Package org.broadinstitute.gatk.utils.recalibration

Examples of org.broadinstitute.gatk.utils.recalibration.RecalibrationReport

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     */
    @Requires("reportFileMap != null")
    private Map<String, RecalibrationReport> buildReportMap(final Map<String, File> reportFileMap) {
        final Map<String,RecalibrationReport> reports = new LinkedHashMap<>(reportFileMap.size());
        for (final Map.Entry<String,File> e : reportFileMap.entrySet()) {
            reports.put(e.getKey(),new RecalibrationReport(e.getValue()));
        }
        return reports;
    }
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                    logger.info("  " + readGroup);
                }
            }
        }

        RecalibrationReport generalReport = null;
        for (File input : inputs) {
            final RecalibrationReport inputReport = new RecalibrationReport(input, allReadGroups);
            if( inputReport.isEmpty() ) { continue; }

            if (generalReport == null)
                generalReport = inputReport;
            else
                generalReport.combine(inputReport);
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Related Classes of org.broadinstitute.gatk.utils.recalibration.RecalibrationReport

  • org.broadinstitute.gatk.engine.report.GATKReport
  • org.broadinstitute.gatk.engine.report.GATKReportTable
  • org.broadinstitute.gatk.tools.walkers.bqsr.AnalyzeCovariates
  • org.broadinstitute.gatk.tools.walkers.bqsr.BQSRGatherer
  • org.broadinstitute.gatk.tools.walkers.bqsr.RecalibrationArgumentCollection
  • org.broadinstitute.gatk.utils.exceptions.ReviewedGATKException
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