diff --git a/public/java/src/org/broadinstitute/sting/gatk/walkers/bqsr/BaseRecalibrator.java b/public/java/src/org/broadinstitute/sting/gatk/walkers/bqsr/BaseRecalibrator.java index e78b9b6fc..ee6a619fd 100755 --- a/public/java/src/org/broadinstitute/sting/gatk/walkers/bqsr/BaseRecalibrator.java +++ b/public/java/src/org/broadinstitute/sting/gatk/walkers/bqsr/BaseRecalibrator.java @@ -179,7 +179,7 @@ public class BaseRecalibrator extends LocusWalker implements TreeRed int numReadGroups = 0; for ( final SAMFileHeader header : getToolkit().getSAMFileHeaders() ) numReadGroups += header.getReadGroups().size(); - recalibrationTables = new RecalibrationTables(requestedCovariates, numReadGroups); + recalibrationTables = new RecalibrationTables(requestedCovariates, numReadGroups, RAC.RECAL_TABLE_UPDATE_LOG); recalibrationEngine = initializeRecalibrationEngine(); recalibrationEngine.initialize(requestedCovariates, recalibrationTables); diff --git a/public/java/src/org/broadinstitute/sting/gatk/walkers/bqsr/RecalibrationArgumentCollection.java b/public/java/src/org/broadinstitute/sting/gatk/walkers/bqsr/RecalibrationArgumentCollection.java index f1f0ce38e..fc7d8a8a4 100755 --- a/public/java/src/org/broadinstitute/sting/gatk/walkers/bqsr/RecalibrationArgumentCollection.java +++ b/public/java/src/org/broadinstitute/sting/gatk/walkers/bqsr/RecalibrationArgumentCollection.java @@ -182,6 +182,10 @@ public class RecalibrationArgumentCollection { @Argument(fullName = "force_platform", shortName = "fP", required = false, doc = "If provided, the platform of EVERY read will be forced to be the provided String. Valid options are illumina, 454, and solid.") public String FORCE_PLATFORM = null; + @Hidden + @Output(fullName = "recal_table_update_log", shortName = "recal_table_update_log", required = false, doc = "If provided, log all updates to the recalibration tables to the given file. For debugging/testing purposes only") + public PrintStream RECAL_TABLE_UPDATE_LOG = null; + public File existingRecalibrationReport = null; public GATKReportTable generateReportTable(final String covariateNames) { diff --git a/public/java/src/org/broadinstitute/sting/utils/collections/LoggingNestedIntegerArray.java b/public/java/src/org/broadinstitute/sting/utils/collections/LoggingNestedIntegerArray.java new file mode 100644 index 000000000..617391714 --- /dev/null +++ b/public/java/src/org/broadinstitute/sting/utils/collections/LoggingNestedIntegerArray.java @@ -0,0 +1,79 @@ +/* + * Copyright (c) 2012 The Broad Institute + * + * Permission is hereby granted, free of charge, to any person + * obtaining a copy of this software and associated documentation + * files (the "Software"), to deal in the Software without + * restriction, including without limitation the rights to use, + * copy, modify, merge, publish, distribute, sublicense, and/or sell + * copies of the Software, and to permit persons to whom the + * Software is furnished to do so, subject to the following + * conditions: + * + * The above copyright notice and this permission notice shall be + * included in all copies or substantial portions of the Software. + * + * THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, + * EXPRESS OR IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES + * OF MERCHANTABILITY, FITNESS FOR A PARTICULAR PURPOSE AND + * NONINFRINGEMENT. IN NO EVENT SHALL THE AUTHORS OR COPYRIGHT + * HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER LIABILITY, + * WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING + * FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR + * THE USE OR OTHER DEALINGS IN THE SOFTWARE. + */ + +package org.broadinstitute.sting.utils.collections; + +import org.broadinstitute.sting.utils.exceptions.ReviewedStingException; + +import java.io.PrintStream; + +/** + * Wrapper around the basic NestedIntegerArray class that logs all updates (ie., all calls to put()) + * to the provided output stream. For testing/debugging purposes. + * + * Log entries are of the following form (fields are tab-separated): + * LABEL VALUE KEY1 KEY2 ... KEY_N + * + * @author David Roazen + */ +public class LoggingNestedIntegerArray extends NestedIntegerArray { + + private PrintStream log; + private String logEntryLabel; + + /** + * + * @param log output stream to which to log update operations + * @param logEntryLabel String that should be prefixed to each log entry + * @param dimensions + */ + public LoggingNestedIntegerArray( PrintStream log, String logEntryLabel, final int... dimensions ) { + super(dimensions); + + if ( log == null ) { + throw new ReviewedStingException("Log output stream must not be null"); + } + this.log = log; + this.logEntryLabel = logEntryLabel != null ? logEntryLabel : ""; + } + + @Override + public void put( final T value, final int... keys ) { + super.put(value, keys); + + StringBuilder logEntry = new StringBuilder(); + + logEntry.append(logEntryLabel); + logEntry.append("\t"); + logEntry.append(value); + for ( int key : keys ) { + logEntry.append("\t"); + logEntry.append(key); + } + + // PrintStream methods all use synchronized blocks internally, so our logging is thread-safe + log.println(logEntry.toString()); + } +} diff --git a/public/java/src/org/broadinstitute/sting/utils/recalibration/RecalibrationTables.java b/public/java/src/org/broadinstitute/sting/utils/recalibration/RecalibrationTables.java index afc8f5065..0dd510245 100644 --- a/public/java/src/org/broadinstitute/sting/utils/recalibration/RecalibrationTables.java +++ b/public/java/src/org/broadinstitute/sting/utils/recalibration/RecalibrationTables.java @@ -25,9 +25,12 @@ package org.broadinstitute.sting.utils.recalibration; +import org.broadinstitute.sting.utils.collections.LoggingNestedIntegerArray; import org.broadinstitute.sting.utils.recalibration.covariates.Covariate; import org.broadinstitute.sting.utils.collections.NestedIntegerArray; +import java.io.PrintStream; + /** * Utility class to facilitate on-the-fly base quality score recalibration. * @@ -52,19 +55,31 @@ public class RecalibrationTables { private final NestedIntegerArray[] tables; public RecalibrationTables(final Covariate[] covariates) { - this(covariates, covariates[TableType.READ_GROUP_TABLE.index].maximumKeyValue() + 1); + this(covariates, covariates[TableType.READ_GROUP_TABLE.index].maximumKeyValue() + 1, null); + } + + public RecalibrationTables(final Covariate[] covariates, final PrintStream log) { + this(covariates, covariates[TableType.READ_GROUP_TABLE.index].maximumKeyValue() + 1, log); } public RecalibrationTables(final Covariate[] covariates, final int numReadGroups) { + this(covariates, numReadGroups, null); + } + + public RecalibrationTables(final Covariate[] covariates, final int numReadGroups, final PrintStream log) { tables = new NestedIntegerArray[covariates.length]; final int qualDimension = covariates[TableType.QUALITY_SCORE_TABLE.index].maximumKeyValue() + 1; final int eventDimension = EventType.values().length; - tables[TableType.READ_GROUP_TABLE.index] = new NestedIntegerArray(numReadGroups, eventDimension); - tables[TableType.QUALITY_SCORE_TABLE.index] = new NestedIntegerArray(numReadGroups, qualDimension, eventDimension); + tables[TableType.READ_GROUP_TABLE.index] = log == null ? new NestedIntegerArray(numReadGroups, eventDimension) : + new LoggingNestedIntegerArray(log, "READ_GROUP_TABLE", numReadGroups, eventDimension); + tables[TableType.QUALITY_SCORE_TABLE.index] = log == null ? new NestedIntegerArray(numReadGroups, qualDimension, eventDimension) : + new LoggingNestedIntegerArray(log, "QUALITY_SCORE_TABLE", numReadGroups, qualDimension, eventDimension); for (int i = TableType.OPTIONAL_COVARIATE_TABLES_START.index; i < covariates.length; i++) - tables[i] = new NestedIntegerArray(numReadGroups, qualDimension, covariates[i].maximumKeyValue()+1, eventDimension); + tables[i] = log == null ? new NestedIntegerArray(numReadGroups, qualDimension, covariates[i].maximumKeyValue()+1, eventDimension) : + new LoggingNestedIntegerArray(log, String.format("OPTIONAL_COVARIATE_TABLE_%d", i - TableType.OPTIONAL_COVARIATE_TABLES_START.index + 1), + numReadGroups, qualDimension, covariates[i].maximumKeyValue()+1, eventDimension); } public NestedIntegerArray getReadGroupTable() {