Reads GATK-style interval list files e.
Represents the mismatches and deletions present in a read that has been aligned to a reference genome.
File that contains a reference assembly that can be broadcasted
Wraps the java Pattern class, to allow for easier regular expression matching (including making the matches/finds methods return Option[Matcher], so that we can flatMap a set of strings with these methods).
Represents a set of reference sequences backed by a .
AttributeUtils is a utility object for parsing optional fields from a BAM file, or the attributes column from an ADAM file.