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Commits on Jan 2, 2019

• Add 'support' for RNA sequence from FASTQ files. Issue marbl#776.

  brianwalenz

  committed
  4a41db9

• Unset the grid task ID environment variable if it is set so our jobs don't get confused when running outside grid control. Issue marbl#1199.

  brianwalenz

  committed
  84576e1

Commits on Dec 21, 2018

• Link to papers for minimum coverage needed, add motivation to not use Illumina for correction. Issue marbl#1187.

  brianwalenz

  committed
  ec32609

• Allow single-task jobs to run even if the machine allows exactly one copy to run. Issue marbl#1186.

  brianwalenz

  committed
  27d47bc

Commits on Dec 20, 2018

• When converting a counting operation to a pass-thru operation, open the input in thread-aware mode.

  brianwalenz

  committed
  7cb336e

• Just some comments.

  brianwalenz

  committed
  c82d844

• Fix return type of functions that don't return values.

  brianwalenz

  committed
  c979289

• Minor changes to debug logging.

  brianwalenz

  committed
  c7d30cb

Commits on Dec 19, 2018

• Parse brackets before saving copies of the filename.

  brianwalenz

  committed
  a5773f9

Commits on Dec 17, 2018

• Add summarize option -split-n to break sequences at N's, then generate statistics.

  brianwalenz

  committed
  d1dba71

• Add option -norealign to turn off read realignment. Issue marbl#1159.

  brianwalenz

  committed
  f6b8d4e

• Update command line error handling to use vector<char*>. Add -VVVV support.

  brianwalenz

  committed
  598f8b5

Commits on Dec 16, 2018

• fix spacing

  skoren

  authored
  56e6099

• Update faq.rst

  skoren

  authored
  2acc905

Commits on Dec 13, 2018

• Add option -1x to force the NG table to always show N000 through N100 regardless of amount of sequence.

  brianwalenz

  committed
  5633efe

Commits on Dec 11, 2018

• Add a compile time option to restrict file names to the Portable Filename Character Set. Issue marbl#1153.

  brianwalenz

  committed
  4b17478

• Cleanup install directions, point to a docer image, discourage use of package managers. Issue marbl#1177.

  brianwalenz

  authored
  49f2f5d

• For jobs configured when they're run, don't prematurely set the concurrency level. Issue marbl#1165.

  brianwalenz

  committed
  bb29f1e

• Check for the output of meryl-configure, not just the shell script, to decide if this needs to run. And don't delete the error output when an error occurs. Issue marbl#1172.

  brianwalenz

  committed
  3a2ecb2

• Use an overlap for recomputing positions if the current placement is within 10% of the expected placement. Issues marbl#1159 and marbl#1168.

  brianwalenz

  committed
  07f59cc

• Check for missing parameters at the end of the command line.

  brianwalenz

  committed
  7478406

Commits on Dec 7, 2018

• Don't allow spaces or slashes in the prefix. Issue marbl#1178.

  brianwalenz

  committed
  c13e82e

Commits on Dec 4, 2018

• Align reads back to consensus to find their true location.

  brianwalenz

  committed
  7db5967

• Update command line usage for -quick: no BAM output.

  brianwalenz

  committed
  a587f70

• Use integers for the amount of memory on each node. Issue marbl#1166.

  brianwalenz

  committed
  da59408

• Fix error configuring jobs with one task. Issue marbl#1166.

  brianwalenz

  committed
  76e87b2

• Trivial bit of code rearrangement for clarity.

  brianwalenz

  committed
  56008b5

Commits on Dec 3, 2018

• Fix reporting of invalid command line parameters.

  brianwalenz

  committed
  e942f4f

• Just some comments on Golomb coding.

  brianwalenz

  committed
  580b3d9

• Use gcc6 by default on FreeBSD.

  brianwalenz

  committed
  905be2d

Commits on Nov 16, 2018

• Rearrange, cleanup a bit.

  brianwalenz

  committed
  5449222

Commits on Nov 15, 2018

• Move unitigConsensus.C out of the libcns/ directory.

  brianwalenz

  committed
  3b80cda

• Remove original 'abacus' consensus algorithm.

  brianwalenz

  committed
  efc928c

• Fix log reporting which read bases are used when the read fails to align to the template.

  brianwalenz

  committed
  9312614

• Remove, finally, the ancient kmer utility libraries.

  brianwalenz

  committed
  f32d0fe

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