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Commits on Jul 22, 2020

• Build in 'build' instead of 'OSTYPE-MACHINETYPE'.

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• Remove unused crud from submakefiles.

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  committed
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Commits on Jul 13, 2020

• Don't change the working directory in meryl-configure; it's already correct. Issue marbl#1740.

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  0d8d7f3

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• Add comment about confusion parameters.

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  dee9262

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• Add utgRepeatConfusedPC and sync bogart -ca/-cp with canu.

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  3c16a58

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• Downgrade class oSH_ovlSco to simple struct.

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• Don't require an output file if output is going to stdout.

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  c6e516a

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Commits on Jul 9, 2020

• Fix inconsistency that could underestimate memory needed for consensus on contigs. Issue marbl#1750.

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Commits on Jul 8, 2020

• Change ovStore data names to be POSIX compliant. Import canu-specific object store methods from meryl-utility. Issue marbl#1732.

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• Check git version, refuse to work with the 1.x series. Issue marbl#1747.

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Commits on Jun 25, 2020

• Use gcc9 instead of clang on FreeBSD.

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  committed
  35ff759

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• Move default initializer from implementation to specification. Oops.

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  committed
  eb1fa42

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• Explicitly initialize arrays, instead of memset().

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  committed
  9661fc4

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• Don't set the clear range if it isn't good. Possibly fixes marbl#1655.

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  b84b065

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• Add options to enable logging.

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  committed
  8baa23e

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• Move logging to a function.

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  committed
  cb72f2a

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• Don't add empty intervals.

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  committed
  e8f8ab6

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• Clean up logging in repeat detect/split, simplify findNext(Prev)ThickestRead.

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  committed
  8de3c0f

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• Fix cute-n-harmless bug that would return false thickest-next-read for the last read in a tig.

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  committed
  cf97d3e

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• Also check if the first read is thickest in findThickestPrevRead().

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  99f0354

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• Remove unused findPrevBestRead() and findNextBestRead().

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  committed
  1667d09

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• Remove reportThickestEdgesInRepeats(); it was just logging.

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  committed
  a8ef81b

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• Split tigs at the ends of confused reads, instead of the repeat region the confused reads are in.

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  committed
  9b0089c

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• Fix error setting end of confused read used for making unitigs.

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  committed
  3aaedfe

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• Use lambda functions for sorting olapDat.

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Commits on Jun 11, 2020

• Adjust kmer histogram size based on coverage; fix out of memory errors. Fixes marbl#1632.

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Commits on May 27, 2020

• Include spur in the set of overlaps that are isOverlapBadQuality().

  

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  committed
  972d01d

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• Do not let a lopsided read rescue a spur path.

  

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Commits on May 15, 2020

• Add option -covgaptype (uncovered default) and associated filters.

  

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• Add options -nocontains, -eM and -eg.

  

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Commits on May 14, 2020

• Add options -nocontains, -eM and -eg.

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  committed
  58e7507

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• Add option -covgaptype (uncovered default) and associated filters.

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  committed
  23512b8

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• Add disabled compile time support for reclassifying contained reads after spurs.

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  19075a9

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• Jiggle order of testing if read/overlap is bad, trying to get some consistency so the multiple tests can be replaced by one.

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  8a86d93

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• Do not let a lopsided read rescue a spur path.

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  committed
  9a779e7

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