diff --git a/protected/java/src/org/broadinstitute/sting/gatk/walkers/bqsr/AdvancedRecalibrationEngine.java b/protected/java/src/org/broadinstitute/sting/gatk/walkers/bqsr/AdvancedRecalibrationEngine.java index 9eca81852..d714ca185 100644 --- a/protected/java/src/org/broadinstitute/sting/gatk/walkers/bqsr/AdvancedRecalibrationEngine.java +++ b/protected/java/src/org/broadinstitute/sting/gatk/walkers/bqsr/AdvancedRecalibrationEngine.java @@ -25,10 +25,14 @@ package org.broadinstitute.sting.gatk.walkers.bqsr; * OTHER DEALINGS IN THE SOFTWARE. */ +import org.broadinstitute.sting.utils.recalibration.covariates.Covariate; import org.broadinstitute.sting.utils.BaseUtils; import org.broadinstitute.sting.utils.classloader.ProtectedPackageSource; import org.broadinstitute.sting.utils.collections.NestedIntegerArray; import org.broadinstitute.sting.utils.pileup.PileupElement; +import org.broadinstitute.sting.utils.recalibration.EventType; +import org.broadinstitute.sting.utils.recalibration.ReadCovariates; +import org.broadinstitute.sting.utils.recalibration.RecalDatum; import org.broadinstitute.sting.utils.recalibration.RecalibrationTables; public class AdvancedRecalibrationEngine extends StandardRecalibrationEngine implements ProtectedPackageSource { diff --git a/protected/java/src/org/broadinstitute/sting/gatk/walkers/compression/reducereads/SyntheticRead.java b/protected/java/src/org/broadinstitute/sting/gatk/walkers/compression/reducereads/SyntheticRead.java index 9ee1a4634..3b9fc0390 100644 --- a/protected/java/src/org/broadinstitute/sting/gatk/walkers/compression/reducereads/SyntheticRead.java +++ b/protected/java/src/org/broadinstitute/sting/gatk/walkers/compression/reducereads/SyntheticRead.java @@ -5,7 +5,7 @@ import net.sf.samtools.Cigar; import net.sf.samtools.CigarElement; import net.sf.samtools.CigarOperator; import net.sf.samtools.SAMFileHeader; -import org.broadinstitute.sting.gatk.walkers.bqsr.EventType; +import org.broadinstitute.sting.utils.recalibration.EventType; import org.broadinstitute.sting.utils.MathUtils; import org.broadinstitute.sting.utils.exceptions.ReviewedStingException; import org.broadinstitute.sting.utils.sam.GATKSAMReadGroupRecord; diff --git a/public/java/src/org/broadinstitute/sting/gatk/walkers/bqsr/BQSRGatherer.java b/public/java/src/org/broadinstitute/sting/gatk/walkers/bqsr/BQSRGatherer.java index 122958ac2..a6d82d5b3 100755 --- a/public/java/src/org/broadinstitute/sting/gatk/walkers/bqsr/BQSRGatherer.java +++ b/public/java/src/org/broadinstitute/sting/gatk/walkers/bqsr/BQSRGatherer.java @@ -28,6 +28,8 @@ package org.broadinstitute.sting.gatk.walkers.bqsr; import org.broadinstitute.sting.commandline.Gatherer; import org.broadinstitute.sting.utils.exceptions.ReviewedStingException; import org.broadinstitute.sting.utils.exceptions.UserException; +import org.broadinstitute.sting.utils.recalibration.RecalUtils; +import org.broadinstitute.sting.utils.recalibration.RecalibrationReport; import java.io.File; import java.io.FileNotFoundException; @@ -71,11 +73,11 @@ public class BQSRGatherer extends Gatherer { if (RAC.recalibrationReport != null && !RAC.NO_PLOTS) { final File recal_out = new File(output.getName() + ".original"); final RecalibrationReport originalReport = new RecalibrationReport(RAC.recalibrationReport); - RecalDataManager.generateRecalibrationPlot(recal_out, originalReport.getRecalibrationTables(), generalReport.getRecalibrationTables(), generalReport.getCovariates(), RAC.KEEP_INTERMEDIATE_FILES); + RecalUtils.generateRecalibrationPlot(recal_out, originalReport.getRecalibrationTables(), generalReport.getRecalibrationTables(), generalReport.getCovariates(), RAC.KEEP_INTERMEDIATE_FILES); } else if (!RAC.NO_PLOTS) { final File recal_out = new File(output.getName() + ".recal"); - RecalDataManager.generateRecalibrationPlot(recal_out, generalReport.getRecalibrationTables(), generalReport.getCovariates(), RAC.KEEP_INTERMEDIATE_FILES); + RecalUtils.generateRecalibrationPlot(recal_out, generalReport.getRecalibrationTables(), generalReport.getCovariates(), RAC.KEEP_INTERMEDIATE_FILES); } generalReport.output(outputFile); 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 b2400a49d..e95a0e6c1 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 @@ -34,6 +34,7 @@ import org.broadinstitute.sting.gatk.filters.MappingQualityUnavailableFilter; import org.broadinstitute.sting.gatk.filters.MappingQualityZeroFilter; import org.broadinstitute.sting.gatk.refdata.RefMetaDataTracker; import org.broadinstitute.sting.gatk.walkers.*; +import org.broadinstitute.sting.utils.recalibration.covariates.Covariate; import org.broadinstitute.sting.utils.baq.BAQ; import org.broadinstitute.sting.utils.classloader.GATKLiteUtils; import org.broadinstitute.sting.utils.collections.Pair; @@ -41,6 +42,9 @@ import org.broadinstitute.sting.utils.exceptions.ReviewedStingException; import org.broadinstitute.sting.utils.exceptions.UserException; import org.broadinstitute.sting.utils.help.DocumentedGATKFeature; import org.broadinstitute.sting.utils.pileup.PileupElement; +import org.broadinstitute.sting.utils.recalibration.QuantizationInfo; +import org.broadinstitute.sting.utils.recalibration.RecalUtils; +import org.broadinstitute.sting.utils.recalibration.RecalibrationReport; import org.broadinstitute.sting.utils.recalibration.RecalibrationTables; import org.broadinstitute.sting.utils.sam.GATKSAMRecord; import org.broadinstitute.sting.utils.sam.ReadUtils; @@ -109,7 +113,7 @@ public class BaseRecalibrator extends LocusWalker implements TreeRed @ArgumentCollection private final RecalibrationArgumentCollection RAC = new RecalibrationArgumentCollection(); // all the command line arguments for BQSR and it's covariates - private QuantizationInfo quantizationInfo; // an object that keeps track of the information necessary for quality score quantization + private QuantizationInfo quantizationInfo; // an object that keeps track of the information necessary for quality score quantization private RecalibrationTables recalibrationTables; @@ -143,12 +147,12 @@ public class BaseRecalibrator extends LocusWalker implements TreeRed throw new UserException.CommandLineException(NO_DBSNP_EXCEPTION); if (RAC.LIST_ONLY) { - RecalDataManager.listAvailableCovariates(logger); + RecalUtils.listAvailableCovariates(logger); System.exit(0); } RAC.recalibrationReport = getToolkit().getArguments().BQSR_RECAL_FILE; // if we have a recalibration file, record it so it goes on the report table - Pair, ArrayList> covariates = RecalDataManager.initializeCovariates(RAC); // initialize the required and optional covariates + Pair, ArrayList> covariates = RecalUtils.initializeCovariates(RAC); // initialize the required and optional covariates ArrayList requiredCovariates = covariates.getFirst(); ArrayList optionalCovariates = covariates.getSecond(); @@ -222,17 +226,17 @@ public class BaseRecalibrator extends LocusWalker implements TreeRed if (readNotSeen(read)) { read.setTemporaryAttribute(SEEN_ATTRIBUTE, true); - RecalDataManager.parsePlatformForRead(read, RAC); - if (RecalDataManager.isColorSpaceConsistent(RAC.SOLID_NOCALL_STRATEGY, read)) { + RecalUtils.parsePlatformForRead(read, RAC); + if (RecalUtils.isColorSpaceConsistent(RAC.SOLID_NOCALL_STRATEGY, read)) { read.setTemporaryAttribute(SKIP_RECORD_ATTRIBUTE, true); continue; } - read.setTemporaryAttribute(COVARS_ATTRIBUTE, RecalDataManager.computeCovariates(read, requestedCovariates)); + read.setTemporaryAttribute(COVARS_ATTRIBUTE, RecalUtils.computeCovariates(read, requestedCovariates)); } if (!ReadUtils.isSOLiDRead(read) || // SOLID bams have inserted the reference base into the read if the color space in inconsistent with the read base so skip