fixed silent substitutions if the Blocksub is true single nuc
fixed annotation it substritution starts befor the txstart
removed debug printouts, fixed StringIndexOutOfBoundsException for
Blocksubstitutions if the AA stays the same but an extra AA is inserted
added correction for overlapping reference/alternate sequences
formating
increased the version number
fixed variant correction
added annotation shift for the 3'UTR
fixed bug in the GFF (FOR ENSEMBL you have to rebuild the serialized
files!!!)
added flag --create-refseq-c for the removal of predicted transcripts
- addded 3'UTR duplication annotation
- fixed run out of 3'UTR
- fixed bug in interval tree were the median is the point
-increased version number
added test for median/point overlap
- really fixed
Merged in latest code from charite repo