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Commits on May 17, 2017

• Fix segfault on reads > 4mb (issue marbl#494), reads >2mb still have limited testing

  skoren

  committed
  f05c815

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• Print citations for software used.

  brianwalenz

  committed
  90e69a6

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Commits on May 16, 2017

• Cleanup error reporting. Issue marbl#495.

  brianwalenz

  committed
  cc950a1

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• Report which algorithm is being run concurrently. Issue marbl#456.

  brianwalenz

  committed
  2ff6652

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• Improve logging of resources to be used. Issue marbl#456.

  brianwalenz

  committed
  de961e5

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Commits on May 15, 2017

• Improve logging, fix problems aligning reads that are entirely simple repeats. Issue marbl#496.

  brianwalenz

  committed
  96ed11f

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Commits on May 12, 2017

• Add BED processing.

  brianwalenz

  committed
  32c8fc8

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• Add threading for BED -> GFA conversion.

  brianwalenz

  committed
  1dff905

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• Big change to process bed, and to convert bed to gfa.

  brianwalenz

  committed
  ca4e385

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• Let gfaSequences and gfaLinks be created from scratch.

  brianwalenz

  committed
  5eaa821

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• Allow sequences to be named tig, utg or ctg.

  brianwalenz

  committed
  37d8a21

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• Add simple .bed reading/writing class.

  brianwalenz

  committed
  36638f6

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• Output a .bed of unitig positions in contigs.

  brianwalenz

  committed
  d7153cc

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• Fix error in tracking source of freshly-split tig. Impacts unitig to contig mapping output.

  brianwalenz

  committed
  8b20550

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• Increase minimum memory for gfa alignments

  skoren

  committed
  0cfea48

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Commits on May 11, 2017

• Make the release version string be 'Canu X.Y'. Issue marbl#481.

  brianwalenz

  committed
  43dc29f

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• Disable stacktrace support for older gcc versions. Report version of the compiler being used. Issue marbl#477.

  brianwalenz

  committed
  b69f212

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Commits on May 10, 2017

• For Torque, set gridEngineArrayMaxJobs based on qmgr reported value for max_job_array_size. Issue marbl#461.

  brianwalenz

  committed
  48b8c0a

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• Report and fail when tigs fail to load correctly. Issue marbl#483.

  brianwalenz

  committed
  40bfeb8

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• Don't place orphan reads back into the orphan they came from. Possibly issue marbl#434.

  brianwalenz

  committed
  119daca

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Commits on May 9, 2017

• If READLEN_BITS is 24 or greater, use a bigger overlap struct.

  brianwalenz

  committed
  700032e

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• Increase size of read metadata from 32 to 64 bits, to allow for longer reads.

  brianwalenz

  committed
  8ca485a

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• Add values for AS_MAX_READLEN_BITS 23 and 24. Issue marbl#478.

  brianwalenz

  committed
  5deaa3e

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• Build a better template for better consensus contiguity.

  brianwalenz

  committed
  1e76077

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• Assert that edlibAlign() lengths are positive.

  brianwalenz

  committed
  d172f1b

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• Increase AS_UTL_readLine() initial line size, fix potential out of bounds.

  brianwalenz

  committed
  7d0c15e

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• Check for algorithm on command line.

  brianwalenz

  committed
  a2b4069

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• Add -threads to command line help.

  brianwalenz

  committed
  4c9e08e

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• Replace 'unitig' with 'tig' in help, comments, logging.

  brianwalenz

  committed
  b6149bf

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• Don't change the directory for alignGFA if not on grid. Issue marbl#485.

  brianwalenz

  committed
  0eec42d

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Commits on May 3, 2017

• Allow extra space >max read length if we are correcting a read == max read length this was causing a crash (issue marbl#478)

  skoren

  committed
  fa3eede

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Commits on Apr 26, 2017

• Standardize making scripts executable. Issue marbl#459.

  brianwalenz

  committed
  63ce8ba

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Commits on Apr 20, 2017

• Add mhap filtering options to the list of options settable without a tag (e.g. mhapFilterUnique auto sets corMhapFilterUnique,obt, and utg).

  skoren

  committed
  f75deef

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• Add span request by default to LSF threading (issues marbl#444, marbl#13)

  skoren

  committed
  1339b2c

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• Switch to edlib alignments for consensus from the start, bump up consensus error rate slightly from the overlap error rate

  skoren

  committed
  c3dea7c

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