it - RAC.SOLID_RECAL_MODE == RecalDataManager.SOLID_RECAL_MODE.DO_NOTHING || - RecalDataManager.isColorSpaceConsistent(read, offset)) + RAC.SOLID_RECAL_MODE == RecalUtils.SOLID_RECAL_MODE.DO_NOTHING || + RecalUtils.isColorSpaceConsistent(read, offset)) recalibrationEngine.updateDataForPileupElement(p, ref.getBase()); // This base finally passed all the checks for a good base, so add it to the big data hashmap } countedSites++; @@ -285,10 +289,10 @@ public class BaseRecalibrator extends LocusWalker implements TreeRed File recalFile = getToolkit().getArguments().BQSR_RECAL_FILE; if (recalFile != null) { RecalibrationReport report = new RecalibrationReport(recalFile); - RecalDataManager.generateRecalibrationPlot(RAC.RECAL_FILE, report.getRecalibrationTables(), recalibrationTables, requestedCovariates, RAC.KEEP_INTERMEDIATE_FILES); + RecalUtils.generateRecalibrationPlot(RAC.RECAL_FILE, report.getRecalibrationTables(), recalibrationTables, requestedCovariates, RAC.KEEP_INTERMEDIATE_FILES); } else - RecalDataManager.generateRecalibrationPlot(RAC.RECAL_FILE, recalibrationTables, requestedCovariates, RAC.KEEP_INTERMEDIATE_FILES); + RecalUtils.generateRecalibrationPlot(RAC.RECAL_FILE, recalibrationTables, requestedCovariates, RAC.KEEP_INTERMEDIATE_FILES); } @@ -309,7 +313,7 @@ public class BaseRecalibrator extends LocusWalker implements TreeRed throw new UserException.CouldNotCreateOutputFile(RAC.RECAL_FILE, "could not be created"); } - RecalDataManager.outputRecalibrationReport(RAC, quantizationInfo, recalibrationTables, requestedCovariates, output); + RecalUtils.outputRecalibrationReport(RAC, quantizationInfo, recalibrationTables, requestedCovariates, output); } } 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 2a94426a7..f04e4a1b3 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 @@ -29,6 +29,7 @@ import org.broad.tribble.Feature; import org.broadinstitute.sting.commandline.*; import org.broadinstitute.sting.gatk.report.GATKReportTable; import org.broadinstitute.sting.utils.Utils; +import org.broadinstitute.sting.utils.recalibration.RecalUtils; import java.io.File; import java.util.Collections; @@ -100,7 +101,7 @@ public class RecalibrationArgumentCollection { * reads which have had the reference inserted because of color space inconsistencies. */ @Argument(fullName = "solid_recal_mode", shortName = "sMode", required = false, doc = "How should we recalibrate solid bases in which the reference was inserted? Options = DO_NOTHING, SET_Q_ZERO, SET_Q_ZERO_BASE_N, or REMOVE_REF_BIAS") - public RecalDataManager.SOLID_RECAL_MODE SOLID_RECAL_MODE = RecalDataManager.SOLID_RECAL_MODE.SET_Q_ZERO; + public RecalUtils.SOLID_RECAL_MODE SOLID_RECAL_MODE = RecalUtils.SOLID_RECAL_MODE.SET_Q_ZERO; /** * CountCovariates and TableRecalibration accept a --solid_nocall_strategy flag which governs how the recalibrator handles @@ -108,7 +109,7 @@ public class RecalibrationArgumentCollection { * their color space tag can not be recalibrated. */ @Argument(fullName = "solid_nocall_strategy", shortName = "solid_nocall_strategy", doc = "Defines the behavior of the recalibrator when it encounters no calls in the color space. Options = THROW_EXCEPTION, LEAVE_READ_UNRECALIBRATED, or PURGE_READ", required = false) - public RecalDataManager.SOLID_NOCALL_STRATEGY SOLID_NOCALL_STRATEGY = RecalDataManager.SOLID_NOCALL_STRATEGY.THROW_EXCEPTION; + public RecalUtils.SOLID_NOCALL_STRATEGY SOLID_NOCALL_STRATEGY = RecalUtils.SOLID_NOCALL_STRATEGY.THROW_EXCEPTION; /** * The context covariate will use a context of this size to calculate it's covariate value for base mismatches @@ -177,41 +178,41 @@ public class RecalibrationArgumentCollection { public GATKReportTable generateReportTable() { GATKReportTable argumentsTable = new GATKReportTable("Arguments", "Recalibration argument collection values used in this run", 2); argumentsTable.addColumn("Argument"); - argumentsTable.addColumn(RecalDataManager.ARGUMENT_VALUE_COLUMN_NAME); + argumentsTable.addColumn(RecalUtils.ARGUMENT_VALUE_COLUMN_NAME); argumentsTable.addRowID("covariate", true); - argumentsTable.set("covariate", RecalDataManager.ARGUMENT_VALUE_COLUMN_NAME, (COVARIATES == null) ? "null" : Utils.join(",", COVARIATES)); + argumentsTable.set("covariate", RecalUtils.ARGUMENT_VALUE_COLUMN_NAME, (COVARIATES == null) ? "null" : Utils.join(",", COVARIATES)); argumentsTable.addRowID("no_standard_covs", true); - argumentsTable.set("no_standard_covs", RecalDataManager.ARGUMENT_VALUE_COLUMN_NAME, DO_NOT_USE_STANDARD_COVARIATES); + argumentsTable.set("no_standard_covs", RecalUtils.ARGUMENT_VALUE_COLUMN_NAME, DO_NOT_USE_STANDARD_COVARIATES); argumentsTable.addRowID("run_without_dbsnp", true); - argumentsTable.set("run_without_dbsnp", RecalDataManager.ARGUMENT_VALUE_COLUMN_NAME, RUN_WITHOUT_DBSNP); + argumentsTable.set("run_without_dbsnp", RecalUtils.ARGUMENT_VALUE_COLUMN_NAME, RUN_WITHOUT_DBSNP); argumentsTable.addRowID("solid_recal_mode", true); - argumentsTable.set("solid_recal_mode", RecalDataManager.ARGUMENT_VALUE_COLUMN_NAME, SOLID_RECAL_MODE); + argumentsTable.set("solid_recal_mode", RecalUtils.ARGUMENT_VALUE_COLUMN_NAME, SOLID_RECAL_MODE); argumentsTable.addRowID("solid_nocall_strategy", true); - argumentsTable.set("solid_nocall_strategy", RecalDataManager.ARGUMENT_VALUE_COLUMN_NAME, SOLID_NOCALL_STRATEGY); + argumentsTable.set("solid_nocall_strategy", RecalUtils.ARGUMENT_VALUE_COLUMN_NAME, SOLID_NOCALL_STRATEGY); argumentsTable.addRowID("mismatches_context_size", true); - argumentsTable.set("mismatches_context_size", RecalDataManager.ARGUMENT_VALUE_COLUMN_NAME, MISMATCHES_CONTEXT_SIZE); + argumentsTable.set("mismatches_context_size", RecalUtils.ARGUMENT_VALUE_COLUMN_NAME, MISMATCHES_CONTEXT_SIZE); argumentsTable.addRowID("indels_context_size", true); - argumentsTable.set("indels_context_size", RecalDataManager.ARGUMENT_VALUE_COLUMN_NAME, INDELS_CONTEXT_SIZE); + argumentsTable.set("indels_context_size", RecalUtils.ARGUMENT_VALUE_COLUMN_NAME, INDELS_CONTEXT_SIZE); argumentsTable.addRowID("mismatches_default_quality", true); - argumentsTable.set("mismatches_default_quality", RecalDataManager.ARGUMENT_VALUE_COLUMN_NAME, MISMATCHES_DEFAULT_QUALITY); + argumentsTable.set("mismatches_default_quality", RecalUtils.ARGUMENT_VALUE_COLUMN_NAME, MISMATCHES_DEFAULT_QUALITY); argumentsTable.addRowID("insertions_default_quality", true); - argumentsTable.set("insertions_default_quality", RecalDataManager.ARGUMENT_VALUE_COLUMN_NAME, INSERTIONS_DEFAULT_QUALITY); + argumentsTable.set("insertions_default_quality", RecalUtils.ARGUMENT_VALUE_COLUMN_NAME, INSERTIONS_DEFAULT_QUALITY); argumentsTable.addRowID("low_quality_tail", true); - argumentsTable.set("low_quality_tail", RecalDataManager.ARGUMENT_VALUE_COLUMN_NAME, LOW_QUAL_TAIL); + argumentsTable.set("low_quality_tail", RecalUtils.ARGUMENT_VALUE_COLUMN_NAME, LOW_QUAL_TAIL); argumentsTable.addRowID("default_platform", true); - argumentsTable.set("default_platform", RecalDataManager.ARGUMENT_VALUE_COLUMN_NAME, DEFAULT_PLATFORM); + argumentsTable.set("default_platform", RecalUtils.ARGUMENT_VALUE_COLUMN_NAME, DEFAULT_PLATFORM); argumentsTable.addRowID("force_platform", true); - argumentsTable.set("force_platform", RecalDataManager.ARGUMENT_VALUE_COLUMN_NAME, FORCE_PLATFORM); + argumentsTable.set("force_platform", RecalUtils.ARGUMENT_VALUE_COLUMN_NAME, FORCE_PLATFORM); argumentsTable.addRowID("quantizing_levels", true); - argumentsTable.set("quantizing_levels", RecalDataManager.ARGUMENT_VALUE_COLUMN_NAME, QUANTIZING_LEVELS); + argumentsTable.set("quantizing_levels", RecalUtils.ARGUMENT_VALUE_COLUMN_NAME, QUANTIZING_LEVELS); argumentsTable.addRowID("keep_intermediate_files", true); - argumentsTable.set("keep_intermediate_files", RecalDataManager.ARGUMENT_VALUE_COLUMN_NAME, KEEP_INTERMEDIATE_FILES); + argumentsTable.set("keep_intermediate_files", RecalUtils.ARGUMENT_VALUE_COLUMN_NAME, KEEP_INTERMEDIATE_FILES); argumentsTable.addRowID("no_plots", true); - argumentsTable.set("no_plots", RecalDataManager.ARGUMENT_VALUE_COLUMN_NAME, NO_PLOTS); + argumentsTable.set("no_plots", RecalUtils.ARGUMENT_VALUE_COLUMN_NAME, NO_PLOTS); argumentsTable.addRowID("recalibration_report", true); - argumentsTable.set("recalibration_report", RecalDataManager.ARGUMENT_VALUE_COLUMN_NAME, recalibrationReport == null ? "null" : recalibrationReport.getAbsolutePath()); + argumentsTable.set("recalibration_report", RecalUtils.ARGUMENT_VALUE_COLUMN_NAME, recalibrationReport == null ? "null" : recalibrationReport.getAbsolutePath()); argumentsTable.addRowID("binary_tag_name", true); - argumentsTable.set("binary_tag_name", RecalDataManager.ARGUMENT_VALUE_COLUMN_NAME, BINARY_TAG_NAME == null ? "null" : BINARY_TAG_NAME); + argumentsTable.set("binary_tag_name", RecalUtils.ARGUMENT_VALUE_COLUMN_NAME, BINARY_TAG_NAME == null ? "null" : BINARY_TAG_NAME); return argumentsTable; } diff --git a/public/java/src/org/broadinstitute/sting/gatk/walkers/bqsr/RecalibrationEngine.java b/public/java/src/org/broadinstitute/sting/gatk/walkers/bqsr/RecalibrationEngine.java index aa62a18bc..38e306939 100644 --- a/public/java/src/org/broadinstitute/sting/gatk/walkers/bqsr/RecalibrationEngine.java +++ b/public/java/src/org/broadinstitute/sting/gatk/walkers/bqsr/RecalibrationEngine.java @@ -1,5 +1,6 @@ package org.broadinstitute.sting.gatk.walkers.bqsr; +import org.broadinstitute.sting.utils.recalibration.covariates.Covariate; import org.broadinstitute.sting.utils.pileup.PileupElement; import org.broadinstitute.sting.utils.recalibration.RecalibrationTables; diff --git a/public/java/src/org/broadinstitute/sting/gatk/walkers/bqsr/StandardRecalibrationEngine.java b/public/java/src/org/broadinstitute/sting/gatk/walkers/bqsr/StandardRecalibrationEngine.java index a24506d07..08c7da754 100644 --- a/public/java/src/org/broadinstitute/sting/gatk/walkers/bqsr/StandardRecalibrationEngine.java +++ b/public/java/src/org/broadinstitute/sting/gatk/walkers/bqsr/StandardRecalibrationEngine.java @@ -25,10 +25,14 @@ package org.broadinstitute.sting.gatk.walkers.bqsr; * OTHER DEALINGS IN THE SOFTWARE. */ +import org.broadinstitute.sting.utils.recalibration.covariates.Covariate; import org.broadinstitute.sting.utils.BaseUtils; import org.broadinstitute.sting.utils.classloader.PublicPackageSource; import org.broadinstitute.sting.utils.collections.NestedIntegerArray; import org.broadinstitute.sting.utils.pileup.PileupElement; +import org.broadinstitute.sting.utils.recalibration.EventType; +import org.broadinstitute.sting.utils.recalibration.ReadCovariates; +import org.broadinstitute.sting.utils.recalibration.RecalDatum; import org.broadinstitute.sting.utils.recalibration.RecalibrationTables; import org.broadinstitute.sting.utils.sam.GATKSAMRecord; diff --git a/public/java/src/org/broadinstitute/sting/utils/classloader/PluginManager.java b/public/java/src/org/broadinstitute/sting/utils/classloader/PluginManager.java index f24bbb636..9a2cb68db 100644 --- a/public/java/src/org/broadinstitute/sting/utils/classloader/PluginManager.java +++ b/public/java/src/org/broadinstitute/sting/utils/classloader/PluginManager.java @@ -168,6 +168,28 @@ public class PluginManager { String pluginName = getName(pluginClass); pluginsByName.put(pluginName, pluginClass); } + + // sort the plugins so the order of elements is deterministic + sortPlugins(plugins); + sortPlugins(interfaces); + } + + /** + * Sorts, in place, the list of plugins according to getName() on each element + * + * @param unsortedPlugins + */ + private final void sortPlugins(final List> unsortedPlugins) { + Collections.sort(unsortedPlugins, new ComparePluginsByName()); + } + + private final class ComparePluginsByName implements Comparator> { + @Override + public int compare(final Class aClass, final Class aClass1) { + String pluginName1 = getName(aClass); + String pluginName2 = getName(aClass1); + return pluginName1.compareTo(pluginName2); + } } /** diff --git a/public/java/src/org/broadinstitute/sting/utils/clipping/ClippingOp.java b/public/java/src/org/broadinstitute/sting/utils/clipping/ClippingOp.java index a4383c3ae..554188bc1 100644 --- a/public/java/src/org/broadinstitute/sting/utils/clipping/ClippingOp.java +++ b/public/java/src/org/broadinstitute/sting/utils/clipping/ClippingOp.java @@ -4,7 +4,7 @@ import com.google.java.contract.Requires; import net.sf.samtools.Cigar; import net.sf.samtools.CigarElement; import net.sf.samtools.CigarOperator; -import org.broadinstitute.sting.gatk.walkers.bqsr.EventType; +import org.broadinstitute.sting.utils.recalibration.EventType; import org.broadinstitute.sting.utils.exceptions.ReviewedStingException; import org.broadinstitute.sting.utils.exceptions.UserException; import org.broadinstitute.sting.utils.sam.GATKSAMRecord; diff --git a/public/java/src/org/broadinstitute/sting/utils/clipping/ReadClipper.java b/public/java/src/org/broadinstitute/sting/utils/clipping/ReadClipper.java index ba9267222..6392ce4ce 100644 --- a/public/java/src/org/broadinstitute/sting/utils/clipping/ReadClipper.java +++ b/public/java/src/org/broadinstitute/sting/utils/clipping/ReadClipper.java @@ -3,7 +3,7 @@ package org.broadinstitute.sting.utils.clipping; import com.google.java.contract.Requires; import net.sf.samtools.CigarElement; import net.sf.samtools.CigarOperator; -import org.broadinstitute.sting.gatk.walkers.bqsr.EventType; +import org.broadinstitute.sting.utils.recalibration.EventType; import org.broadinstitute.sting.utils.exceptions.ReviewedStingException; import org.broadinstitute.sting.utils.sam.GATKSAMRecord; import org.broadinstitute.sting.utils.sam.ReadUtils; diff --git a/public/java/src/org/broadinstitute/sting/utils/fragments/FragmentUtils.java b/public/java/src/org/broadinstitute/sting/utils/fragments/FragmentUtils.java index c6eec24f1..851272673 100644 --- a/public/java/src/org/broadinstitute/sting/utils/fragments/FragmentUtils.java +++ b/public/java/src/org/broadinstitute/sting/utils/fragments/FragmentUtils.java @@ -4,7 +4,7 @@ import net.sf.samtools.Cigar; import net.sf.samtools.CigarElement; import net.sf.samtools.CigarOperator; import net.sf.samtools.SAMRecord; -import org.broadinstitute.sting.gatk.walkers.bqsr.EventType; +import org.broadinstitute.sting.utils.recalibration.EventType; import org.broadinstitute.sting.utils.collections.Pair; import org.broadinstitute.sting.utils.exceptions.ReviewedStingException; import org.broadinstitute.sting.utils.pileup.PileupElement; diff --git a/public/java/src/org/broadinstitute/sting/utils/recalibration/BaseRecalibration.java b/public/java/src/org/broadinstitute/sting/utils/recalibration/BaseRecalibration.java index b5f7ad046..c09eb0063 100644 --- a/public/java/src/org/broadinstitute/sting/utils/recalibration/BaseRecalibration.java +++ b/public/java/src/org/broadinstitute/sting/utils/recalibration/BaseRecalibration.java @@ -27,7 +27,7 @@ package org.broadinstitute.sting.utils.recalibration; import net.sf.samtools.SAMTag; import net.sf.samtools.SAMUtils; -import org.broadinstitute.sting.gatk.walkers.bqsr.