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Commits on Sep 9, 2016

• Add mtRandomExponential().

  brianwalenz

  committed
  3b526ea

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• Don't use the maximum number of processes when configuring, and report failures better. Issue marbl#250.

  brianwalenz

  committed
  7cbe266

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Commits on Sep 6, 2016

• Fix dump from gatekeeper

  skoren

  committed
  4f6f0fd

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Commits on Sep 2, 2016

• Don't gzip compress snappy compressed ovb files.

  brianwalenz

  committed
  71dcf22

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• Don't let PBS/Torque or PBSPro split array jobs into multiple submissions. Issue marbl#246.

  brianwalenz

  committed
  e7e78b4

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• Use PBS_ARRAY_INDEX to get the job number, not PBS_ARRAY_ID. Issue marbl#246.

  brianwalenz

  committed
  be3b612

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• Don't wipe out the name for single-element arrays. Issue marbl#246.

  brianwalenz

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Commits on Sep 1, 2016

• Fix issues with older gnuplot versions.

  brianwalenz

  committed
  ee7b32a

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• Add gridEngine=PBSPro. Issues marbl#166 and marbl#246.

  brianwalenz

  committed
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Commits on Aug 31, 2016

• Actually _use_ the new gnuplot configuration. Issue marbl#218.

  brianwalenz

  committed
  a2951ae

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• Add configuration options for gnuplot, and auto-detect which image format to use. Report errors too. Issue marbl#218.

  brianwalenz

  committed
  a7771c8

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• Enable snappy compression of raw overlaps. Add conversion from uncompressed to compressed format.

  brianwalenz

  committed
  3208c21

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• Remove extraneous logging.

  brianwalenz

  committed
  791d41d

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Commits on Aug 30, 2016

• Add snappy 1.1.3, and support for it in ovFile (but disabled).

  brianwalenz

  committed
  24c976d

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• Realphabetize. Kind of.

  brianwalenz

  committed
  2aa24a3

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• printf() formatting.

  brianwalenz

  committed
  dc739ff

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• Add function to return type of compressed file, use it.

  brianwalenz

  committed
  f1eedb1

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• Don't write small buffers, unless the last one.

  brianwalenz

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  5fbdf74

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• Whitespace.

  brianwalenz

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  7dbb287

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• Move buffer reading/writing to helper functions.

  brianwalenz

  committed
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• If the end reads are not placed, don't place the orphan or bubble.

  brianwalenz

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  525f903

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• Report number of uniq and rept bubbles.

  brianwalenz

  committed
  730fda6

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• Cleanup; use nReads instead of bubble->ufpath.size().

  brianwalenz

  committed
  f7f9176

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• Change coordinate format in logs.

  brianwalenz

  committed
  9110aca

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• Remove stray include of sys/types.h.

  brianwalenz

  committed
  dd08542

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• Copy correction and trimming figures to the correct directory.

  brianwalenz

  committed
  668e385

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• Clean up command line error handling.

  brianwalenz

  committed
  24ea005

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• Update library dependencies

  skoren

  committed
  2814ec7

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• Try again, this time with the files not symlinks

  skoren

  committed
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• Add experimental support using edlib (https://github.com/Martinsos/edlib) to compute alignments after MHAP overlapping. Clean up alignment driver code. Only tested on bacteria.

  skoren

  committed
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Commits on Aug 26, 2016

• Check for implausible genome size, and fail if so.

  brianwalenz

  committed
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Commits on Aug 25, 2016

• Improve filtering to discard more edges, and to improve logging.

  brianwalenz

  committed
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• Don't add 'isContig' labels, only remove them, when rebuilding.

  brianwalenz

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• Enable a bit more logging, ifdef'd turned on.

  brianwalenz

  committed
  d384085

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• Don't find edges off the spur end of a partially aligned read.

  brianwalenz

  committed
  dbd7e5d

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