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Commits on Jan 27, 2021

• Enable utgReAlign by default, so that overlapper=mhap (instead of -fast) works correctly. Issue marbl#1872.

  brianwalenz

  committed
  db0a8da

• Guard against integer overflow when correcting reads with LOTS of evidence. Issue marbl#1875.

  brianwalenz

  committed
  7bffb10

• Update submodules.

  brianwalenz

  committed
  15dd498

• Move the .git directory out of the way before building binaries.

  brianwalenz

  committed
  13ffb40

Commits on Jan 26, 2021

• Fix out of bounds issue marbl#1878

  skoren

  committed
  e90f476

Commits on Dec 11, 2020

• Check for out of bounds while adjusting band, not just the first time (fix marbl#1845)

  skoren

  committed
  af771ef

Commits on Dec 1, 2020

• Update utility/ again. Don't use isdigit() or isspsace().

  brianwalenz

  committed
  095ed09

Commits on Nov 30, 2020

• Update meryl/ and utility/: 'types.H' changes and 64-mer lookups.

  brianwalenz

  committed
  aa43bb5

Commits on Nov 13, 2020

• Update tag

  skoren

  committed
  76b1263

• Fix crash with tiny alignments and fix incorrect check for circularization

  skoren

  committed
  4b8448f

• Add functions to get non-contained first/last read and standardize their usage

  skoren

  committed
  ab08d0c

• Switch to non-vectorized version

  skoren

  committed
  a58af29

Commits on Nov 6, 2020

• Fix crash circularizing teeny-tiny tigs.

  brianwalenz

  committed
  4dd74b5

Commits on Nov 4, 2020

• Fix -nofilter so it works, require exactly one filter name per option instance.

  brianwalenz

  committed
  61ade1a

• Switch utgcns to use parasail/edlib instead of libSSW for circularization.

  brianwalenz

  committed
  9a27705

• Add -mavx2 and CFLAGS.

  brianwalenz

  committed
  dd9fa9b

Commits on Nov 3, 2020

• Update utility/; splitHaplotype to new merylExactLookup interface.

  brianwalenz

  committed
  0b39efc

Commits on Oct 27, 2020

• Don't emit blank lines in the -coverage report. Fixes 563d049.

  brianwalenz

  committed
  604f7fc

Commits on Oct 22, 2020

• Turn off trimming for pacbio-hifi and fix so it runs; possibly broken in 6c17278.

  brianwalenz

  committed
  fcd7f96

Commits on Oct 21, 2020

• Output read names unless option '-id' is supplied.

  brianwalenz

  committed
  ef09dea

• Output to stdout if no -O option supplied.

  brianwalenz

  committed
  6a64765

Commits on Oct 20, 2020

• Make mean,stddev,median,mad local variables instead of class members.

  brianwalenz

  committed
  504b7b4

Commits on Oct 19, 2020

• Update faq.rst

  skoren

  authored
  2caad53

Commits on Oct 5, 2020

• Simplify (a little bit) flow of repeat detection, add comments, fix debugging.

  brianwalenz

  committed
  d51c25a

• Distinguish between repeat and unique when the split point is exactly between segments. Issue marbl#1806.

  brianwalenz

  committed
  8bed3e9

• Add a blank line after an overlap picture.

  brianwalenz

  committed
  563d049

Commits on Sep 29, 2020

• Add a script for generating the bias figures.

  brianwalenz

  committed
  37c2d43

Commits on Sep 27, 2020

• Rename local variables for consistency.

  brianwalenz

  committed
  ad130cc

• Fix error resetting the library range to dump; convert to strongly typed enum to prevent similar errors.

  brianwalenz

  committed
  a8b31c7

• Add asserts that the range to dump is valid.

  brianwalenz

  committed
  0e22969

Commits on Sep 25, 2020

• Update readSamplingBias, with example results.

  brianwalenz

  committed
  1c120b0

• Fix warnings caused by the prefix table.

  brianwalenz

  committed
  c40e7f5

• Fix warnings generated by white space.

  brianwalenz

  committed
  8313da1

• Fix a few broken links.

  brianwalenz

  committed
  feb2874

• Remove obsolete errorRate parameter.

  brianwalenz

  committed
  35acf32

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