Interface SequencingQcMetricsService

All Known Implementing Classes:

SequencingQcMetricsServiceImpl

public interface SequencingQcMetricsService

Reads the per-sample sequencing QC metrics the RNA-Seq pipeline's MultiQC report carries, and joins them to the experiment's bioAssays.

Read depth is also held on BioAssay itself, but mapping rate, duplication, GC and mismatch rate are only in the report — the schema has nowhere to put them — so the report has to be read either way.

Author:

gembro

See Also:

• SequencingQcMetrics

Method Summary

Modifier and Type	Method	Description
Optional<SequencingQcMetrics>	getSequencingQcMetrics(ExpressionExperiment ee)	Obtain the sequencing QC metrics for an experiment.

Method Details

getSequencingQcMetrics

Optional<SequencingQcMetrics> getSequencingQcMetrics(ExpressionExperiment ee)
                                              throws IOException

Obtain the sequencing QC metrics for an experiment.

The experiment's bioAssays must already be thawed (ExpressionExperimentService.thawBioAssays(ExpressionExperiment)): this reads their accessions and read counts.

Returns:

the metrics, or Optional.empty() when the experiment has neither a MultiQC report nor a read count on any assay, i.e. when there is nothing to show.

Throws:

IOException - if the report exists but cannot be read