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Commits on Aug 7, 2015

• Cleanup bogart implementation.

  brianwalenz

  committed
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Commits on Aug 5, 2015

• Fix bash bug ("33>file" vs "33 > file"), improve logging of unitigs in store.

  brianwalenz

  committed
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Commits on Aug 3, 2015

• Report unitig sizes if the tigStore exists.

  brianwalenz

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Commits on Jul 29, 2015

• Set local max coverage for correction to 10x estimated coverage.

  brianwalenz

  committed
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• Don't set local max coverage if it isn't defined.

  brianwalenz

  committed
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Commits on Jul 28, 2015

• Remove two stray ${asm} prefixes on filenames, remove (already disabled) utgcnsfix.

  brianwalenz

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Commits on Jul 23, 2015

• Missing backslash in ca3g resubmission script.

  brianwalenz

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Commits on Jul 21, 2015

• Write a message about where the final trimmed reads are.

  brianwalenz

  committed
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Commits on Jul 1, 2015

• Update path to falcon for dev cluster.

  brianwalenz

  committed
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Commits on Jun 17, 2015

• Don't redirect utgcns output to a file.

  brianwalenz

  committed
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Commits on Jun 16, 2015

• Fix formatting of the bin directory in shell scripts.

  brianwalenz

  committed
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• Pass the four error rates to bogart (finally).

  brianwalenz

  committed
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• Detect missing files (only the first one) passed in via -pacbio* or -nanopore*.

  brianwalenz

  committed
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• Remove the 'stage' based restarts, back to make style restarts. Redo overlap partitioning,

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  brianwalenz

  committed
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Commits on Jun 15, 2015

• Minor tweaks to correction; use 40x instead of 50x coverage for deciding the minimum

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  brianwalenz

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Commits on Jun 10, 2015

• Expand corMaxEvidenceCoverage into one for global and one for local filtering.

  brianwalenz

  committed
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• Correctly detect undef merylMemory, and reset to 2/3*max.

  brianwalenz

  committed
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Commits on Jun 6, 2015

• Add gobs of logging. Three bugs fixed. In filterCorrectionOverlaps.C, the wrong length

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  brianwalenz

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Commits on Jun 3, 2015

• Set default error rate to 0.01. Cleanup logging.

  brianwalenz

  committed
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• Set default error rate to 0.01. Cleanup logging.

  brianwalenz

  committed
  9839c73

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Commits on May 29, 2015

• Find ca3g.pl in the bin directory, not from the command line.

  brianwalenz

  committed
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• Set default error rates based on yeast tests.

  brianwalenz

  committed
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• Increase minReadLength to 1000 and minOverlapLength to 500.

  brianwalenz

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• Remove merylSegments.

  brianwalenz

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• Reenable cleanup after installing.

  brianwalenz

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Commits on May 28, 2015

• Show error rates at the start of a run.

  brianwalenz

  committed
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• Dead code.

  brianwalenz

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• Add global filtering of overlaps.

  brianwalenz

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Commits on May 26, 2015

• Decrease 'run' error rates from 2% to 0.5%, show error rates at start of pipeline.

  brianwalenz

  committed
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• Among gobs of small changes:

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Commits on May 14, 2015

• Remove useless logging.

  brianwalenz

  committed
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• A variety of minor changes:

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  brianwalenz

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• Remove tiny bit of dead code.

  brianwalenz

  committed
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• Add 'ovl' to overlapper parameters.

  brianwalenz

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• Change format of checkpoint/stage strings.

  brianwalenz

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