*; +import org.broadinstitute.sting.utils.recalibration.covariates.Covariate; import org.broadinstitute.sting.utils.MathUtils; import org.broadinstitute.sting.utils.QualityUtils; import org.broadinstitute.sting.utils.collections.NestedIntegerArray; @@ -103,7 +103,7 @@ public class BaseRecalibration { } } - RecalDataManager.computeCovariates(read, requestedCovariates, readCovariates); // compute all covariates for the read + RecalUtils.computeCovariates(read, requestedCovariates, readCovariates); // compute all covariates for the read for (final EventType errorModel : EventType.values()) { // recalibrate all three quality strings if (disableIndelQuals && errorModel != EventType.BASE_SUBSTITUTION) { read.setBaseQualities(null, errorModel); diff --git a/public/java/src/org/broadinstitute/sting/gatk/walkers/bqsr/EventType.java b/public/java/src/org/broadinstitute/sting/utils/recalibration/EventType.java similarity index 96% rename from public/java/src/org/broadinstitute/sting/gatk/walkers/bqsr/EventType.java rename to public/java/src/org/broadinstitute/sting/utils/recalibration/EventType.java index 2650f0f8d..1c84518eb 100644 --- a/public/java/src/org/broadinstitute/sting/gatk/walkers/bqsr/EventType.java +++ b/public/java/src/org/broadinstitute/sting/utils/recalibration/EventType.java @@ -1,4 +1,4 @@ -package org.broadinstitute.sting.gatk.walkers.bqsr; +package org.broadinstitute.sting.utils.recalibration; import org.broadinstitute.sting.utils.exceptions.ReviewedStingException; diff --git a/public/java/src/org/broadinstitute/sting/gatk/walkers/bqsr/QuantizationInfo.java b/public/java/src/org/broadinstitute/sting/utils/recalibration/QuantizationInfo.java similarity index 78% rename from public/java/src/org/broadinstitute/sting/gatk/walkers/bqsr/QuantizationInfo.java rename to public/java/src/org/broadinstitute/sting/utils/recalibration/QuantizationInfo.java index fb3aef949..2b67d12a9 100644 --- a/public/java/src/org/broadinstitute/sting/gatk/walkers/bqsr/QuantizationInfo.java +++ b/public/java/src/org/broadinstitute/sting/utils/recalibration/QuantizationInfo.java @@ -1,11 +1,9 @@ -package org.broadinstitute.sting.gatk.walkers.bqsr; +package org.broadinstitute.sting.utils.recalibration; import org.broadinstitute.sting.gatk.report.GATKReportTable; import org.broadinstitute.sting.utils.MathUtils; import org.broadinstitute.sting.utils.QualityUtils; import org.broadinstitute.sting.utils.collections.NestedIntegerArray; -import org.broadinstitute.sting.utils.recalibration.QualQuantizer; -import org.broadinstitute.sting.utils.recalibration.RecalibrationTables; import java.util.Arrays; import java.util.List; @@ -41,7 +39,7 @@ public class QuantizationInfo { for (final RecalDatum value : qualTable.getAllValues()) { final RecalDatum datum = value; final int empiricalQual = MathUtils.fastRound(datum.getEmpiricalQuality()); // convert the empirical quality to an integer ( it is already capped by MAX_QUAL ) - qualHistogram[empiricalQual] += datum.numObservations; // add the number of observations for every key + qualHistogram[empiricalQual] += datum.getNumObservations(); // add the number of observations for every key } empiricalQualCounts = Arrays.asList(qualHistogram); // histogram with the number of observations of the empirical qualities quantizeQualityScores(quantizationLevels); @@ -70,15 +68,15 @@ public class QuantizationInfo { } public GATKReportTable generateReportTable() { - GATKReportTable quantizedTable = new GATKReportTable(RecalDataManager.QUANTIZED_REPORT_TABLE_TITLE, "Quality quantization map", 3); - quantizedTable.addColumn(RecalDataManager.QUALITY_SCORE_COLUMN_NAME); - quantizedTable.addColumn(RecalDataManager.QUANTIZED_COUNT_COLUMN_NAME); - quantizedTable.addColumn(RecalDataManager.QUANTIZED_VALUE_COLUMN_NAME); + GATKReportTable quantizedTable = new GATKReportTable(RecalUtils.QUANTIZED_REPORT_TABLE_TITLE, "Quality quantization map", 3); + quantizedTable.addColumn(RecalUtils.QUALITY_SCORE_COLUMN_NAME); + quantizedTable.addColumn(RecalUtils.QUANTIZED_COUNT_COLUMN_NAME); + quantizedTable.addColumn(RecalUtils.QUANTIZED_VALUE_COLUMN_NAME); for (int qual = 0; qual <= QualityUtils.MAX_QUAL_SCORE; qual++) { - quantizedTable.set(qual, RecalDataManager.QUALITY_SCORE_COLUMN_NAME, qual); - quantizedTable.set(qual, RecalDataManager.QUANTIZED_COUNT_COLUMN_NAME, empiricalQualCounts.get(qual)); - quantizedTable.set(qual, RecalDataManager.QUANTIZED_VALUE_COLUMN_NAME, quantizedQuals.get(qual)); + quantizedTable.set(qual, RecalUtils.QUALITY_SCORE_COLUMN_NAME, qual); + quantizedTable.set(qual, RecalUtils.QUANTIZED_COUNT_COLUMN_NAME, empiricalQualCounts.get(qual)); + quantizedTable.set(qual, RecalUtils.QUANTIZED_VALUE_COLUMN_NAME, quantizedQuals.get(qual)); } return quantizedTable; } diff --git a/public/java/src/org/broadinstitute/sting/gatk/walkers/bqsr/ReadCovariates.java b/public/java/src/org/broadinstitute/sting/utils/recalibration/ReadCovariates.java similarity index 97% rename from public/java/src/org/broadinstitute/sting/gatk/walkers/bqsr/ReadCovariates.java rename to public/java/src/org/broadinstitute/sting/utils/recalibration/ReadCovariates.java index 5e907237d..c86bd4deb 100644 --- a/public/java/src/org/broadinstitute/sting/gatk/walkers/bqsr/ReadCovariates.java +++ b/public/java/src/org/broadinstitute/sting/utils/recalibration/ReadCovariates.java @@ -1,4 +1,4 @@ -package org.broadinstitute.sting.gatk.walkers.bqsr; +package org.broadinstitute.sting.utils.recalibration; /** * The object temporarily held by a read that describes all of it's covariates. diff --git a/public/java/src/org/broadinstitute/sting/gatk/walkers/bqsr/RecalDatum.java b/public/java/src/org/broadinstitute/sting/utils/recalibration/RecalDatum.java similarity index 77% rename from public/java/src/org/broadinstitute/sting/gatk/walkers/bqsr/RecalDatum.java rename to public/java/src/org/broadinstitute/sting/utils/recalibration/RecalDatum.java index ed4e769b1..43ff54378 100755 --- a/public/java/src/org/broadinstitute/sting/gatk/walkers/bqsr/RecalDatum.java +++ b/public/java/src/org/broadinstitute/sting/utils/recalibration/RecalDatum.java @@ -1,4 +1,4 @@ -package org.broadinstitute.sting.gatk.walkers.bqsr; +package org.broadinstitute.sting.utils.recalibration; /* * Copyright (c) 2009 The Broad Institute @@ -56,12 +56,12 @@ public class RecalDatum { /** * number of bases seen in total */ - long numObservations; + private long numObservations; /** * number of bases seen that didn't match the reference */ - long numMismatches; + private long numMismatches; /** * used when calculating empirical qualities to avoid division by zero @@ -82,16 +82,16 @@ public class RecalDatum { } public RecalDatum(final RecalDatum copy) { - this.numObservations = copy.numObservations; - this.numMismatches = copy.numMismatches; + this.numObservations = copy.getNumObservations(); + this.numMismatches = copy.getNumMismatches(); this.estimatedQReported = copy.estimatedQReported; this.empiricalQuality = copy.empiricalQuality; } public synchronized void combine(final RecalDatum other) { final double sumErrors = this.calcExpectedErrors() + other.calcExpectedErrors(); - increment(other.numObservations, other.numMismatches); - estimatedQReported = -10 * Math.log10(sumErrors / this.numObservations); + increment(other.getNumObservations(), other.getNumMismatches()); + estimatedQReported = -10 * Math.log10(sumErrors / getNumObservations()); empiricalQuality = UNINITIALIZED; } @@ -100,7 +100,8 @@ public class RecalDatum { private synchronized final void calcEmpiricalQuality() { // cache the value so we don't call log over and over again final double doubleMismatches = (double) (numMismatches + SMOOTHING_CONSTANT); - final double doubleObservations = (double) (numObservations + SMOOTHING_CONSTANT); + // smoothing is one error and one non-error observation, for example + final double doubleObservations = (double) (numObservations + SMOOTHING_CONSTANT + SMOOTHING_CONSTANT); final double empiricalQual = -10 * Math.log10(doubleMismatches / doubleObservations); empiricalQuality = Math.min(empiricalQual, (double) QualityUtils.MAX_RECALIBRATED_Q_SCORE); } @@ -125,7 +126,7 @@ public class RecalDatum { @Override public String toString() { - return String.format("%d,%d,%d", numObservations, numMismatches, (byte) Math.floor(getEmpiricalQuality())); + return String.format("%d,%d,%d", getNumObservations(), getNumMismatches(), (byte) Math.floor(getEmpiricalQuality())); } public String stringForCSV() { @@ -133,7 +134,7 @@ public class RecalDatum { } private double calcExpectedErrors() { - return (double) this.numObservations * qualToErrorProb(estimatedQReported); + return (double) getNumObservations() * qualToErrorProb(estimatedQReported); } private double qualToErrorProb(final double qual) { @@ -170,15 +171,42 @@ public class RecalDatum { // //--------------------------------------------------------------------------------------------------------------- - synchronized void increment(final long incObservations, final long incMismatches) { - numObservations += incObservations; - numMismatches += incMismatches; + public long getNumObservations() { + return numObservations; + } + + public synchronized void setNumObservations(final long numObservations) { + this.numObservations = numObservations; empiricalQuality = UNINITIALIZED; } - synchronized void increment(final boolean isError) { - numObservations++; - numMismatches += isError ? 1:0; + public long getNumMismatches() { + return numMismatches; + } + + public synchronized void setNumMismatches(final long numMismatches) { + this.numMismatches = numMismatches; empiricalQuality = UNINITIALIZED; } + + public synchronized void incrementNumObservations(final long by) { + numObservations += by; + empiricalQuality = UNINITIALIZED; + } + + public synchronized void incrementNumMismatches(final long by) { + numMismatches += by; + empiricalQuality = UNINITIALIZED; + } + + public synchronized void increment(final long incObservations, final long incMismatches) { + incrementNumObservations(incObservations); + incrementNumMismatches(incMismatches); + } + + public synchronized void increment(final boolean isError) { + incrementNumObservations(1); + if ( isError ) + incrementNumMismatches(1); + } } diff --git a/public/java/src/org/broadinstitute/sting/gatk/walkers/bqsr/RecalDataManager.java b/public/java/src/org/broadinstitute/sting/utils/recalibration/RecalUtils.java similarity index 96% rename from public/java/src/org/broadinstitute/sting/gatk/walkers/bqsr/RecalDataManager.java rename to public/java/src/org/broadinstitute/sting/utils/recalibration/RecalUtils.java index f40a62d53..fe6ef7018 100644 --- a/public/java/src/org/broadinstitute/sting/gatk/walkers/bqsr/RecalDataManager.java +++ b/public/java/src/org/broadinstitute/sting/utils/recalibration/RecalUtils.java @@ -23,11 +23,13 @@ * THE USE OR OTHER DEALINGS IN THE SOFTWARE. */ -package org.broadinstitute.sting.gatk.walkers.bqsr; +package org.broadinstitute.sting.utils.recalibration; import org.apache.log4j.Logger; import org.broadinstitute.sting.gatk.report.GATKReport; import org.broadinstitute.sting.gatk.report.GATKReportTable; +import org.broadinstitute.sting.gatk.walkers.bqsr.RecalibrationArgumentCollection; +import org.broadinstitute.sting.utils.recalibration.covariates.*; import org.broadinstitute.sting.utils.BaseUtils; import org.broadinstitute.sting.utils.R.RScriptExecutor; import org.broadinstitute.sting.utils.Utils; @@ -39,7 +41,6 @@ import org.broadinstitute.sting.utils.exceptions.DynamicClassResolutionException import org.broadinstitute.sting.utils.exceptions.ReviewedStingException; import org.broadinstitute.sting.utils.exceptions.UserException; import org.broadinstitute.sting.utils.io.Resource; -import org.broadinstitute.sting.utils.recalibration.RecalibrationTables; import org.broadinstitute.sting.utils.sam.GATKSAMReadGroupRecord; import org.broadinstitute.sting.utils.sam.GATKSAMRecord; import org.broadinstitute.sting.utils.sam.ReadUtils; @@ -59,7 +60,7 @@ import java.util.*; * This class holds the parsing methods that are shared between CountCovariates and TableRecalibration. */ -public class RecalDataManager { +public class RecalUtils { public final static String ARGUMENT_REPORT_TABLE_TITLE = "Arguments"; public final static String QUANTIZED_REPORT_TABLE_TITLE = "Quantized"; public final static String READGROUP_REPORT_TABLE_TITLE = "RecalTable0"; @@ -85,13 +86,108 @@ public class RecalDataManager { private static final String SCRIPT_FILE = "BQSR.R"; - private static final Pair covariateValue = new Pair(RecalDataManager.COVARIATE_VALUE_COLUMN_NAME, "%s"); - private static final Pair covariateName = new Pair(RecalDataManager.COVARIATE_NAME_COLUMN_NAME, "%s"); - private static final Pair eventType = new Pair(RecalDataManager.EVENT_TYPE_COLUMN_NAME, "%s"); - private static final Pair empiricalQuality = new Pair(RecalDataManager.EMPIRICAL_QUALITY_COLUMN_NAME, "%.4f"); - private static final Pair estimatedQReported = new Pair(RecalDataManager.ESTIMATED_Q_REPORTED_COLUMN_NAME, "%.4f"); - private static final Pair nObservations = new Pair(RecalDataManager.NUMBER_OBSERVATIONS_COLUMN_NAME, "%d"); - private static final Pair nErrors = new Pair(RecalDataManager.NUMBER_ERRORS_COLUMN_NAME, "%d"); + private static final Pair covariateValue = new Pair(RecalUtils.COVARIATE_VALUE_COLUMN_NAME, "%s"); + private static final Pair covariateName = new Pair(RecalUtils.COVARIATE_NAME_COLUMN_NAME, "%s"); + private static final Pair eventType = new Pair(RecalUtils.EVENT_TYPE_COLUMN_NAME, "%s"); + private static final Pair empiricalQuality = new Pair(RecalUtils.EMPIRICAL_QUALITY_COLUMN_NAME, "%.4f"); + private static final Pair estimatedQReported = new Pair(RecalUtils.ESTIMATED_Q_REPORTED_COLUMN_NAME, "%.4f"); + private static final Pair nObservations = new Pair(RecalUtils.NUMBER_OBSERVATIONS_COLUMN_NAME, "%d"); + private static final Pair nErrors = new Pair(RecalUtils.NUMBER_ERRORS_COLUMN_NAME, "%d"); + + /** + * Generates two lists : required covariates and optional covariates based on the user's requests. + * + * Performs the following tasks in order: + * 1. Adds all requierd covariates in order + * 2. Check if the user asked to use the standard covariates and adds them all if that's the case + * 3. Adds all covariates requested by the user that were not already added by the two previous steps + * + * @param argumentCollection the argument collection object for the recalibration walker + * @return a pair of ordered lists : required covariates (first) and optional covariates (second) + */ + public static Pair, ArrayList> initializeCovariates(RecalibrationArgumentCollection argumentCollection) { + final List> covariateClasses = new PluginManager(Covariate.class).getPlugins(); + final List> requiredClasses = new PluginManager(RequiredCovariate.class).getPlugins(); + final List> standardClasses = new PluginManager(StandardCovariate.class).getPlugins(); + + final ArrayList requiredCovariates = addRequiredCovariatesToList(requiredClasses); // add the required covariates + ArrayList optionalCovariates = new ArrayList(); + if (!argumentCollection.DO_NOT_USE_STANDARD_COVARIATES) + optionalCovariates = addStandardCovariatesToList(standardClasses); // add the standard covariates if -standard was specified by the user + + if (argumentCollection.COVARIATES != null) { // parse the -cov arguments that were provided, skipping over the ones already specified + for (String requestedCovariateString : argumentCollection.COVARIATES) { + boolean foundClass = false; + for (Class covClass : covariateClasses) { + if (requestedCovariateString.equalsIgnoreCase(covClass.getSimpleName())) { // -cov argument matches the class name for an implementing class + foundClass = true; + if (!requiredClasses.contains(covClass) && + (argumentCollection.DO_NOT_USE_STANDARD_COVARIATES || !standardClasses.contains(covClass))) { + try { + final Covariate covariate = covClass.newInstance(); // now that we've found a matching class, try to instantiate it + optionalCovariates.add(covariate); + } catch (Exception e) { + throw new DynamicClassResolutionException(covClass, e); + } + } + } + } + + if (!foundClass) { + throw new UserException.CommandLineException("The requested covariate type (" + requestedCovariateString + ") isn't a valid covariate option. Use --list to see possible covariates."); + } + } + } + return new Pair, ArrayList>(requiredCovariates, optionalCovariates); + } + + /** + * Adds the required covariates to a covariate list + * + * Note: this method really only checks if the classes object has the expected number of required covariates, then add them by hand. + * + * @param classes list of classes to add to the covariate list + * @return the covariate list + */ + private static ArrayList addRequiredCovariatesToList(List> classes) { + ArrayList dest = new ArrayList(classes.size()); + if (classes.size() != 2) + throw new ReviewedStingException("The number of required covariates has changed, this is a hard change in the code and needs to be inspected"); + + dest.add(new ReadGroupCovariate()); // enforce the order with RG first and QS next. + dest.add(new QualityScoreCovariate()); + return dest; + } + + /** + * Adds the standard covariates to a covariate list + * + * @param classes list of classes to add to the covariate list + * @return the covariate list + */ + private static ArrayList addStandardCovariatesToList(List> classes) { + ArrayList dest = new ArrayList(classes.size()); + for (Class covClass : classes) { + try { + final Covariate covariate = (Covariate) covClass.newInstance(); + dest.add(covariate); + } catch (Exception e) { + throw new DynamicClassResolutionException(covClass, e); + } + } + return dest; + } + + public static void listAvailableCovariates(Logger logger) { + // Get a list of all available covariates + final List> covariateClasses = new PluginManager(Covariate.class).getPlugins(); + + // Print and exit if that's what was requested + logger.info("Available covariates:"); + for (Class covClass : covariateClasses) + logger.info(covClass.getSimpleName()); + logger.info(""); + } public enum SOLID_RECAL_MODE { @@ -152,64 +248,6 @@ public class RecalDataManager { } } - /** - * Generates two lists : required covariates and optional covariates based on the user's requests. - * - * Performs the following tasks in order: - * 1. Adds all requierd covariates in order - * 2. Check if the user asked to use the standard covariates and adds them all if that's the case - * 3. Adds all covariates requested by the user that were not already added by the two previous steps - * - * @param argumentCollection the argument collection object for the recalibration walker - * @return a pair of ordered lists : required covariates (first) and optional covariates (second) - */ - public static Pair, ArrayList> initializeCovariates(RecalibrationArgumentCollection argumentCollection) { - final List> covariateClasses = new PluginManager(Covariate.class).getPlugins(); - final List> requiredClasses = new PluginManager(RequiredCovariate.class).getPlugins(); - final List> standardClasses = new PluginManager(StandardCovariate.class).getPlugins(); - - final ArrayList requiredCovariates = addRequiredCovariatesToList(requiredClasses); // add the required covariates - ArrayList optionalCovariates = new ArrayList(); - if (!argumentCollection.DO_NOT_USE_STANDARD_COVARIATES) - optionalCovariates = addStandardCovariatesToList(standardClasses); // add the standard covariates if -standard was specified by the user - - if (argumentCollection.COVARIATES != null) { // parse the -cov arguments that were provided, skipping over the ones already specified - for (String requestedCovariateString : argumentCollection.COVARIATES) { - boolean foundClass = false; - for (Class covClass : covariateClasses) { - if (requestedCovariateString.equalsIgnoreCase(covClass.getSimpleName())) { // -cov argument matches the class name for an implementing class - foundClass = true; - if (!requiredClasses.contains(covClass) && - (argumentCollection.DO_NOT_USE_STANDARD_COVARIATES || !standardClasses.contains(covClass))) { - try { - final Covariate covariate = covClass.newInstance(); // now that we've found a matching class, try to instantiate it - optionalCovariates.add(covariate); - } catch (Exception e) { - throw new DynamicClassResolutionException(covClass, e); - } - } - } - } - - if (!foundClass) { - throw new UserException.CommandLineException("The requested covariate type (" + requestedCovariateString + ") isn't a valid covariate option. Use --list to see possible covariates."); - } - } - } - return new Pair, ArrayList>(requiredCovariates, optionalCovariates); - } - - public static void listAvailableCovariates(Logger logger) { - // Get a list of all available covariates - final List> covariateClasses = new PluginManager(Covariate.class).getPlugins(); - - // Print and exit if that's what was requested - logger.info("Available covariates:"); - for (Class covClass : covariateClasses) - logger.info(covClass.getSimpleName()); - logger.info(""); - } - private static List generateReportTables(final RecalibrationTables recalibrationTables, final Covariate[] requestedCovariates) { List result = new LinkedList(); int reportTableIndex = 0; @@ -272,8 +310,8 @@ public class RecalDataManager { reportTable.set(rowIndex, columnNames.get(columnIndex++).getFirst(), datum.getEmpiricalQuality()); 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.numObservations); - reportTable.set(rowIndex, columnNames.get(columnIndex).getFirst(), datum.numMismatches); + reportTable.set(rowIndex, columnNames.get(columnIndex++).getFirst(), datum.getNumObservations()); + reportTable.set(rowIndex, columnNames.get(columnIndex).getFirst(), datum.getNumMismatches()); rowIndex++; } @@ -320,7 +358,7 @@ public class RecalDataManager { files.getFirst().close(); final RScriptExecutor executor = new RScriptExecutor(); - executor.addScript(new Resource(SCRIPT_FILE, RecalDataManager.class)); + executor.addScript(new Resource(SCRIPT_FILE, RecalUtils.class)); executor.addArgs(csvFileName.getAbsolutePath()); executor.addArgs(plotFileName.getAbsolutePath()); executor.exec(); @@ -480,14 +518,14 @@ public class RecalDataManager { */ public static boolean isColorSpaceConsistent(final SOLID_NOCALL_STRATEGY strategy, final GATKSAMRecord read) { if (ReadUtils.isSOLiDRead(read)) { // If this is a SOLID read then we have to check if the color space is inconsistent. This is our only sign that SOLID has inserted the reference base - if (read.getAttribute(RecalDataManager.COLOR_SPACE_INCONSISTENCY_TAG) == null) { // Haven't calculated the inconsistency array yet for this read - final Object attr = read.getAttribute(RecalDataManager.COLOR_SPACE_ATTRIBUTE_TAG); + if (read.getAttribute(RecalUtils.COLOR_SPACE_INCONSISTENCY_TAG) == null) { // Haven't calculated the inconsistency array yet for this read + final Object attr = read.getAttribute(RecalUtils.COLOR_SPACE_ATTRIBUTE_TAG); if (attr != null) { byte[] colorSpace; if (attr instanceof String) colorSpace = ((String) attr).getBytes(); else - throw new UserException.MalformedBAM(read, String.format("Value encoded by %s in %s isn't a string!", RecalDataManager.COLOR_SPACE_ATTRIBUTE_TAG, read.getReadName())); + throw new UserException.MalformedBAM(read, String.format("Value encoded by %s in %s isn't a string!", RecalUtils.COLOR_SPACE_ATTRIBUTE_TAG, read.getReadName())); byte[] readBases = read.getReadBases(); // Loop over the read and calculate first the inferred bases from the color and then check if it is consistent with the read if (read.getReadNegativeStrandFlag()) @@ -501,7 +539,7 @@ public class RecalDataManager { inconsistency[i] = (byte) (thisBase == readBases[i] ? 