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Commits on Jul 10, 2018

• Merge pull request marbl#992 from godotgildor/master

  Show description for 7e6d8f8
  brianwalenz

  authored
  7e6d8f8

• Initialize the number of overlaps per file to zero. Argh. Issue marbl#959.

  brianwalenz

  committed
  51947ae

• Fix indenting and call it 'minimap', not 'mmap', in messages.

  brianwalenz

  committed
  958060a

• Don't declare the precompute done if the fasta exists, declare it done if the mmi exists. Issue marbl#990.

  brianwalenz

  committed
  3e44731

• Remove a tiny bit of dead code when dumping fasta for precompute.

  brianwalenz

  committed
  054a3b9

• Check for existence of minimap2 in bin directory before starting the assembly. Issue marbl#990.

  brianwalenz

  committed
  abb716c

• Add conditional compilation symbol IGNORE_FLIPPED_OVERLAPS.

  brianwalenz

  committed
  07c0b04

Commits on Jun 25, 2018

• Convert kmers-to-ignore to lowercase so they can be found in the hash table.

  brianwalenz

  committed
  683fa2f

Commits on Jun 21, 2018

• Fix integer overflow when counting the number of overlaps in a single file. CHANGES FILE FORMAT of .oc files. Issue marbl#959.

  brianwalenz

  committed
  6b0d22a

• Fix errors configuring large overlap files, and/or reads with lots of overlaps. Issue marbl#959.

  brianwalenz

  committed
  f2e2efc

Commits on Jun 19, 2018

• Refuse to allow relative paths for java and gnuplot. Issue marbl#962.

  brianwalenz

  committed
  49267eb

• Use the string equality test for comparing strings in makeAbsolute().

  brianwalenz

  committed
  6867945

• Check for a too-small memory limit. Fix minor typo in logging.

  brianwalenz

  committed
  33e9fe5

• Add (an overly) verbose mode for (maybe) helping to debug why bucketizer is failing. Issue marbl#959.

  brianwalenz

  committed
  3a2e695

• Force rerunning of ovStoreBucketizer even if the create#### directory exists. Issue marbl#959.

  brianwalenz

  committed
  d6cf139

• Correctly count the number of jobs to run when deciding if grid jobs should run here and now.

  brianwalenz

  committed
  fa6d0bb

• When creating frequentMers.ignore, accept either FASTA or single-line kmer data.

  brianwalenz

  committed
  18449c5

• Make AS_UTL_closeFile() NULL the file handle.

  brianwalenz

  committed
  61757b5

• Add AS_UTL_createEmptyFile().

  brianwalenz

  committed
  f1fd9e2

Commits on Jun 15, 2018

• Disable a block of unused code that fails to compile with gcc8. Issue marbl#927.

  brianwalenz

  committed
  f251336

Commits on Jun 13, 2018

• Pass the correct args to setWorkDirectory().

  brianwalenz

  committed
  be1d566

Commits on Jun 11, 2018

• Write the load.dat summary BEFORE closing the file. Issue marbl#885.

  brianwalenz

  committed
  9b49a02

Commits on Jun 8, 2018

• Update command line usage.

  brianwalenz

  committed
  cb1c899

• Remove unused CA8 compatibility format.

  brianwalenz

  committed
  d9a0856

• Make overlapImport import the formats that ovStoreDump dumps.

  brianwalenz

  committed
  724f08c

• Read 'skip' kmers from either fasta or single line formatted files.

  brianwalenz

  committed
  1273e9b

• Explicitly declare the 'environ' global.

  brianwalenz

  committed
  7586311

Commits on May 23, 2018

• Add skipLine(). Not used in Canu.

  brianwalenz

  committed
  2ff48f3

Commits on May 22, 2018

• Add some text about restarting. Issue marbl#921.

  brianwalenz

  committed
  2499979

Commits on May 16, 2018

• Remove semicolon from shell echo string.

  brianwalenz

  committed
  81ba837

• Add command line usage, fix and/or implement the broken and/or missing dump options.

  brianwalenz

  committed
  aad86c6

• When dumping metadata, do so inclusively.

  brianwalenz

  committed
  d0bb3cf

• Rearrange shell code to not emit stuff when not in cloud mode.

  brianwalenz

  committed
  639df79

• Don't delete the overlap store if saveOverlaps is set!

  brianwalenz

  committed
  6de2967

• Actually process inclusively, as the usage text says we do.

  brianwalenz

  committed
  bb7e178

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