hammerlab/genomic-utils

Name: genomic-utils

Owner: Hammer Lab

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

Created: 2016-12-10 17:02:27.0

Updated: 2016-12-10 17:28:40.0

Pushed: 2018-01-13 21:06:19.0

Homepage: null

Size: 29

Language: Scala

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README

genomic-utils

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.