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Commits on Nov 24, 2021

• Allow dumps of disjoint ranges.

  brianwalenz

  committed
  c5b776d

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Commits on Nov 19, 2021

• Fix crash when increasing overlap beyond the tig length

  skoren

  committed
  cda11f7

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Commits on Nov 17, 2021

• Dump read name and tig name translations

  skoren

  committed
  be31361

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Commits on Nov 12, 2021

• Clean up logging

  skoren

  committed
  5079c3d

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• Update partitioning to support putting a read into more than 1 partition

  skoren

  committed
  412b5e0

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• Log errors

  skoren

  committed
  dc5863f

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• Allow consensus to handle duplicate reads (e.g. same read multiple times in a contig or across contigs)

  skoren

  committed
  209f67e

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• Fix the infinite loop fix which just disabled increasing error rate, doh

  skoren

  committed
  3b53c16

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• Fix infinite loop bug w/0% error rate

  skoren

  committed
  453819d

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• Allow overlap to be resized up/down, don't force alignment when there is no overlap

  skoren

  committed
  f4110f6

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• Add min coverage on the ends of contigs

  skoren

  committed
  be7cd75

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• Fix array resize error; fix memory leak.

  brianwalenz

  committed
  8c40b4e

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Commits on Nov 11, 2021

• sort tigs again

  brianwalenz

  committed
  0a79d57

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• Fix minor bugs.

  brianwalenz

  committed
  0e2fb68

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Commits on Nov 10, 2021

• Allow sqCache to load reads from fasta/fastq, add layoutToPackage.

  brianwalenz

  committed
  5353e05

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• Remove, TEMPORARILY, splitHaplotype from the build, due to meryl-lookup interface changes.

  brianwalenz

  committed
  65ce518

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Commits on Oct 18, 2021

• Guard against OG == nullptr when called from layoutReads.

  brianwalenz

  committed
  08b0347

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Commits on Oct 8, 2021

• Fix invalid load check

  skoren

  committed
  1c62138

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Commits on Oct 1, 2021

• Fix runs with <100 reads (marbl#2035)

  skoren

  committed
  7fb66bb

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Commits on Sep 16, 2021

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

  brianwalenz

  committed
  4702e33

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Commits on Sep 7, 2021

• Fix usage text. @fishercera marbl#686

  brianwalenz

  committed
  407ae11

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Commits on Aug 26, 2021

• Revert IND constants changed in cb94432.

  brianwalenz

  committed
  6c41938

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• Add license text.

  brianwalenz

  committed
  79f0cbd

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Commits on Aug 13, 2021

• Rewrite correction memory configuration.

  brianwalenz

  committed
  dee8c6e

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• Indent creation of correctReads.sh,

  brianwalenz

  committed
  5983fc3

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• Simplify call to getAllowedResources().

  brianwalenz

  committed
  806081d

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• Tidy up cor and cns settings.

  brianwalenz

  committed
  7332aec

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Commits on Aug 5, 2021

• Update quick-start.rst

  skoren

  authored
  f265325

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Commits on Aug 4, 2021

• Autoset read correction memory

  skoren

  committed
  27e2db7

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• Bump version number.

  brianwalenz

  committed
  110d1ad

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Commits on Aug 3, 2021

• Trim back noisy alignments to the real alignment.

  brianwalenz

  committed
  ea2b03d

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• Change default corErrorRate from 50 to 30 (nanopore) and 30 to 25 (pacbio).

  brianwalenz

  committed
  741911c

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• Extend so it will report time on arbitrary jobs.

  brianwalenz

  committed
  0e603ad

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Commits on Aug 2, 2021

• Fix/simplify setting of thread limit.

  brianwalenz

  committed
  b626dbe

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• Fix issues with invalid SGE date/time strings.

  brianwalenz

  committed
  0f1c290

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