changed MySQL db connections to use .my.cnf instead of passwords
Rewrite of Grch37LiteGaf and addition of GTF code for generating GAF4 from input gencode gtf. gtfToGAF.py replaces makeGeneSet.py, makeTranscriptSet.py and makeExonSet.py
fixed mislabeled featureCoordinates and compositeCoordinates
removed redundant header
removed obsolete defs; corrected gtf tag parsing; removed chrY PARs from output
removed bug that only printed exons of last transcripts to the exon.genome file; removed duplicate exons
added capability to create junctions from GTF
changed MySql authorization method
unfinished code for converting gaf to valid GTF:minus strand split starts and stops have not been added
added split starts and stops for min strand using newly defined functions. Must rework plus strand splits to do the same
reworked plus strand split starts and stops to separate functions
fixed issues with incomplete transcripts. These now create warnings in the output GAF, which can then be used to correct reading frame in gafToGtf.py
added featureToComposite output; renamed and uniquefied junctions
added RefSeqs to FeatureInfo field
split gafToGtf.py into program and functions
changed feature info for junctions
added RefSeq IDs; fixed bug that resulted in different numbers of exonStarts and exonEnds in genes
added gene info to junction_transcript gaf; cleaned up how the script deals with empty gene objects
added option to allow complete blocks only, needed for mapping exons to genes
final polishing of GAF4.0 scripts