proposal for a package htsjdk.tribble.gtf

[lindenb]

Hi all,

here is a proposal for a new package htsjdk.tribble.gtf

Description

htsjdk contains a gff3 codec but is still missing a GTF codec. I wrote a few classes parsing the a GTF. Some parts were copied from the gff3 package.

# constants
src/main/java/htsjdk/tribble/gtf/GtfConstants.java

# an interface describing a GTF record
# it comes with default methods to get the gene_id, gene_name, transcript_id, etc...
src/main/java/htsjdk/tribble/gtf/GtfFeature.java

# an implementation of GtfFeature
src/main/java/htsjdk/tribble/gtf/GtfFeatureImpl.java

# the GTF parser
src/main/java/htsjdk/tribble/gtf/GtfCodec.java 

some tests have been added:

# test the properties of GtfFeature
src/test/java/htsjdk/tribble/gtf/GtfFeatureTest.java

# test the Codec
src/test/java/htsjdk/tribble/gtf/GtfCodecTest.java

and some files for the tests were added too:

./src/test/resources/htsjdk/tribble/gtf/gencode.v43.annotation.gtf
./src/test/resources/htsjdk/tribble/gtf/gencode.vM32.annotation.gtf.gz.tbi
./src/test/resources/htsjdk/tribble/gtf/gencode.vM32.annotation.gtf.gz

Comparaison with the gff3 package:

• some parts were copied from the gff3 package
• for now I want to keep this simple for a first PR, so there is no implementation of the 'tree' building ( chromosme > gene > transcript > exon > etc... )
• I didn't implemented the writer, I didn't fully implemented the UTF-8 escaping...

Things to think about before submitting:

• [X] Make sure your changes compile and new tests pass locally.
• [X] Add new tests or update existing ones:
  • A bug fix should include a test that previously would have failed and passes now.
  • New features should come with new tests that exercise and validate the new functionality.
• [X] Extended the README / documentation, if necessary
• [X] Check your code style.
• [X] Write a clear commit title and message
  • The commit message should describe what changed and is targeted at htsjdk developers
  • Breaking changes should be mentioned in the commit message.