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brianwalenz

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Commits on Feb 27, 2020

• Restore the -covgapolap and -lopsided parameters initially set in 8b1d9d1 and, somehow, removed in f1e89e4.

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  1b0cd4b

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• Don't recompute contained reads after we start removing edges, and do recompute best edges for reads that had edges removed.

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  1be21ca

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• Change the scoring of lopsided edges so it makes sense, and to not declare something lopsided if the overlap covers a large fraction of the read.

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  c4ff60b

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• Add some much needed whitespace.

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Commits on Feb 25, 2020

• Check for each submodule using standard make method.

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  779c342

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• Make make explicitly initialize submodules before doing anything.

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  f97f66e

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• Adjust header files to compile with submodules.

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  47b5074

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• Remove AS_global.C and AS_global.H. Hugs.

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  1705a99

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• Add meryl and meryl-utility submodules.

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  46da3ca

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• Remove meryl and utility in preparation for submodules.

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  c3ac4b8

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Commits on Feb 24, 2020

• Update docs on building a release.

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  d521766

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• Bump version numbers.

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  f4d0264

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• Tell git to ignore canu_version.H.

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  committed
  32d2abf

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• Update for the last copyright update.

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  committed
  d54c48c

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• Update authorship in copyright blurb.

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  d5fd693

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• Remove stray whitespace.

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  ef22127

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• Remove hacks to skip old kmer-project code base.

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  75f68b7

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• Clarify what -test does.

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  cf3b8ec

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• Add S.Nurk as an approved author.

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  caf4883

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• Add some comments on the origin of optimize.

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  committed
  1d9e863

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• Disable second round of lopsided. Details in comments.

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Commits on Feb 21, 2020

• Make 'pairwise align' read fasta/fastq and not skip lines in the second file.

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  9492acc

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• Set default -covgapolap (500) and -lopsided (nobest 50) options to agree with Canu.

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  committed
  f1e89e4

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• Make tgStoreDump -layout behave reasonably. Remove -layout-verbose.

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  bd43f89

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• Add logging of the edges we replace spur-path edges with.

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  af5a174

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• Add a second pass of lopsided detection after spurs are flagged and removed.

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  633b8d4

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• Implement new rule for calling a confused edge (if external is bigger than internal) but leave it disabled until we can test. And fix a printf format.

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  0de2cf5

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Commits on Feb 18, 2020

• More reliably set the version string; don't try to parse the directory name to get it.

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  6cfdadd

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Commits on Feb 14, 2020

• Fix sneaky bug that was discarding all read placements if the first tig was a potential orphan.

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  7ae7a09

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• Require that both ends be covered by overlaps for a tig to be a potential orphan/bubble.

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  3bc4eb8

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• Update logging to easier search for non-potential-orphans.

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  662f080

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• A safer strategy for enabling debugging on a specific tig.

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  51bab5d

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Commits on Feb 13, 2020

• Add shift-register emit(), fix printing of state, command line options.

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  01f6a6e

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• When ignoring reads, ignore in all copies of the metadata. Issue marbl#1619.

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  d9130cc

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Commits on Feb 12, 2020

• Add kmerIterator interface to return something for every base; use that to report N bases in meryl-lookup output.

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  4724187

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