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Commits on Feb 7, 2014

• add m. durling --config option to flatfile-to-json.pl

  rbuels

  committed
  1ec4639

• clarify POD about --clientConfig behavior

  rbuels

  committed
  9127726

Commits on Dec 13, 2013

• add nameAttributes support to flatfile-to-json and biodb-to-json

  rbuels

  committed
  11c099b

Commits on Dec 5, 2013

• add --metadata arg to flatfile-to-json.pl

  rbuels

  committed
  18e085c

• in-passing cleanups and doc improvements

  rbuels

  committed
  00febf3

Commits on Oct 28, 2013

• tweak POD for --maxLookback option

  rbuels

  committed
  584a3c7

Commits on Oct 2, 2013

• upgrade to Bio::GFF3::LowLevel::Parser 1.7, and use its new max_lookback method

  rbuels

  committed
  5fb859a

Commits on Aug 29, 2013

• add a note that the genbank adaptor can only handle one gene at a time

  rbuels

  committed
  978b3ef

Commits on Jul 29, 2013

• add docs on --trackType option to flatfile-to-json.pl

  rbuels

  committed
  616bbf8

• improve --gbk option docs in flatfile-to-json.pl

  rbuels

  committed
  ad83470

• Merge branch 'genbank_flatfile'

  Show description for f1a98ed
  rbuels

  committed
  f1a98ed

Commits on Jul 24, 2013

• add --noSubfeature option to flatfile-to-json.pl

  rbuels

  committed
  5a71902

Commits on Jul 10, 2013

• added some files to start supporting GBK files in flatfile-to-json.pl

  justaddcoffee

  committed
  4034b63

Commits on Aug 28, 2012

• add a note about memory usage to the flatfile-to-json.pl POD

  rbuels

  committed
  352909d

Commits on Aug 11, 2012

• add more doc about the flatfile-to-json.pl --type option

  rbuels

  committed
  b340b3e

Commits on Jun 27, 2012

• move perl libs to src/perl5

  rbuels

  committed
  1ff8041

• move perl modules to lib/perl5

  rbuels

  committed
  71b1fe3

Commits on Jun 12, 2012

• remove references to unused --autocomplete command-line options

  rbuels

  committed
  9621f2c

Commits on Apr 13, 2012

• further move Bio::JBrowse::Script namespace to Bio::JBrowse::Cmd to appease dzil

  rbuels

  committed
  9acfffc

• move Script::* Perl modules into the Bio::JBrowse::Script namespace

  rbuels

  committed
  6a56c1e

Commits on Apr 10, 2012

• change the --cssClass arg to flatfile-to-json.pl to be --className, to match what shows up eventually in the configuration. --cssClass still works though, for backcompat

  rbuels

  committed
  2f1344f

Commits on Apr 6, 2012

• better document --type option to flatfile-to-json.pl

  rbuels

  committed
  2dbf7c6

Commits on Apr 3, 2012

• make perl tests and scripts use a local::lib at extlib/ if present

  rbuels

  committed
  fde4605

Commits on Mar 22, 2012

• fix some misformatting in flatfile-to-json.pl POD

  rbuels

  committed
  6309182

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

  Show description for 5e0feda
  rbuels

  committed
  5e0feda

Commits on Mar 19, 2012

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

  rbuels

  committed
  7524eac

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

  rbuels

  committed
  f5f2389

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

  rbuels

  committed
  ac9613d

Commits on Feb 29, 2012

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

  rbuels

  committed
  cc4b505

Commits on Feb 27, 2012

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

  rbuels

  committed
  add96da

Commits on Feb 23, 2012

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

  rbuels

  committed
  29f9276

Commits on Feb 21, 2012

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

  rbuels

  committed
  aaee552

• 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

  rbuels

  committed
  c4a6a31

Commits on Feb 16, 2012

• add missing use to flatfile-to-json

  rbuels

  committed
  222559c

• remove erroneously-committed Carp::Always line

  rbuels

  committed
  e72f054

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