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Commits on Sep 3, 2010

• Pair-matching in the presence of multiply-mapped reads is more complicated than I thought; reverting the pair matching code

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  Mitch Skinner

  committed
  c06893f

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• Revert "finish streaming pair matcher"

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  Mitch Skinner

  committed
  c8c7b57

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Commits on Sep 1, 2010

• finish streaming pair matcher

  

  Mitch Skinner

  committed
  9801043

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Commits on Aug 31, 2010

• don't try to share subfeatures if they're not already shared

  

  Mitch Skinner

  committed
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Commits on Aug 6, 2010

• Make extraData an optional parameter for flatfile-to-json.pl for flatfiles as well

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  asw12

  authored and

  Mitch Skinner

  committed
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• Print an error if a type argument isn't matching anything in the GFF

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  asw12

  authored and

  Mitch Skinner

  committed
  8a5cccd

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• Change the order error messages are printed in flatfile-to-json.pl

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  asw12

  authored and

  Mitch Skinner

  committed
  e776361

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• Don't add tracks to trackInfo.js when no features are present on that track

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  asw12

  authored and

  Mitch Skinner

  committed
  6febe0f

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• get labels if autocomplete is on

  

  Mitch Skinner

  committed
  7d4880a

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Commits on Mar 28, 2010

• make top-level nclist more compact, omit IDs for bam files

  

  Mitch Skinner

  committed
  6f10d1f

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Commits on Mar 19, 2010

• add parameter to set NCL chunk size (temp. hack until we make NCList.pm smarter about chunking)

  

  Mitch Skinner

  committed
  11b1ffe

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Commits on Mar 8, 2010

• reduce bam memory usage by iterating and flattening as we go

  

  Mitch Skinner

  committed
  c44ea96

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Commits on Nov 20, 2009

• add a version of Caroline Johnston's Bio::DB::Sam patch

  

  Mitch Skinner

  committed
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• Merge branch 'master' into lazyfeatures

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  Mitch Skinner

  committed
  599a8fb

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Commits on Oct 21, 2009

• allow the ID callback to vary

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  Mitch Skinner

  committed
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• stop requiring GFFs to have sequence-region headers

  

  Mitch Skinner

  committed
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Commits on Oct 19, 2009

• change shebang line

  

  Mitch Skinner

  committed
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Commits on Sep 29, 2009

• check for required parameters in flatfile-to-json

  

  Mitch Skinner

  committed
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Commits on Sep 13, 2009

• server-calculated histograms; evenly size lazy feature chunks

  

  Mitch Skinner

  committed
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Commits on Jul 17, 2009

• don't barf if there's no segment

  

  Mitch Skinner

  committed
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Commits on Jul 1, 2009

• require JSON version 2

  

  Mitch Skinner

  committed
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Commits on Jun 12, 2009

• add client config and BED type parameters

  

  Mitch Skinner

  committed
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Commits on Jun 5, 2009

• bed support

  

  Mitch Skinner

  committed
  7eeba41

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• rename gff-to-json to flatfile-to-json

  

  Mitch Skinner

  committed
  f6656a3

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