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Removing testing scaffolding from delocalized BQSR. The output recal table reports the data as doubles instead of integers. This changes the mapping-based BQSR integration tests. Final intermediate push before delocalized BQSR replaces previous BQSR.

This commit is contained in:
Ryan Poplin 2012-09-19 10:39:06 -04:00
parent f4ac92e95c
commit 0ea543e1fd
3 changed files with 8 additions and 8 deletions
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4
public/java/src/org/broadinstitute/sting/utils/recalibration/RecalDatum.java
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@ -199,11 +199,11 @@ public class RecalDatum {
@Override @Override
public String toString() { public String toString() {
return String.format("%d,%d,%d", Math.round(getNumObservations()), Math.round(getNumMismatches()), (byte) Math.floor(getEmpiricalQuality())); return String.format("%.2f,%,2f,%.2f", getNumObservations(), getNumMismatches(), getEmpiricalQuality());
} }
public String stringForCSV() { public String stringForCSV() {
return String.format("%s,%d,%.2f", toString(), (byte) Math.floor(getEstimatedQReported()), getEmpiricalQuality() - getEstimatedQReported()); return String.format("%s,%.2f,%.2f", toString(), getEstimatedQReported(), getEmpiricalQuality() - getEstimatedQReported());
} }
// /** // /**

8
public/java/src/org/broadinstitute/sting/utils/recalibration/RecalUtils.java
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@ -92,8 +92,8 @@ public class RecalUtils {
private static final Pair<String, String> eventType = new Pair<String, String>(RecalUtils.EVENT_TYPE_COLUMN_NAME, "%s"); private static final Pair<String, String> eventType = new Pair<String, String>(RecalUtils.EVENT_TYPE_COLUMN_NAME, "%s");
private static final Pair<String, String> empiricalQuality = new Pair<String, String>(RecalUtils.EMPIRICAL_QUALITY_COLUMN_NAME, "%.4f"); private static final Pair<String, String> empiricalQuality = new Pair<String, String>(RecalUtils.EMPIRICAL_QUALITY_COLUMN_NAME, "%.4f");
private static final Pair<String, String> estimatedQReported = new Pair<String, String>(RecalUtils.ESTIMATED_Q_REPORTED_COLUMN_NAME, "%.4f"); private static final Pair<String, String> estimatedQReported = new Pair<String, String>(RecalUtils.ESTIMATED_Q_REPORTED_COLUMN_NAME, "%.4f");
private static final Pair<String, String> nObservations = new Pair<String, String>(RecalUtils.NUMBER_OBSERVATIONS_COLUMN_NAME, "%d"); private static final Pair<String, String> nObservations = new Pair<String, String>(RecalUtils.NUMBER_OBSERVATIONS_COLUMN_NAME, "%.2f");
private static final Pair<String, String> nErrors = new Pair<String, String>(RecalUtils.NUMBER_ERRORS_COLUMN_NAME, "%d"); private static final Pair<String, String> nErrors = new Pair<String, String>(RecalUtils.NUMBER_ERRORS_COLUMN_NAME, "%.2f");
/** /**
* Generates two lists : required covariates and optional covariates based on the user's requests. * Generates two lists : required covariates and optional covariates based on the user's requests.
@ -318,8 +318,8 @@ public class RecalUtils {
reportTable.set(rowIndex, columnNames.get(columnIndex++).getFirst(), datum.getEmpiricalQuality()); reportTable.set(rowIndex, columnNames.get(columnIndex++).getFirst(), datum.getEmpiricalQuality());
if (tableIndex == RecalibrationTables.TableType.READ_GROUP_TABLE.index) if (tableIndex == RecalibrationTables.TableType.READ_GROUP_TABLE.index)
reportTable.set(rowIndex, columnNames.get(columnIndex++).getFirst(), datum.getEstimatedQReported()); // we only add the estimated Q reported in the RG table reportTable.set(rowIndex, columnNames.get(columnIndex++).getFirst(), datum.getEstimatedQReported()); // we only add the estimated Q reported in the RG table
reportTable.set(rowIndex, columnNames.get(columnIndex++).getFirst(), Math.round(datum.getNumObservations())); reportTable.set(rowIndex, columnNames.get(columnIndex++).getFirst(), datum.getNumObservations());
reportTable.set(rowIndex, columnNames.get(columnIndex).getFirst(), Math.round(datum.getNumMismatches())); reportTable.set(rowIndex, columnNames.get(columnIndex).getFirst(), datum.getNumMismatches());
rowIndex++; rowIndex++;
} }

4
public/java/src/org/broadinstitute/sting/utils/recalibration/RecalibrationReport.java
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@ -194,8 +194,8 @@ public class RecalibrationReport {
} }
private RecalDatum getRecalDatum(final GATKReportTable reportTable, final int row, final boolean hasEstimatedQReportedColumn) { private RecalDatum getRecalDatum(final GATKReportTable reportTable, final int row, final boolean hasEstimatedQReportedColumn) {
final long nObservations = (Long) reportTable.get(row, RecalUtils.NUMBER_OBSERVATIONS_COLUMN_NAME); final double nObservations = (Double) reportTable.get(row, RecalUtils.NUMBER_OBSERVATIONS_COLUMN_NAME);
final long nErrors = (Long) reportTable.get(row, RecalUtils.NUMBER_ERRORS_COLUMN_NAME); final double nErrors = (Double) reportTable.get(row, RecalUtils.NUMBER_ERRORS_COLUMN_NAME);
final double empiricalQuality = (Double) reportTable.get(row, RecalUtils.EMPIRICAL_QUALITY_COLUMN_NAME); final double empiricalQuality = (Double) reportTable.get(row, RecalUtils.EMPIRICAL_QUALITY_COLUMN_NAME);
// the estimatedQreported column only exists in the ReadGroup table // the estimatedQreported column only exists in the ReadGroup table