GetLibrary returns the library for the given record's read group.

GetR1R2Orientation returns an orientation byte containing orientations for both R1 and R2.

NewTestOutput returns different string filename for the different output formats.

ParseLocation returns a physical location given an Illumina style read name.

ReadRecords reads the records from path and returns them as a slice, in order.

SetupAndMark does some minimal setup for validating opts, and creating provider and then runs mark().

IlluminaReadName5Fields is the number of columns in a 5 field read name.

IlluminaReadName5FieldsTileField is 0-based field number that contains the tileName for 5 field read names.

IlluminaReadName7Fields is the number of columns in a 5 field read name.

IlluminaReadName7FieldsTileField is 0-based field number that contains the tileName for 7 field read names.

IlluminaReadName8Fields is the number of columns in a 5 field read name.

IlluminaReadName8FieldsTileField is 0-based field number that contains the tileName for 8 field read names.

MarkDuplicates implements duplicate marking.

Metrics contains metrics from mark duplicates.

MetricsCollection contains metrics computed by Mark.

Opts for mark-duplicates.

PhysicalLocation describes a read's physical location on the flow cell.

TileOpticalDetector detects optical duplicates with a tile.

BagProcessorFactory creates BagProcessors.

OpticalDetector is a general interface for optical duplicate detection.

BagProcessor takes the set of bags from a particular shard, and returns the same set of reads, but the reads may now be bagged differently.