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@hsiaoyi0504 hsiaoyi0504 released this 23 Jul 22:54
· 228 commits to master since this release
v1.4.1
7b81684

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.
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