hammerlab/genomic-readsets

Library for representing and working with sets of genomic-sequencing reads, e.g. BAM files.

hammerlab/case-app

Type-level & seamless command-line argument parsing for Scala

hammerlab/test-utils

Unit-testing utilities

hammerlab/args4s

Scala-focused OptionHandlers for args4j

hammerlab/filter-bam

Stand-alone utility for filtering a BAM file to specific genomic regions, using Apache Spark.

hammerlab/genomic-reference

Utilities for representing and working with reference genomes

hammerlab/path-utils

Scala convenience-wrapper for java.nio.file.Path