Nucleotide
,DNANucleotide
andRNANucleotide
are renamed toNucleicAcid
,DNA
andRNA
, 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 theeachoverlap
function exported fromBio.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
andAminoAcid
) are moved to BioSymbols.jl and re-exported fromBio.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)