support for long-read RNA-seq data: funannotate train and funannotate update can take PacBio isoSeq (--pacbio_isoseq), Nanopore cDNA reads (--nanopore_cdna), and Nanopore direct mRNA (--nanopore_mrna). fix for important bug in transcript alignments in funannotate predict -- bug in previous versions related to multi-exon crick alignments not getting correctly parsed into GFF3 alignments soft masking is now decoupled from funannotate predict, this is now done with funannotate mask. Reason for this switch is to allow more flexibility in how the assembly is soft masked -- this can be done externally with another program. This change will allow users that don't have access to RepBase to use an alternative from RepeatMasker/RepeatModeler. One alternative is RED -- I wrote a wrapper for called RedMask funannotate predict can now run without GeneMark being installed -- again to accommodate users that may be unable to use GeneMark due to licensing. Note you can pass gene predictions from any external program to --other_gff and they will be handed off to Evidence Modeler. spaces in either strain or isolate name will be stripped #180 default program for funannotate clean changed to minimap2 #176 fix errors in partial gene models derived from using EVM script to generate proteins, this is now done internally using exact coordinates #184 added --soft_mask option to funannotate predict which will control the option with same name in GeneMark, i.e. default is --soft_mask 5000 which means that repeat regions less than 5 kb will be ignored for GeneMark prediction, those greater than 5 kb will be fed to Genemark. #185 bug fixes for tbl file generation. all tRNA models will be partial #184 improvement to how data from funannotate train is used in prediction steps Slight changes for clarity to funannotate predict flags for evidence alignments:--protein_evidence Proteins to map to genome (prot1.fa prot2.fa uniprot.fa). Default: uniprot.fa --protein_alignments Pre-computed exonerate protein alignments (see docs for format) --transcript_evidence mRNA/ESTs to align to genome (trans1.fa ests.fa trinity.fa). Default: none --transcript_alignments Pre-computed transcript alignments in GFF3 format added funannotate util bam2gff3 script to convert coordsorted RNA-seq BAM alignments to GFF3 compatible alignment file. fix bug for input of files+weight in funannotate predict -- script would get hung up if you passed --other_gff snap_alignemnts.gff3:5 #191 allow for non-standard LocusTags - will now split on last underscore #191