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Commits on Jan 11, 2023

• Make minkmer parameter non-positional

  skoren

  committed
  4b563b5

• Enable use of minimum kmer count to filter matches

  skoren

  committed
  2c5dd8c

Commits on Dec 21, 2021

• Fix check for hash table overflow

  skoren

  committed
  af0f896

Commits on Dec 20, 2021

• Add some extra space to the hash table to avoid cases where we are unable to load the last few reads

  skoren

  committed
  dd10d72

Commits on Dec 17, 2021

• Allow one read's worth of slush when loading data into hash

  skoren

  committed
  165ff44

Commits on Sep 16, 2021

• Add .ovb as an input type; allow filtering of imported overlaps. Issue marbl#2022.

  brianwalenz

  committed
  4702e33

Commits on Aug 2, 2021

• Fix/simplify setting of thread limit.

  brianwalenz

  committed
  b626dbe

Commits on Mar 31, 2021

• Add a new method for pruning the DP matrix and a bunch of logging, all disabled.

  brianwalenz

  committed
  8ebd75b

• Update debug outputs.

  brianwalenz

  committed
  49cca44

• Disable logging of parameters.

  brianwalenz

  committed
  3d724de

• Update utility: array flags; (big) remove 'using namespace std'.

  brianwalenz

  committed
  93b3149

• Add option --alignnoise to artifically raise the DP pruning threshold.

  brianwalenz

  committed
  8788abf

Commits on Feb 4, 2021

• Test for file existence in -k option to avoid call to isdigit().

  brianwalenz

  committed
  bf4b369

Commits on Aug 12, 2020

• Choose the longest overlap when identity is the same.

  brianwalenz

  committed
  88590e7

Commits on Jul 29, 2020

• Add MODULE definition, remove unused SUBMAKEFILES definitions in submakefiles, update submodules for same.

  brianwalenz

  committed
  fd66ed8

• Remove empty SUBMODULES definition in submakefiles.

  brianwalenz

  committed
  97e9767

Commits on Jul 22, 2020

• Remove unused crud from submakefiles.

  brianwalenz

  committed
  ff5d6f7

Commits on May 12, 2020

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

  brianwalenz

  committed
  4be7010

Commits on Mar 27, 2020

• Simplify license text included in source files.

  brianwalenz

  committed
  9ff09f1

Commits on Mar 25, 2020

• Fix const-ness of string parameters.

  brianwalenz

  committed
  65b20f0

Commits on Feb 25, 2020

• Adjust header files to compile with submodules.

  brianwalenz

  committed
  47b5074

Commits on Feb 21, 2020

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

  brianwalenz

  committed
  9492acc

Commits on Dec 3, 2019

• Fix issue where reads with many many many overlaps might be skipped in overlapPair and ovStoreDump.

  brianwalenz

  committed
  c8fbbff

Commits on Sep 10, 2019

• Move debug print to be after values are set. (D'oh!)

  brianwalenz

  committed
  be1cf18

• Ensure the length of the read is actually the read length.

  brianwalenz

  committed
  fd3c118

Commits on Jul 5, 2019

• Implement version 8 of seqStore. Working, but not complete and not well tested.

  brianwalenz

  committed
  40763d8

Commits on Jun 28, 2019

• Add import of paf format, fix paf dump which was missing () for proper operation order, add identity to paf dump

  skoren

  committed
  360a37d

Commits on Apr 25, 2019

• Print more details about the alignment.

  brianwalenz

  committed
  1bdf420

Commits on Apr 22, 2019

• Add mode to align sequence to reference and return number of indel etc.

  brianwalenz

  committed
  d9215b3

Commits on Apr 11, 2019

• Set the sqStore pointer in ovOverlap when the seqStore is opened. Fixes a race condition when an array of overlaps is allocated, which reset the pointer. And it's simpler code.

  brianwalenz

  committed
  033bee3

Commits on Feb 8, 2019

• Move edlib to utility/.

  brianwalenz

  committed
  b241431

Commits on Jan 10, 2019

• Allow matches to N (and n) ambiguity bases. Based on Martinsos/edlib@92f6a3f.

  brianwalenz

  committed
  3a3c336

Commits on Oct 22, 2018

• Update copyright info.

  brianwalenz

  committed
  fcc3fe1

Commits on Sep 17, 2018

• Remove the original 'project kmer' meryl and associated libraries. Roughly 14.5 years old in its current form.

  brianwalenz

  committed
  728f687

Commits on Aug 13, 2018

• Slightly cleanup to show that we always have a sqStore object.

  brianwalenz

  committed
  dc324a8

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