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Commits on Mar 29, 2018

• Fix crash from race in std::set when finding zombie reads. Issue marbl#844.

  brianwalenz

  committed
  01744a6

Commits on Mar 16, 2018

• Allow a read with only container overlaps to form a contig. Issue marbl#818.

  brianwalenz

  committed
  967fcea

• If a read has no dovetail overlaps, use the error rate of its best overlap (for estimating global error rates).

  brianwalenz

  committed
  3b70634

Commits on Jan 30, 2018

• Replace unguarded fclose() with AS_UTL_closeFile().

  brianwalenz

  committed
  90fa2bd

• Report the correct number of suspicious edges found and discarded.

  brianwalenz

  committed
  6d1b84d

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 Jul 6, 2017

• Don't make best edges to singletons.

  brianwalenz

  committed
  8401731

Commits on Jan 20, 2017

• Add disabled code for filtering reads when the error rate in best overlaps differs greatly.

  brianwalenz

  committed
  3554998

Commits on Jan 12, 2017

• Add options to disable Best Overlap Graph read and overlap filtering.

  brianwalenz

  committed
  f835936

Commits on Nov 30, 2016

• In reportBestEdges(), close each file individually, not only if all files are opened.

  brianwalenz

  committed
  d6371b9

• Set errno=0 before fopen().

  brianwalenz

  committed
  3040de4

Commits on Nov 22, 2016

• Use snprintf() instead of sprintf().

  brianwalenz

  committed
  8ae92b9

Commits on Nov 21, 2016

• Update copyright message.

  brianwalenz

  committed
  bbbdcd0

Commits on Oct 17, 2016

• Fix gcc6 C++11 warnings. Issue marbl#270.

  brianwalenz

  committed
  37c7d79

Commits on Sep 29, 2016

• Set 'filtered' flag on high-error overlaps.

  brianwalenz

  committed
  abc3e67

• Remove const from things that want overlaps. We'll later be setting flags.

  brianwalenz

  committed
  de6d34d

• Expand BAToverlapInt to include BAToverlap, rename the former and remove the latter.

  brianwalenz

  committed
  190a8cb

Commits on Aug 21, 2016

• Use singular form when reporting one thread.

  brianwalenz

  committed
  f322902

Commits on Aug 12, 2016

• Rename FragmentInfo to ReadInfo, beacuse they're reads, and it stores their info.

  brianwalenz

  committed
  63459ac

• Call reads 'reads' instead of 'frags' and 'fragments'.

  brianwalenz

  committed
  4e74215

Commits on Aug 9, 2016

• Dead code; reconstructRepeats().

  brianwalenz

  committed
  46a8cec

Commits on Aug 5, 2016

• Initialize output graph file pointer to NULL.

  brianwalenz

  committed
  69f9cc5

Commits on Jun 14, 2016

• Log file changes; rename logs and write stats to individual files.

  brianwalenz

  committed
  d3dce1f

Commits on Jun 13, 2016

• Log actually useful statistics on edge filtering.

  brianwalenz

  committed
  e65ceb1

• Report spur reads to *.best.spurs.

  brianwalenz

  committed
  5dfbcb2

Commits on May 23, 2016

• Output best edges as GFA.

  brianwalenz

  committed
  fa135a1

Commits on May 18, 2016

• Update copyrights.

  brianwalenz

  committed
  1ef3359

Commits on May 10, 2016

• Reenable logging of spur reads.

  brianwalenz

  committed
  7a8a263

Commits on May 4, 2016

• Add atomics around counters.

  brianwalenz

  committed
  44a985c

Commits on Apr 28, 2016

• Organize and cleanup header files.

  brianwalenz

  committed
  127be84

Commits on Apr 22, 2016

• Add knobs. Report arrival rate histogram. Change logging.

  brianwalenz

  committed
  4c15630

Commits on Apr 19, 2016

• Report final best edges before removing them from contained reads.

  brianwalenz

  committed
  978096d

• Cleanup logging. A lot.

  brianwalenz

  committed
  0585437

• Don't report contained reads as singletons.

  brianwalenz

  committed
  2a3c3bf

Commits on Apr 18, 2016

• Change formatting of best edge score logging.

  brianwalenz

  committed
  ecb9f40

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