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Misc cleanup

This commit is contained in:
Eric Banks 2012-06-15 10:39:19 -04:00
parent 0c218e4822
commit 783b7f6899
1 changed files with 1 additions and 6 deletions
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7
public/java/src/org/broadinstitute/sting/utils/recalibration/BaseRecalibration.java
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@ -44,9 +44,7 @@ public class BaseRecalibration {
private final static int MAXIMUM_RECALIBRATED_READ_LENGTH = 5000; private final static int MAXIMUM_RECALIBRATED_READ_LENGTH = 5000;
private final ReadCovariates readCovariates; private final ReadCovariates readCovariates;
private final QuantizationInfo quantizationInfo; // histogram containing the map for qual quantization (calculated after recalibration is done) private final QuantizationInfo quantizationInfo; // histogram containing the map for qual quantization (calculated after recalibration is done)
private final LinkedHashMap<BQSRKeyManager, Map<Long, RecalDatum>> keysAndTablesMap; // quick access reference to the read group table and its key manager
private final KeysAndTables keysAndTables; private final KeysAndTables keysAndTables;
private final Covariate[] requestedCovariates; // list of all covariates to be used in this calculation private final Covariate[] requestedCovariates; // list of all covariates to be used in this calculation
@ -80,7 +78,6 @@ public class BaseRecalibration {
tables[type.index] = mapEntry.getValue(); tables[type.index] = mapEntry.getValue();
} }
} }
} }
/** /**
@ -92,8 +89,7 @@ public class BaseRecalibration {
public BaseRecalibration(final File RECAL_FILE, int quantizationLevels) { public BaseRecalibration(final File RECAL_FILE, int quantizationLevels) {
RecalibrationReport recalibrationReport = new RecalibrationReport(RECAL_FILE); RecalibrationReport recalibrationReport = new RecalibrationReport(RECAL_FILE);
keysAndTablesMap = recalibrationReport.getKeysAndTablesMap(); keysAndTables = new KeysAndTables(recalibrationReport.getKeysAndTablesMap());
keysAndTables = new KeysAndTables(keysAndTablesMap);
requestedCovariates = recalibrationReport.getRequestedCovariates(); requestedCovariates = recalibrationReport.getRequestedCovariates();
quantizationInfo = recalibrationReport.getQuantizationInfo(); quantizationInfo = recalibrationReport.getQuantizationInfo();
if (quantizationLevels == 0) // quantizationLevels == 0 means no quantization, preserve the quality scores if (quantizationLevels == 0) // quantizationLevels == 0 means no quantization, preserve the quality scores
@ -113,7 +109,6 @@ public class BaseRecalibration {
*/ */
protected BaseRecalibration(final QuantizationInfo quantizationInfo, final LinkedHashMap<BQSRKeyManager, Map<Long, RecalDatum>> keysAndTablesMap, final Covariate[] requestedCovariates) { protected BaseRecalibration(final QuantizationInfo quantizationInfo, final LinkedHashMap<BQSRKeyManager, Map<Long, RecalDatum>> keysAndTablesMap, final Covariate[] requestedCovariates) {
this.quantizationInfo = quantizationInfo; this.quantizationInfo = quantizationInfo;
this.keysAndTablesMap = keysAndTablesMap;
keysAndTables = new KeysAndTables(keysAndTablesMap); keysAndTables = new KeysAndTables(keysAndTablesMap);
this.requestedCovariates = requestedCovariates; this.requestedCovariates = requestedCovariates;
readCovariates = new ReadCovariates(MAXIMUM_RECALIBRATED_READ_LENGTH, requestedCovariates.length); readCovariates = new ReadCovariates(MAXIMUM_RECALIBRATED_READ_LENGTH, requestedCovariates.length);