| Class | Description |
|---|---|
| CheckIlluminaDirectory |
Program to check a lane of an Illumina output directory.
|
| ClusterDataToSamConverter |
Takes ClusterData provided by an IlluminaDataProvider into one or two SAMRecords,
as appropriate, and optionally marking adapter sequence.
|
| CollectIlluminaBasecallingMetrics |
A Command line tool to collect Illumina Basecalling metrics for a sequencing run
Requires a Lane and an input file of Barcodes to expect.
|
| CollectIlluminaLaneMetrics |
Command-line wrapper around
CollectIlluminaLaneMetrics.IlluminaLaneMetricsCollector. |
| CollectIlluminaLaneMetrics.IlluminaLaneMetricsCollector |
Utility for collating Tile records from the Illumina TileMetrics file into lane-level and phasing-level metrics.
|
| ExtractIlluminaBarcodes |
Determine the barcode for each read in an Illumina lane.
|
| ExtractIlluminaBarcodes.BarcodeMetric |
Metrics produced by the ExtractIlluminaBarcodes program that is used to parse data in
the basecalls directory and determine to which barcode each read should be assigned.
|
| ExtractIlluminaBarcodes.PerTileBarcodeExtractor |
Extracts barcodes and accumulates metrics for an entire tile.
|
| ExtractIlluminaBarcodes.PerTileBarcodeExtractor.BarcodeMatch |
Utility class to hang onto data about the best match for a given barcode
|
| IlluminaBasecallingMetrics |
Metric for Illumina Basecalling that stores means and standard deviations on a per-barcode per-lane basis.
|
| IlluminaBasecallsConverter<CLUSTER_OUTPUT_RECORD> |
Manages the conversion of Illumina basecalls into some output format.
|
| IlluminaBasecallsToFastq | |
| IlluminaBasecallsToSam |
IlluminaBasecallsToSam transforms a lane of Illumina data file formats (bcl, locs, clocs, qseqs, etc.) into
SAM or BAM file format.
|
| IlluminaLaneMetrics |
Embodies characteristics that describe a lane.
|
| IlluminaPhasingMetrics |
Metrics for Illumina Basecalling that stores median phasing and prephasing percentages on a per-template-read, per-lane basis.
|
| LanePhasingMetricsCollector |
Helper class used to transform tile data for a lane into a collection of IlluminaPhasingMetrics
|
| MarkIlluminaAdapters |
Command line program to mark the location of adapter sequences.
|
| NewIlluminaBasecallsConverter<CLUSTER_OUTPUT_RECORD> |
| Enum | Description |
|---|---|
| DistanceMetric | |
| IlluminaBasecallsToFastq.ReadNameFormat |
Simple switch to control the read name format to emit.
|