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busco internal run now uses the local augustus config path, so hopefully write access to $AUGUSTUS_CONFIG_PATH is no longer required
long reads are now processed to remove forward slashes from names if present -- this was causing problems with PASA #326#250
added augustus hints file generation when using RNA-seq data. Also added a check for --transcript_evidence if found in --transcript_alignments, ie so extra transcripts can be added instead of only those used to generate alignments in funannotate train. #360
fix typo in funannotate check
fix for proteinortho issue in funannotate compare#350