Create array design (feature) importer for GTF files

[Nicklas Nordborg]

A description of the GTF file format can be found at: ​http://www.ensembl.org/info/website/upload/gff.html

The importer should use "transcript_id" as the feature id. Reporter id is either the "gene_id" or "transcript_id" with an optional prefix (eg. hg19).

[Nicklas Nordborg]

(In [5764]) Fixes #1624: Create array design (feature) importer for GTF files

• Created GtfReporterMapImporter and two configurations that uses transcript_id/gene_id for reporter ids. The GTF importer builds on the ReporterMapFlatFileImporter but has less configuration options. Eg. it is locked to use FEATURE_ID for identifying features.
• Added a new parameter to the regular ReporterMapFlatFileImporter that makes it possible to limit a configuration to certain platforms. This is used to hide genepix, illumina, etc. when using the sequencing platform.
• Added SEQUENCING platform and SEQUENCING_EXPRESSION variant.
• Created a GTF validator that hooks into the fileset validation extension point for array designs and extracts the number of unique transcript_id:s from the GTF file.

[Nicklas Nordborg]

(In [5771]) References #1624: Create array design (feature) importer for GTF files

The default configuration now uses transcript_id@seqname as the reporter and feature id. We discovered that this is needed to make up a unique id for all entries that we want to track in array design features and raw data.

[Nicklas Nordborg]

(In [5772]) References #1624: Create array design (feature) importer for GTF files

Fixed incorrect mapping for reporter id.

[Nicklas Nordborg]

(In [5787]) References #1624: Create array design (feature) importer for GTF files

The importer should not be shared to everyone, since the other array design importers are not.