0 : 1); prevBase = readBases[i]; } - read.setAttribute(RecalDataManager.COLOR_SPACE_INCONSISTENCY_TAG, inconsistency); + read.setAttribute(RecalUtils.COLOR_SPACE_INCONSISTENCY_TAG, inconsistency); } else if (strategy == SOLID_NOCALL_STRATEGY.THROW_EXCEPTION) // if the strategy calls for an exception, throw it throw new UserException.MalformedBAM(read, "Unable to find color space information in SOLiD read. First observed at read with name = " + read.getReadName() + " Unfortunately this .bam file can not be recalibrated without color space information because of potential reference bias."); @@ -545,7 +583,7 @@ public class RecalDataManager { * @return Returns true if the base was inconsistent with the color space */ public static boolean isColorSpaceConsistent(final GATKSAMRecord read, final int offset) { - final Object attr = read.getAttribute(RecalDataManager.COLOR_SPACE_INCONSISTENCY_TAG); + final Object attr = read.getAttribute(RecalUtils.COLOR_SPACE_INCONSISTENCY_TAG); if (attr != null) { final byte[] inconsistency = (byte[]) attr; // NOTE: The inconsistency array is in the direction of the read, not aligned to the reference! @@ -691,40 +729,4 @@ public class RecalDataManager { } - /** - * Adds the required covariates to a covariate list - * - * Note: this method really only checks if the classes object has the expected number of required covariates, then add them by hand. - * - * @param classes list of classes to add to the covariate list - * @return the covariate list - */ - private static ArrayList addRequiredCovariatesToList(List> classes) { - ArrayList dest = new ArrayList(classes.size()); - if (classes.size() != 2) - throw new ReviewedStingException("The number of required covariates has changed, this is a hard change in the code and needs to be inspected"); - - dest.add(new ReadGroupCovariate()); // enforce the order with RG first and QS next. - dest.add(new QualityScoreCovariate()); - return dest; - } - - /** - * Adds the standard covariates to a covariate list - * - * @param classes list of classes to add to the covariate list - * @return the covariate list - */ - private static ArrayList addStandardCovariatesToList(List> classes) { - ArrayList dest = new ArrayList(classes.size()); - for (Class covClass : classes) { - try { - final Covariate covariate = (Covariate) covClass.newInstance(); - dest.add(covariate); - } catch (Exception e) { - throw new DynamicClassResolutionException(covClass, e); - } - } - return dest; - } } diff --git a/public/java/src/org/broadinstitute/sting/gatk/walkers/bqsr/RecalibrationReport.java b/public/java/src/org/broadinstitute/sting/utils/recalibration/RecalibrationReport.java similarity index 82% rename from public/java/src/org/broadinstitute/sting/gatk/walkers/bqsr/RecalibrationReport.java rename to public/java/src/org/broadinstitute/sting/utils/recalibration/RecalibrationReport.java index e69cf4d69..e6ab9e38b 100644 --- a/public/java/src/org/broadinstitute/sting/gatk/walkers/bqsr/RecalibrationReport.java +++ b/public/java/src/org/broadinstitute/sting/utils/recalibration/RecalibrationReport.java @@ -1,11 +1,12 @@ -package org.broadinstitute.sting.gatk.walkers.bqsr; +package org.broadinstitute.sting.utils.recalibration; import org.broadinstitute.sting.gatk.report.GATKReport; import org.broadinstitute.sting.gatk.report.GATKReportTable; +import org.broadinstitute.sting.gatk.walkers.bqsr.*; +import org.broadinstitute.sting.utils.recalibration.covariates.Covariate; import org.broadinstitute.sting.utils.QualityUtils; import org.broadinstitute.sting.utils.collections.NestedIntegerArray; import org.broadinstitute.sting.utils.collections.Pair; -import org.broadinstitute.sting.utils.recalibration.RecalibrationTables; import java.io.File; import java.io.PrintStream; @@ -33,13 +34,13 @@ public class RecalibrationReport { public RecalibrationReport(final File RECAL_FILE) { final GATKReport report = new GATKReport(RECAL_FILE); - argumentTable = report.getTable(RecalDataManager.ARGUMENT_REPORT_TABLE_TITLE); + argumentTable = report.getTable(RecalUtils.ARGUMENT_REPORT_TABLE_TITLE); RAC = initializeArgumentCollectionTable(argumentTable); - GATKReportTable quantizedTable = report.getTable(RecalDataManager.QUANTIZED_REPORT_TABLE_TITLE); + GATKReportTable quantizedTable = report.getTable(RecalUtils.QUANTIZED_REPORT_TABLE_TITLE); quantizationInfo = initializeQuantizationTable(quantizedTable); - Pair, ArrayList> covariates = RecalDataManager.initializeCovariates(RAC); // initialize the required and optional covariates + Pair, ArrayList> covariates = RecalUtils.initializeCovariates(RAC); // initialize the required and optional covariates ArrayList requiredCovariates = covariates.getFirst(); ArrayList optionalCovariates = covariates.getSecond(); requestedCovariates = new Covariate[requiredCovariates.size() + optionalCovariates.size()]; @@ -57,13 +58,13 @@ public class RecalibrationReport { for (Covariate cov : requestedCovariates) cov.initialize(RAC); // initialize any covariate member variables using the shared argument collection - recalibrationTables = new RecalibrationTables(requestedCovariates, countReadGroups(report.getTable(RecalDataManager.READGROUP_REPORT_TABLE_TITLE))); + recalibrationTables = new RecalibrationTables(requestedCovariates, countReadGroups(report.getTable(RecalUtils.READGROUP_REPORT_TABLE_TITLE))); - parseReadGroupTable(report.getTable(RecalDataManager.READGROUP_REPORT_TABLE_TITLE), recalibrationTables.getTable(RecalibrationTables.TableType.READ_GROUP_TABLE)); + parseReadGroupTable(report.getTable(RecalUtils.READGROUP_REPORT_TABLE_TITLE), recalibrationTables.getTable(RecalibrationTables.TableType.READ_GROUP_TABLE)); - parseQualityScoreTable(report.getTable(RecalDataManager.QUALITY_SCORE_REPORT_TABLE_TITLE), recalibrationTables.getTable(RecalibrationTables.TableType.QUALITY_SCORE_TABLE)); + parseQualityScoreTable(report.getTable(RecalUtils.QUALITY_SCORE_REPORT_TABLE_TITLE), recalibrationTables.getTable(RecalibrationTables.TableType.QUALITY_SCORE_TABLE)); - parseAllCovariatesTable(report.getTable(RecalDataManager.ALL_COVARIATES_REPORT_TABLE_TITLE), recalibrationTables); + parseAllCovariatesTable(report.getTable(RecalUtils.ALL_COVARIATES_REPORT_TABLE_TITLE), recalibrationTables); } @@ -85,7 +86,7 @@ public class RecalibrationReport { private int countReadGroups(final GATKReportTable reportTable) { Set readGroups = new HashSet(); for ( int i = 0; i < reportTable.getNumRows(); i++ ) - readGroups.add(reportTable.get(i, RecalDataManager.READGROUP_COLUMN_NAME).toString()); + readGroups.add(reportTable.get(i, RecalUtils.READGROUP_COLUMN_NAME).toString()); return readGroups.size(); } @@ -139,17 +140,17 @@ public class RecalibrationReport { \ */ private void parseAllCovariatesTable(final GATKReportTable reportTable, final RecalibrationTables recalibrationTables) { for ( int i = 0; i < reportTable.getNumRows(); i++ ) { - final Object rg = reportTable.get(i, RecalDataManager.READGROUP_COLUMN_NAME); + final Object rg = reportTable.get(i, RecalUtils.READGROUP_COLUMN_NAME); tempCOVarray[0] = requestedCovariates[0].keyFromValue(rg); - final Object qual = reportTable.get(i, RecalDataManager.QUALITY_SCORE_COLUMN_NAME); + final Object qual = reportTable.get(i, RecalUtils.QUALITY_SCORE_COLUMN_NAME); tempCOVarray[1] = requestedCovariates[1].keyFromValue(qual); - final String covName = (String)reportTable.get(i, RecalDataManager.COVARIATE_NAME_COLUMN_NAME); + final String covName = (String)reportTable.get(i, RecalUtils.COVARIATE_NAME_COLUMN_NAME); final int