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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

• Fix minor logging inconsistencies.

  brianwalenz

  committed
  ed5a947

Commits on Nov 10, 2018

• Make gcc48 happy by declaring swv::operator<() const. Issue marbl#1148.

  brianwalenz

  committed
  a50e26a

Commits on Nov 9, 2018

• Fix failure when no alignment can be found, presumably because of N's in the read(s). Issue marbl#1142.

  brianwalenz

  committed
  ceda4d6

• For tigs loaded via import, write the layout and read sequences to <input>.layout and <input>.fasta.

  brianwalenz

  committed
  71c8011

Commits on Nov 7, 2018

• Remove unused and terrible 'logo'.

  brianwalenz

  committed
  e364f14

• Add a reasonably useless test of file reading and writing.

  brianwalenz

  committed
  618f916

• Add an option to dump the Fibonacci numbers.

  brianwalenz

  committed
  a71902b

• Remove now extremely out-of-date documentation on running commands in canu.

  brianwalenz

  committed
  55913c5

• Remove now extremely out-of-date documentation on correcting reads.

  brianwalenz

  committed
  cf61a50

• Remove a hack to make alignGFA work both on and off grid when under PBS control.

  brianwalenz

  committed
  11368b2

• Add -haplotype option to usage output.

  brianwalenz

  committed
  e9acc9d

• Add option -haplotype to stop after haplotype-specific reads are generated, and before assemblies are started. Issue marbl#1140.

  brianwalenz

  committed
  3eecfcd

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