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Commits on May 12, 2020

• Drop the 'duplicate' overlap with the fewest matching bases, not the one with the fewest errors.

  brianwalenz

  committed
  017e2f4

• Don't complain about too little memory to load overlaps until after we compute how many overlap to load.

  brianwalenz

  committed
  b8c687c

• Add toString(Overlap_t) to report the type of overlap.

  brianwalenz

  committed
  4be7010

Commits on May 11, 2020

• Parse genome size as float to avoid overflowing with genomes >4gb

  skoren

  committed
  c1e4ac2

Commits on May 8, 2020

• Add utility to convert a list of reads to contig layouts.

  brianwalenz

  committed
  790f3cb

• Adjust logging to handle the lack of a BestOverlapGraph.

  brianwalenz

  committed
  550e9ec

• Check that the (required) genome size command line parameter is supplied.

  brianwalenz

  committed
  a055ca4

• Bend to gcc's idiotic suggestion that parens are needed to make an unambiguous if-if-else construct unambiguous.

  brianwalenz

  committed
  855a9ba

Commits on May 5, 2020

• Extend covGap to include reads not fully covered by overlaps.

  brianwalenz

  committed
  698a743

• Fix executive memory to not ignore minMemory

  skoren

  committed
  33ab421

• Cleanup style, comments and indenting a bit.

  brianwalenz

  committed
  7690ceb

• Remove unused variable 'toUnassembled'.

  brianwalenz

  committed
  a712d22

• Update confusion parameters (-ca and -cp) to agree with canu.

  brianwalenz

  committed
  7c05085

• Merge 'confusion_fixed_rebased' into masster.

  brianwalenz

  committed
  60b105e

Commits on Apr 28, 2020

• Revert "temporarily adding -D most to bogart"

  Show description for d636a78
  snurk

  committed
  d636a78

• dead code clean-up

  snurk

  committed
  5d8ad06

• Update confusion criteria for all assemblies with HiFi thresholds less strict by default

  skoren

  committed
  daf9c94

• Do not place bubbles with too many locations since they're probably repeats and not bubbles

  skoren

  committed
  96a5428

• Fix print formatting

  skoren

  committed
  c753ca4

• Reset orphans to not be backbone reads when they are placed

  skoren

  committed
  be51024

• Allow bubbles to not be covered by a few intervals, we don't expect bubbles to be fully covered anyway

  skoren

  committed
  00f278c

• Switch bubbles back to using the input error rate and require 1% (for now) of a read to be placed for both confusion and bubbles

  skoren

  committed
  c277874

Commits on Apr 27, 2020

• Fix race in flagging reads as coverage-gap.

  brianwalenz

  committed
  9e30b7a

Commits on Apr 24, 2020

• Add -readlen option to set a range of read lengths to use, instead of just a min like -mr does.

  brianwalenz

  committed
  1abc58e

• Add option to ignore some jobs, fix reporting of wall clock for SGE (maybe Slurm too), change order of output columns.

  brianwalenz

  committed
  db291dc

Commits on Apr 22, 2020

• Add -coverage option to report simple statistics on the coverage of a read by its overlaps.

  brianwalenz

  committed
  03cbc37

Commits on Apr 21, 2020

• submodule update

  snurk

  committed
  3a9394d

Commits on Apr 15, 2020

• Special case Us and convert them to Ts implicitly (issue marbl#1680)

  skoren

  committed
  64dd9f1

Commits on Apr 14, 2020

• Do not check non-backbone reads for confusion, allow reads contained in repeats to be checked for confusion

  skoren

  committed
  214d94e

• Adjust bubble placements to require at least half the read to be placed and auto-set threshold based on provided -eg parameter

  skoren

  committed
  bbd03d2

• Adjust assembly graph building to use only overlaps below provided threshold, default uses all

  skoren

  committed
  bd40516

Commits on Apr 9, 2020

• Report versions in use to stdout, not stderr.

  brianwalenz

  committed
  4e92526

Commits on Apr 7, 2020

• Fix logging/debug printf().

  brianwalenz

  committed
  30715d7

Commits on Apr 2, 2020

• Update to do orphan placement in two rounds, also update orphan placement critera and include bfaf2ad from master

  skoren

  committed
  28392ba

• Update utility tag

  skoren

  committed
  01281b5

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