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Commits on Feb 14, 2012

• fix gff3 subfeature fetching in flatfile-to-json.pl

  rbuels

  committed
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• flatfile-to-json getting closer to working

  rbuels

  committed
  e8fce25

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• make flatfile-to-json actually pay attention to the --type argument and filter with it

  rbuels

  committed
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• ported flatfile-to-json to the new loading API, with some tests. needs more tests still though

  rbuels

  committed
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• to be more consistent, change --tracklabel arg of flatfile-to-json to trackLabel (but with backcompat to the old capitalization)

  rbuels

  committed
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Commits on Feb 13, 2012

• write POD for flatfile-to-json.pl and migrate to Pod::Usage

  rbuels

  committed
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Commits on Jan 30, 2012

• global replace of trackInfo.js -> trackInfo.json and refSeqs.js -> refSeqs.json

  rbuels

  committed
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Commits on Feb 26, 2011

• call seq_id on the right thing

  

  Mitch Skinner

  committed
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• use ref to check for non-string seq_id values

  

  Mitch Skinner

  committed
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• separate names.json output from JsonGenerator, use feature counts to calculate max histogram

  

  Mitch Skinner

  committed
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Commits on Feb 14, 2011

• change clientConfig example in usage message

  

  Mitch Skinner

  committed
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• add usage messages

  

  Mitch Skinner

  committed
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Commits on Feb 10, 2011

• get flatfile-to-json.pl working, hand names to JsonGenerator early, remove unused JsonGenerator constructor argument

  

  Mitch Skinner

  committed
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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
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• Revert "finish streaming pair matcher"

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  Mitch Skinner

  committed
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Commits on Sep 1, 2010

• finish streaming pair matcher

  

  Mitch Skinner

  committed
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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

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  Mitch Skinner

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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
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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
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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
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• get labels if autocomplete is on

  

  Mitch Skinner

  committed
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Commits on Mar 28, 2010

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

  

  Mitch Skinner

  committed
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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
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Commits on Mar 8, 2010

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

  

  Mitch Skinner

  committed
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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

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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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