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justaddcoffee

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Commits on Jul 22, 2013

• changed regex to match either join or complement for coordinates while doing Genbank parsing

  justaddcoffee

  committed
  5c6ebc6

• changed regex to match either join or complement for coordinates while doing Genbank parsing

  justaddcoffee

  committed
  962dc32

• fixed tests for type feature in Genbank file parsing, removed garbage attributes from parsed Genbank JSON

  justaddcoffee

  committed
  c408c2c

• added a few more test fixtures for Genbank file parsing

  justaddcoffee

  committed
  5059833

• added a few more test fixtures for Genbank file parsing

  justaddcoffee

  committed
  4d99842

Commits on Jul 16, 2013

• added tests/code to set type in features/subfeatures in parsed Genbank JSON

  justaddcoffee

  committed
  5be9582

• moved code to calculate offset for region GBK files to a separate method, for tidiness

  justaddcoffee

  committed
  7e0dc62

• added tests/code to support Genbank files describing subregions of chromosomes

  justaddcoffee

  committed
  e3b3330

• changed JSON in parsed Genbank records so attributes with no value are marked 'null'

  justaddcoffee

  committed
  daa1a2e

• added tests for setting coordinates correctly when parsing Genbank records that are partial records from a chromosome (basically just need to add a number to the feature coordinates corresponding t…

  Show description for 7e1e167
  justaddcoffee

  committed
  7e1e167

• added code to pass test for setting custom type via commandline in flatfile-to-json.pl

  justaddcoffee

  committed
  ec94f45

• added test for setting track type via commandline flag in flatfile-to-json.pl (not passing)

  justaddcoffee

  committed
  30581f2

Commits on Jul 15, 2013

• added tests and code to check subfeatures in JSON after Genbank parsing

  justaddcoffee

  committed
  b3316ff

• added tests for subfeatures in Genbank parsing

  justaddcoffee

  committed
  b77acec

• fixed unit test for subfeatures in Genbank parsing

  justaddcoffee

  committed
  7352b94

• added trivial subfeatures to pass subfeature test in Benbank.pm

  justaddcoffee

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  8d0cc5c

• removed diag from cssName test

  justaddcoffee

  committed
  755a94a

• added test for setting of default and custom cssName

  justaddcoffee

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  b0dda64

• added (failing) test for setting of subfeatures when parsing Genbank files

  justaddcoffee

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  03fff41

• merged with branch

  justaddcoffee

  committed
  402763b

• added tests/code for attributes being set correctly in Genbank parsed JSON

  justaddcoffee

  committed
  cc97d81

• added code to pass test for correct setting of start/stop

  justaddcoffee

  committed
  cf11b96

• added (another) fix to GenBankParser.pm to fix parsing of coordinates, which was broken because Genbank starting inserting newlines inside of join tokens.

  justaddcoffee

  committed
  e7fe333

• added (another) fix to GenBankParser.pm to fix parsing of coordinates, which was broken because Genbank starting inserting newlines inside of join tokens.

  justaddcoffee

  committed
  7152bf8

• added (another) fix to GenBankParser.pm to fix parsing of coordinates, which was broken because Genbank starting inserting newlines inside of join tokens.

  justaddcoffee

  committed
  bde127c

• added tests for start/end of Genbank parsed features, and cheat code to pass test

  justaddcoffee

  committed
  952161f

Commits on Jul 11, 2013

• merged

  justaddcoffee

  committed
  be8d845

• fixed test for parsing of attributes in gbk files to include some stuff I was manually deleting before - for now I'm just going to put everything into the JSON, need to confer with Rob/Gregg to dec…

  Show description for 825fc32
  justaddcoffee

  committed
  825fc32

• added test for correct attributes in genbank file parsing

  justaddcoffee

  committed
  12c8269

• fixed GenBankParser - this parser was written in 2008, and it looks like many keywords changed.

  justaddcoffee

  committed
  4a02c70

Commits on Jul 10, 2013

• added module required by GenBankParser.pm (Readonly.pm)

  justaddcoffee

  committed
  148a0cc

• trivial edit to comments in Genbank.pm

  justaddcoffee

  committed
  2f5aa3c

• changed stuff in flatfile-to-json.pm to accept --gbk flag

  justaddcoffee

  committed
  b165218

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

  justaddcoffee

  committed
  4034b63

Commits on Dec 15, 2012

• gff3 inloading: added tests and code for multiple mRNAs

  justaddcoffee

  committed
  b7cca3f

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