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Commits on Mar 27, 2020

• Simplify license text included in source files.

  brianwalenz

  committed
  9ff09f1

Commits on Mar 25, 2020

• A little bit more const-ness needed to compile on Linux.

  brianwalenz

  committed
  bb1f87d

• 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 24, 2020

• Update authorship in copyright blurb.

  brianwalenz

  committed
  d5fd693

• Remove stray whitespace.

  brianwalenz

  committed
  ef22127

Commits on Nov 19, 2019

• Properly check if contig sequence exists

  skoren

  committed
  792e5fb

Commits on Nov 15, 2019

• Some fixes to previous commit, don't stop when we hit the end of A since we'd never relax the error rate criteria that way. Increase tolerance for erate and length as well.

  skoren

  committed
  d35232d

• Clean up bed alignment, use only the contigs size change for the ratio, and ensure we try all attempts to expand region until we run out of sequence

  skoren

  committed
  ca4243f

Commits on Nov 14, 2019

• Use ratio when computing the unitig positions within contigs too

  skoren

  committed
  39afb6d

• Try trimming sequence when aligning to see if we can find a shorter match, use updated length for error rate tolerance

  skoren

  committed
  43ddb77

• Pass error rate to gfa alignment rather than hard-coding, use ratio of original to post-consensus length to adjust alignment positions

  skoren

  committed
  26ed56f

Commits on Jul 15, 2019

• Remove support for 'gapped' consensus sequence.

  brianwalenz

  committed
  92f8c95

Commits on Jul 21, 2018

• Fold reverse-complementing into 'sequence' library.

  brianwalenz

  committed
  1674b22

Commits on Jul 20, 2018

• Make utility/files.H and utility/strings.H.

  brianwalenz

  committed
  ce12198

• Rename 'AS_UTL/' to 'utility/'.

  brianwalenz

  committed
  fb95293

Commits on May 1, 2018

• Reimplement splitToWords so it can split path names too.

  brianwalenz

  committed
  0b4ce31

Commits on Apr 18, 2018

• Rename gatekeeper/gkpStore to sequence store/seqStore. Existing assemblies should be upgradable by just renaming *.gkpStore to *.seqStore.

  brianwalenz

  committed
  01d1823

Commits on Jan 30, 2018

• Replace unguarded fclose() with AS_UTL_closeFile().

  brianwalenz

  committed
  90fa2bd

Commits on Jan 17, 2018

• Delete seqsp object, instead of seqsp array.

  brianwalenz

  committed
  032fcc5

• Fix minor memory leak.

  brianwalenz

  committed
  83609ba

Commits on Jan 10, 2018

• Fix printf() formatting (maybe).

  brianwalenz

  committed
  151c34f

Commits on Nov 20, 2017

• Fix VN tag in GFA output to correctly report version of GFA used. Issue marbl#706.

  brianwalenz

  committed
  35757b4

Commits on Oct 6, 2017

• Install files in more proper locations. Issue marbl#563.

  brianwalenz

  committed
  cce9f5d

Commits on Aug 14, 2017

• Update copyright info.

  brianwalenz

  committed
  9e9bd67

Commits on Jul 26, 2017

• In BED mode, don't align the whole unitig to the contig, only look for the ends.

  brianwalenz

  committed
  344f1f6

Commits on Jun 24, 2017

• Make a copy of sequences before reverse complementing.

  brianwalenz

  committed
  96eec22

Commits on Jun 13, 2017

• If the BED utg to ctg is outside the ctg cns sequence, adjust instead of crashing.

  brianwalenz

  committed
  5f2312e

Commits on Jun 12, 2017

• Fix error in reporting BED percent identity.

  brianwalenz

  committed
  4a57f3d

Commits on May 12, 2017

• Add threading for BED -> GFA conversion.

  brianwalenz

  committed
  1dff905

• Big change to process bed, and to convert bed to gfa.

  brianwalenz

  committed
  ca4e385

• Let gfaSequences and gfaLinks be created from scratch.

  brianwalenz

  committed
  5eaa821

• Allow sequences to be named tig, utg or ctg.

  brianwalenz

  committed
  37d8a21

• Add simple .bed reading/writing class.

  brianwalenz

  committed
  36638f6

Commits on Apr 17, 2017

• Update copyrights.

  brianwalenz

  committed
  5ad2434

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