apr 7, 2017

• Fallback to maxMemory and maxThreads if qhost returns nothing. Issue marbl#392.

  brianwalenz

  committed
  ae428fc

• Note minimum ovsMemory size.

  brianwalenz

  committed
  d98b66f

• Describe memory values.

  brianwalenz

  committed
  fbf01a6

• Note that -pacbio-corrected et al. do not do correction. Note that -d is not required.

  brianwalenz

  committed
  b0f1430

• Note that boolean values are true/false/1/0.

  brianwalenz

  committed
  808ff17

• Add some text about grid engine support.

  brianwalenz

  committed
  71992df

• Add GFA link alignment to the pipeline.

  brianwalenz

  committed
  b276a79

• Remove gkpStore requirement. Check command line for errors. Improve status output.

  brianwalenz

  committed
  9987f87

Commits on Apr 6, 2017

• Simplify ovStoreBuild -evalues processing; remove memory mapped file.

  brianwalenz

  committed
  10e6510

Commits on Apr 5, 2017

• Add directions to FTP us stuff.

  brianwalenz

  committed
  82bf1d3

• Fix more printf() format warnings.

  brianwalenz

  committed
  77e7c63

• Fix a handful of problems resulting in crashes on (suspected) non-repetitive data. Issues marbl#408 and marbl#413.

  brianwalenz

  committed
  9253adb

Commits on Apr 4, 2017

• Reset GFA sequence length based on consensus length.

  brianwalenz

  committed
  63e2ea3

• Add better GFA support, better alignments, and multithread.

  brianwalenz

  committed
  9a4d0ae

• Move alignGFA from utgcns/ to gfa/.

  brianwalenz

  committed
  2a1fd99

• Add AS_UTL_readLine().

  brianwalenz

  committed
  1e3dcde

Commits on Apr 3, 2017

• Set a default bucket size for the read length histogram. Issue marbl#436.

  brianwalenz

  committed
  0efa80e

Commits on Mar 30, 2017

• Don't append ../ to 'trimmedReads' that aren't made by canu. Issue marbl#434.

  brianwalenz

  committed
  fb75616

• Update errorRate to correctedErrorRate. Issue marbl#430.

  brianwalenz

  committed
  540dd7c

• Fix undefined usage of snprintf. Issue marbl#432.

  brianwalenz

  committed
  b94bfdc

Commits on Mar 29, 2017

• Iterate over consensusConfigure() and consensusCheck() so non-grid runs rewrite the script on the second iteration.

  brianwalenz

  committed
  f4ef049

• Use relative paths for partitioned gkpStore links back to the original store.

  brianwalenz

  committed
  b44580e

• Add missing minReadLength and minOverlapLength. Issue marbl#410.

  brianwalenz

  committed
  f709be2

• Set default major.minor version, report snapshot or release when compiling.

  brianwalenz

  committed
  8c6e9a9

• Compute alignments for GFA edges and populate the CIGAR string. Issue marbl#428.

  brianwalenz

  committed
  49439a6

• Swap order of sequences in GFA links. Issue marbl#416.

  brianwalenz

  committed
  73fd8a1

Commits on Mar 28, 2017

• Update faq.rst

  skoren

  authored
  74942c1

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