BioJava

removing dependency that is not needed.

more info in pom

addint release module config

Added support for taking a fasta contig/chromosome file and a fasta gene file where exons are upper case and mapping the genes to chromosome sequences with exon and cds regions. You can then write the chromosome sequence out to a gff3 file.

Modifications to the translation code to increase speed. Also found bugs with stop codon handling

Allowing translations to be case insensitive. Test case also added

Added method setProxySequenceReader and getProxySequenceReader to AbstractSequence to allow lazy instantiation of Sequence class. Checking in the beginning of handling Features with more to come.

Added method setProxySequenceReader and getProxySequenceReader to AbstractSequence to allow lazy instantiation of Sequence class. Checking in the beginning of handling Features with more to come.

updating new Atom nr. to match results after altLocs are being parsed.

making parsing less verbose