| BarcodeExtractor |
BarcodeExtractor is used to match barcodes and collect barcode match metrics.
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| BarcodeExtractor.BarcodeMatch |
Utility class to hang onto data about the best match for a given barcode
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| 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.
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| 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).
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| BasecallsConverterBuilder<CLUSTER_OUTPUT_RECORD> |
BasecallsConverterBuilder creates and configures BasecallsConverter objects.
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| CheckIlluminaDirectory |
Program to check a lane of an Illumina output directory.
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| ClusterDataToSamConverter |
Takes ClusterData provided by an IlluminaDataProvider into one or two SAMRecords,
as appropriate, and optionally marking adapter sequence.
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| 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.
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| CollectIlluminaLaneMetrics |
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| CollectIlluminaLaneMetrics.IlluminaLaneMetricsCollector |
Utility for collating Tile records from the Illumina TileMetrics file into lane-level and phasing-level metrics.
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| ExtractBarcodesProgram |
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| ExtractIlluminaBarcodes |
Determine the barcode for each read in an Illumina lane.
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| ExtractIlluminaBarcodes.PerTileBarcodeExtractor |
Extracts barcodes and accumulates metrics for an entire tile.
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| IlluminaBasecallingMetrics |
Metric for Illumina Basecalling that stores means and standard deviations on a per-barcode per-lane basis.
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| IlluminaBasecallsToFastq |
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| IlluminaBasecallsToSam |
IlluminaBasecallsToSam transforms a lane of Illumina data file formats (bcl, locs, clocs, qseqs, etc.) into
SAM, BAM or CRAM file format.
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| IlluminaLaneMetrics |
Embodies characteristics that describe a lane.
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| IlluminaPhasingMetrics |
Metrics for Illumina Basecalling that stores median phasing and prephasing percentages on a per-template-read, per-lane basis.
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| LanePhasingMetricsCollector |
Helper class used to transform tile data for a lane into a collection of IlluminaPhasingMetrics
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| MarkIlluminaAdapters |
Command line program to mark the location of adapter sequences.
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| 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).
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| 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).
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