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Commits on Mar 22, 2012

• refactored flatfile-to-json.pl to use Bio::GFF3::LowLevel::Parser,

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Commits on Mar 19, 2012

• there is not really any reason to make flatfile-to-json users have the reference sequences beforehand

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Commits on Mar 7, 2012

• rewrite flatfile-to-json.pl filtering logic to recursively check subfeatures if the parent feature does not pass the filtering rule

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• make flatfile-to-json.pl doc suggest using --getSubfeatures instead of --getSubs

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Commits on Feb 29, 2012

• move refSeqs.json into the seq/ subdirectory, leaving just trackList.json in the top level of the data

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Commits on Feb 27, 2012

• remove some unnecessary uses of Data::Dump and Data::Dumper

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Commits on Feb 23, 2012

• fix some configuration problems with biodb-to-json and flatfile-to-json

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Commits on Feb 21, 2012

• add note explicitly disavowing GFF2 and GTF support to flatfile-to-json

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• give bioperlflattener a default subroutine to use for fetching feature labels, which is actually the label-fetching code moved into there from flatfile-to-json.pl

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Commits on Feb 16, 2012

• add missing use to flatfile-to-json

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• remove erroneously-committed Carp::Always line

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• remove not-implemented --extraData option from flatfile-to-json.pl

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Commits on Feb 15, 2012

• remove some unnecessary code cruft, thanks to tests.

  rbuels

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• add --trackLabel to bam-to-json.pl, and make it a required arg

  rbuels

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• make sure all the scripts i have been over accept either --help, -h, or -? for displaying the extended help

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Commits on Feb 14, 2012

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

  rbuels

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• flatfile-to-json getting closer to working

  rbuels

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

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

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

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Commits on Feb 13, 2012

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

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Commits on Jan 30, 2012

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

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Commits on Feb 26, 2011

• call seq_id on the right thing

  

  Mitch Skinner

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• use ref to check for non-string seq_id values

  

  Mitch Skinner

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

  

  Mitch Skinner

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Commits on Feb 14, 2011

• change clientConfig example in usage message

  

  Mitch Skinner

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• add usage messages

  

  Mitch Skinner

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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

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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

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• Revert "finish streaming pair matcher"

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  Mitch Skinner

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Commits on Sep 1, 2010

• finish streaming pair matcher

  

  Mitch Skinner

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Commits on Aug 31, 2010

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

  

  Mitch Skinner

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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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  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

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  Mitch Skinner

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

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  asw12

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  Mitch Skinner

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