Hadoop-BAM is a Java library for the manipulation of files in common bioinformatics formats using the Hadoop MapReduce framework

Scala-focused OptionHandlers for args4j

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

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

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

Unit-testing utilities