hammerlab / genomic-utils

Utilities for working with genomic bases, cigar strings, and phred scores.

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genomic-utils

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Utilities for working with genomic bases, cigar strings, and phred scores.

  • Bases wraps a Vector[Base], and implements BasesBuffer, with Int length
    • well-suited for sub-contig-sized genomic-sequences, e.g. reads.
  • BasesBuffer is a more general interface that can also be implemented for contig-sized sequences (often with Long length); see Contig.
  • Base wraps a Byte, and only a maximum of 5 are instantiated (A, C, G, T, and N).
  • All "wrapping" referenced above uses value classes and carries no run-time cost.