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NEWS.md

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Bio.jl v0.5.0 Release Notes

  • Nucleotide, DNANucleotide and RNANucleotide are renamed to NucleicAcid, DNA and RNA, respectively (#391).
  • Support VCF and BCF file formats (#378).
  • Support APIs for Entrez Programming Utilities (#350).
  • Support GFF3 file format (#138).
  • Support BigWig file format (#352, #452).
  • Sequence names are ordered lexicographically by default (#291).
  • Computing genomic distances using the MASH algorithm is introduced (#415).
  • New FASTQ reader does not support multiline sequence and quality (#448).
  • IO APIs are reorganized into submodules:
    • Bio.Seq.FASTAReader => Bio.Seq.FASTA.Reader (#413).
    • Bio.Seq.FASTQReader => Bio.Seq.FASTQ.Reader (#448).
    • Bio.Seq.TwoBitReader => Bio.Seq.TwoBit.Reader (#431).
    • Bio.Intervals.BEDReader => Bio.Intervals.BED.Reader (#418).
    • Bio.Intervals.BigBedReader => Bio.Intervals.BigBed.Reader (#452)
    • Bio.Align.SAMReader => Bio.Align.SAM.Reader (#440)
    • Bio.Align.BAMReader => Bio.Align.BAM.Reader (#440)
  • Overloaded Base.intersect methods for intervals are removed. Use the eachoverlap function exported from Bio.Intervals instead (#426).
  • A reader for the ABIF format by Applied Biosystems is introduced (#353).
  • Newlines are removed by default when printing a long sequence (#441).
  • Definitions of biological symbols (DNA, RNA and AminoAcid) are moved to BioSymbols.jl and re-exported from Bio.Seq (#443).
  • Definitions of types and methods in Bio.Phylo have been moved to [Phylogenies.jl], and re-exported from Bio.Phylo (#438).
  • Add a macro that enables writing kmers as string literals (kmer"ACGT"; #446)