Package picard.illumina
package picard.illumina
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ClassDescriptionBarcodeExtractor is used to match barcodes and collect barcode match metrics.Utility class to hang onto data about the best match for a given barcodeMetrics 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.BasecallsConverter<CLUSTER_OUTPUT_RECORD>BasecallsConverter utilizes an underlying IlluminaDataProvider to convert parsed and decoded sequencing data from standard Illumina formats to specific output records (FASTA records/SAM records).BasecallsConverter.ClusterDataConverter<OUTPUT_RECORD>Interface that defines a converter that takes ClusterData and returns OUTPUT_RECORD type objects.BasecallsConverter.ConvertedClusterDataWriter<OUTPUT_RECORD>Interface that defines a writer that will write out OUTPUT_RECORD type objects.BasecallsConverterBuilder<CLUSTER_OUTPUT_RECORD>BasecallsConverterBuilder creates and configures BasecallsConverter objects.Program to check a lane of an Illumina output directory.Takes ClusterData provided by an IlluminaDataProvider into one or two SAMRecords, as appropriate, and optionally marking adapter sequence.A Command line tool to collect Illumina Basecalling metrics for a sequencing run Requires a Lane and an input file of Barcodes to expect.Command-line wrapper around
CollectIlluminaLaneMetrics.IlluminaLaneMetricsCollector.Utility for collating Tile records from the Illumina TileMetrics file into lane-level and phasing-level metrics.Determine the barcode for each read in an Illumina lane.Extracts barcodes and accumulates metrics for an entire tile.Metric for Illumina Basecalling that stores means and standard deviations on a per-barcode per-lane basis.Simple switch to control the read name format to emit.IlluminaBasecallsToSam transforms a lane of Illumina data file formats (bcl, locs, clocs, qseqs, etc.) into SAM, BAM or CRAM file format.Embodies characteristics that describe a lane.Metrics for Illumina Basecalling that stores median phasing and prephasing percentages on a per-template-read, per-lane basis.Helper class used to transform tile data for a lane into a collection of IlluminaPhasingMetricsCommand line program to mark the location of adapter sequences.SortedBasecallsConverter<CLUSTER_OUTPUT_RECORD>SortedBasecallsConverter utilizes an underlying IlluminaDataProvider to convert parsed and decoded sequencing data from standard Illumina formats to specific output records (FASTA records/SAM records).UnsortedBasecallsConverter<CLUSTER_OUTPUT_RECORD>UnortedBasecallsConverter utilizes an underlying IlluminaDataProvider to convert parsed and decoded sequencing data from standard Illumina formats to specific output records (FASTA records/SAM records).