Class AbstractMexSingleCellDataLoaderConfigurer
java.lang.Object
ubic.gemma.core.loader.expression.singleCell.AbstractMexSingleCellDataLoaderConfigurer
- All Implemented Interfaces:
DataLoaderConfigurer<MexSingleCellDataLoader,,SingleCellDataLoaderConfig> SingleCellDataLoaderConfigurer<MexSingleCellDataLoader>
- Direct Known Subclasses:
GeoMexSingleCellDataLoaderConfigurer,MexSingleCellDataLoaderConfigurer
public abstract class AbstractMexSingleCellDataLoaderConfigurer
extends Object
implements SingleCellDataLoaderConfigurer<MexSingleCellDataLoader>
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Field Summary
Fields -
Constructor Summary
ConstructorsModifierConstructorDescriptionprotectedAbstractMexSingleCellDataLoaderConfigurer(Path cellRangerPrefix) -
Method Summary
Modifier and TypeMethodDescriptionCreate aDataLoaderfrom the given configuration.protected booleanDetect if a MEX dataset is using the 10x Chromium Sequencing platform.protected abstract Stringdetect10xChemistry(String sampleName, Path sampleDir) Detect the chemistry used by a 10x dataset.protected abstract Stringdetect10xGenome(String sampleName, Path sampleDir) Detect the genome used by a 10x dataset.protected booleandetectUnfiltered(String sampleName, Path sampleDir) Detect if a MEX dataset is unfiltered.
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Field Details
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log
protected final org.apache.commons.logging.Log log
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Constructor Details
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AbstractMexSingleCellDataLoaderConfigurer
- Parameters:
cellRangerPrefix- path to an installation of Cell Ranger, required if 10x filtering is deemed necessary,MexSingleCellDataLoaderConfig.getApply10xFilter().
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Method Details
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configureLoader
Description copied from interface:DataLoaderConfigurerCreate aDataLoaderfrom the given configuration.- Specified by:
configureLoaderin interfaceDataLoaderConfigurer<MexSingleCellDataLoader,SingleCellDataLoaderConfig>
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getSampleNames
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getSampleDirs
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detect10x
Detect if a MEX dataset is using the 10x Chromium Sequencing platform. -
detectUnfiltered
Detect if a MEX dataset is unfiltered. -
detect10xGenome
Detect the genome used by a 10x dataset. -
detect10xChemistry
Detect the chemistry used by a 10x dataset.
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