This release contains the following changes:
- now GFF3 toolkit supports Windows 41 and Mac 48 as well
- add a new argument for gff3_merge, `--all` 35
- `--all:` auto-assignment replace tags for all transcript features. (default: Only automatically assign replace tags for the transcript without replace tags)
- add new arguments for gff3_sort, `--sort_template` and `--isoform_sort` 38
- `--sort_template`: A file that indicates the sorting order of features within a gene model
- `--isoform`: Sort multi-isoform gene models by feature type (default: False)
- add new argument for gff3_to_fastsa, `--embedded_fasta` 39
- `--embedded_fasta`: Specify this option if you want to extract sequence from embedded fasta.
- remove old APIs 46
Bug fixes:
- fixed a bug in which gff3_fix failed if the phase of the first CDS is missing. Set the initial phase as 0, if phase missing. 40
- fixed a bug in which gff3_merge only gets the user-defined transcripts from -u1 file. Now, it will get the user-defined transcripts from both -u1 and -u2 files.
- fixed a bug in which gff3_to_fasta failed if the input gff3 file pass all the QC check without detecting any formatting error.