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Commits on Feb 24, 2016

• Add support for minimap as an overlapper option

  skoren

  committed
  26569bb

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• Convert to compiled falcon_sense from os-specific binaries and include necessary code

  skoren

  committed
  7a58403

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Commits on Feb 22, 2016

• Respect DESTDIR and PREFIX. Issue marbl#46.

  brianwalenz

  committed
  853c5c7

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Commits on Feb 12, 2016

• Add (incomplete) GFA output.

  brianwalenz

  committed
  302cd08

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Commits on Feb 6, 2016

• Replace the full computation of the number of errors allowed with a partial compute and an estimate.

  brianwalenz

  committed
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Commits on Feb 5, 2016

• Remove tabs.

  brianwalenz

  committed
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Commits on Dec 28, 2015

• update make file to include pbdagcon includes

  skoren

  committed
  603579c

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Commits on Dec 21, 2015

• Build libcanu, not libCA.

  brianwalenz

  committed
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Commits on Dec 3, 2015

• Encode sequence as 2-bit values. If the sequence cannot be 2-bit encoded, it is stored as

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  brianwalenz

  committed
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Commits on Nov 23, 2015

• Rewrite utgcns 'quick' mode to be more correct, and probably more faster.

  brianwalenz

  committed
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Commits on Oct 27, 2015

• Add initial (and poor) version of an overlap statistics generator, committed

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  brianwalenz

  committed
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Commits on Aug 18, 2015

• Remove AS_UTL_heap. Unused.

  brianwalenz

  committed
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• Remove AS_UTL_Hash. Unused in existing code.

  brianwalenz

  committed
  3b92fcc

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• Remove, finally, the VarArray. It was a clever variable length array for C,

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  brianwalenz

  committed
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• Tidy up main.mk, remove several unused main.mk from subdirectories.

  brianwalenz

  committed
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Commits on Aug 14, 2015

• Add coverage stat and bogus unitig filters.

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  brianwalenz

  committed
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Commits on Aug 12, 2015

• Change the tgStore constructor to take a 'type' instead of three bool flags to

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  brianwalenz

  committed
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Commits on Aug 11, 2015

• Remove unitigger, sorry Clark.

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  brianwalenz

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Commits on Jul 26, 2015

• Remove obsolete utgcns/libNDalign/Display_Alignment.C

  brianwalenz

  committed
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Commits on Jul 23, 2015

• Add stddev.C to the build.

  brianwalenz

  committed
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Commits on Jul 21, 2015

• Finish renaming overlapInCore's liboverlap (prefixEditDistance) to utgcns's libNDalign.

  brianwalenz

  committed
  21af79e

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• Copy overlapInCore/liboverlap to utgcns/libNDalign.

  brianwalenz

  committed
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Commits on Jul 8, 2015

• Make unitigConsensus a class with a built-in driver function. Add support for

  Show description for 9d3c975
  brianwalenz

  committed
  9d3c975

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• Remove useless alignment/overlap.C driver.

  brianwalenz

  committed
  a675bfd

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Commits on Jun 25, 2015

• Fix overlapper Display_Alignment() routine.

  brianwalenz

  committed
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Commits on Jun 23, 2015

• Fix many issues in seed finding in overlapAlign. Engineering to support readConsensus.

  brianwalenz

  committed
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Commits on Jun 18, 2015

• Compile overlapErrorAdjustment/analyzeAlignment.

  brianwalenz

  committed
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Commits on Jun 3, 2015

• Add prefixEditDistance.C to the build; file added a few revisions ago.

  brianwalenz

  committed
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Commits on Jun 2, 2015

• Precompute the prefixEditDistance Edit_Match_Limit array. Very big.

  brianwalenz

  committed
  bcdda14

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Commits on May 28, 2015

• Add global filtering of overlaps.

  brianwalenz

  committed
  8b5d32c

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Commits on May 14, 2015

• Add program to load ascii overlaps to either binary ovb or a store.

  brianwalenz

  committed
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Commits on Apr 22, 2015

• Revive the simple mer counter.

  brianwalenz

  committed
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Commits on Apr 15, 2015

• Rename AS_OBT to overlapBasedTrimming.

  brianwalenz

  committed
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• Remove the old chimera/spur algorithms, clean up what is left of the splitting code.

  brianwalenz

  committed
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Commits on Apr 13, 2015

• Engineering. Rename binaries, move overlap reader to ovStore itself.

  brianwalenz

  committed
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