API reference¶
The API reference is generated from the KDoc comments in the source with
Dokka, and is rebuilt
alongside this site from the current master branch.
Released versions¶
Documentation for each published release is hosted on javadoc.io:
Packages at a glance¶
biokotlin.seq¶
Immutable, type-safe sequences. NucSeq covers DNA and RNA over the full IUPAC
alphabet, ProteinSeq covers peptides, and NucMSA/ProteinMSA represent
multiple sequence alignments. Sequence records (NucSeqRecord,
ProteinSeqRecord) attach identifiers and annotations.
Because sequences are immutable, they are safe to share across threads, and
NucSeq stores unambiguous DNA at two bits per base.
biokotlin.seqIO¶
Reading and writing sequence files. reader() returns a SequenceIterator for
FASTA and FASTQ; NucSeqIO and ProteinSeqIO are the typed entry points, and
GVCFReader walks GVCF records.
biokotlin.featureTree¶
GFF3 parsing into an immutable tree that mirrors the structure genome databases
use: genome → chromosome/scaffold/contig and gene → transcript →
exon, coding sequence, leader, and terminator. Genome.fromFile(path) is the
entry point, and MutableGenome.fromFile(path) gives you an editable copy.
biokotlin.genome¶
Genomic intervals (SRange) with flanking, intersection, and BED helpers;
GenomicFeatures for loading a GFF into a data frame; and MAF tooling for
coverage and identity statistics and for MAFToGVCF conversion.
biokotlin.kmer¶
Two-bit encoded k-mers up to 32 bp. Kmer is a value class over a Long;
KmerSet, KmerMultiSet, and KmerBigSet hold collections at different
size/speed tradeoffs, and KmerIO persists them.
biokotlin.data¶
NCBI genetic code tables. CodonTable(1) or CodonTable("Standard") selects a
table for NucSeq.translate().
biokotlin.util¶
Shared IO helpers (bufferedReader, bufferedWriter) plus VCF and GVCF
utilities used by the tooling in
biokotlin-tools.