covIndex = optionalCovariateIndexes.get(covName); - final Object covValue = reportTable.get(i, RecalDataManager.COVARIATE_VALUE_COLUMN_NAME); + final Object covValue = reportTable.get(i, RecalUtils.COVARIATE_VALUE_COLUMN_NAME); tempCOVarray[2] = requestedCovariates[RecalibrationTables.TableType.OPTIONAL_COVARIATE_TABLES_START.index + covIndex].keyFromValue(covValue); - final EventType event = EventType.eventFrom((String)reportTable.get(i, RecalDataManager.EVENT_TYPE_COLUMN_NAME)); + final EventType event = EventType.eventFrom((String)reportTable.get(i, RecalUtils.EVENT_TYPE_COLUMN_NAME)); tempCOVarray[3] = event.index; recalibrationTables.getTable(RecalibrationTables.TableType.OPTIONAL_COVARIATE_TABLES_START.index + covIndex).put(getRecalDatum(reportTable, i, false), tempCOVarray); @@ -164,11 +165,11 @@ public class RecalibrationReport { */ private void parseQualityScoreTable(final GATKReportTable reportTable, final NestedIntegerArray qualTable) { for ( int i = 0; i < reportTable.getNumRows(); i++ ) { - final Object rg = reportTable.get(i, RecalDataManager.READGROUP_COLUMN_NAME); + final Object rg = reportTable.get(i, RecalUtils.READGROUP_COLUMN_NAME); tempQUALarray[0] = requestedCovariates[0].keyFromValue(rg); - final Object qual = reportTable.get(i, RecalDataManager.QUALITY_SCORE_COLUMN_NAME); + final Object qual = reportTable.get(i, RecalUtils.QUALITY_SCORE_COLUMN_NAME); tempQUALarray[1] = requestedCovariates[1].keyFromValue(qual); - final EventType event = EventType.eventFrom((String)reportTable.get(i, RecalDataManager.EVENT_TYPE_COLUMN_NAME)); + final EventType event = EventType.eventFrom((String)reportTable.get(i, RecalUtils.EVENT_TYPE_COLUMN_NAME)); tempQUALarray[2] = event.index; qualTable.put(getRecalDatum(reportTable, i, false), tempQUALarray); @@ -183,9 +184,9 @@ public class RecalibrationReport { */ private void parseReadGroupTable(final GATKReportTable reportTable, final NestedIntegerArray rgTable) { for ( int i = 0; i < reportTable.getNumRows(); i++ ) { - final Object rg = reportTable.get(i, RecalDataManager.READGROUP_COLUMN_NAME); + final Object rg = reportTable.get(i, RecalUtils.READGROUP_COLUMN_NAME); tempRGarray[0] = requestedCovariates[0].keyFromValue(rg); - final EventType event = EventType.eventFrom((String)reportTable.get(i, RecalDataManager.EVENT_TYPE_COLUMN_NAME)); + final EventType event = EventType.eventFrom((String)reportTable.get(i, RecalUtils.EVENT_TYPE_COLUMN_NAME)); tempRGarray[1] = event.index; rgTable.put(getRecalDatum(reportTable, i, true), tempRGarray); @@ -193,13 +194,13 @@ public class RecalibrationReport { } private RecalDatum getRecalDatum(final GATKReportTable reportTable, final int row, final boolean hasEstimatedQReportedColumn) { - final long nObservations = (Long) reportTable.get(row, RecalDataManager.NUMBER_OBSERVATIONS_COLUMN_NAME); - final long nErrors = (Long) reportTable.get(row, RecalDataManager.NUMBER_ERRORS_COLUMN_NAME); - final double empiricalQuality = (Double) reportTable.get(row, RecalDataManager.EMPIRICAL_QUALITY_COLUMN_NAME); + final long nObservations = (Long) reportTable.get(row, RecalUtils.NUMBER_OBSERVATIONS_COLUMN_NAME); + final long nErrors = (Long) reportTable.get(row, RecalUtils.NUMBER_ERRORS_COLUMN_NAME); + final double empiricalQuality = (Double) reportTable.get(row, RecalUtils.EMPIRICAL_QUALITY_COLUMN_NAME); final double estimatedQReported = hasEstimatedQReportedColumn ? // the estimatedQreported column only exists in the ReadGroup table - (Double) reportTable.get(row, RecalDataManager.ESTIMATED_Q_REPORTED_COLUMN_NAME) : // we get it if we are in the read group table - Byte.parseByte((String) reportTable.get(row, RecalDataManager.QUALITY_SCORE_COLUMN_NAME)); // or we use the reported quality if we are in any other table + (Double) reportTable.get(row, RecalUtils.ESTIMATED_Q_REPORTED_COLUMN_NAME) : // we get it if we are in the read group table + Byte.parseByte((String) reportTable.get(row, RecalUtils.QUALITY_SCORE_COLUMN_NAME)); // or we use the reported quality if we are in any other table final RecalDatum datum = new RecalDatum(nObservations, nErrors, (byte)1); datum.setEstimatedQReported(estimatedQReported); @@ -218,8 +219,8 @@ public class RecalibrationReport { final Long[] counts = new Long[QualityUtils.MAX_QUAL_SCORE + 1]; for ( int i = 0; i < table.getNumRows(); i++ ) { final byte originalQual = (byte)i; - final Object quantizedObject = table.get(i, RecalDataManager.QUANTIZED_VALUE_COLUMN_NAME); - final Object countObject = table.get(i, RecalDataManager.QUANTIZED_COUNT_COLUMN_NAME); + final Object quantizedObject = table.get(i, RecalUtils.QUANTIZED_VALUE_COLUMN_NAME); + final Object countObject = table.get(i, RecalUtils.QUANTIZED_COUNT_COLUMN_NAME); final byte quantizedQual = Byte.parseByte(quantizedObject.toString()); final long quantizedCount = Long.parseLong(countObject.toString()); quals[originalQual] = quantizedQual; @@ -239,7 +240,7 @@ public class RecalibrationReport { for ( int i = 0; i < table.getNumRows(); i++ ) { final String argument = table.get(i, "Argument").toString(); - Object value = table.get(i, RecalDataManager.ARGUMENT_VALUE_COLUMN_NAME); + Object value = table.get(i, RecalUtils.ARGUMENT_VALUE_COLUMN_NAME); if (value.equals("null")) value = null; // generic translation of null values that were printed out as strings | todo -- add this capability to the GATKReport @@ -250,10 +251,10 @@ public class RecalibrationReport { RAC.DO_NOT_USE_STANDARD_COVARIATES = Boolean.parseBoolean((String) value); else if (argument.equals("solid_recal_mode")) - RAC.SOLID_RECAL_MODE = RecalDataManager.SOLID_RECAL_MODE.recalModeFromString((String) value); + RAC.SOLID_RECAL_MODE = RecalUtils.SOLID_RECAL_MODE.recalModeFromString((String) value); else if (argument.equals("solid_nocall_strategy")) - RAC.SOLID_NOCALL_STRATEGY = RecalDataManager.SOLID_NOCALL_STRATEGY.nocallStrategyFromString((String) value); + RAC.SOLID_NOCALL_STRATEGY = RecalUtils.SOLID_NOCALL_STRATEGY.nocallStrategyFromString((String) value); else if (argument.equals("mismatches_context_size")) RAC.MISMATCHES_CONTEXT_SIZE = Integer.parseInt((String) value); @@ -307,7 +308,7 @@ public class RecalibrationReport { } public void output(PrintStream output) { - RecalDataManager.outputRecalibrationReport(argumentTable, quantizationInfo, recalibrationTables, requestedCovariates, output); + RecalUtils.outputRecalibrationReport(argumentTable, quantizationInfo, recalibrationTables, requestedCovariates, output); } public RecalibrationArgumentCollection getRAC() { 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 0416b5eb9..f37e69c9a 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 +25,7 @@ package org.broadinstitute.sting.utils.recalibration; -import org.broadinstitute.sting.gatk.walkers.bqsr.Covariate; -import org.broadinstitute.sting.gatk.walkers.bqsr.EventType; -import org.broadinstitute.sting.gatk.walkers.bqsr.RecalDatum; +import org.broadinstitute.sting.utils.recalibration.covariates.Covariate; import org.broadinstitute.sting.utils.collections.NestedIntegerArray; /** diff --git a/public/java/src/org/broadinstitute/sting/gatk/walkers/bqsr/BinaryTagCovariate.java b/public/java/src/org/broadinstitute/sting/utils/recalibration/covariates/BinaryTagCovariate.java similarity index 89% rename from public/java/src/org/broadinstitute/sting/gatk/walkers/bqsr/BinaryTagCovariate.java rename to public/java/src/org/broadinstitute/sting/utils/recalibration/covariates/BinaryTagCovariate.java index a89586c2c..cebdebf9d 100644 --- a/public/java/src/org/broadinstitute/sting/gatk/walkers/bqsr/BinaryTagCovariate.java +++ b/public/java/src/org/broadinstitute/sting/utils/recalibration/covariates/BinaryTagCovariate.java @@ -1,5 +1,7 @@ -package org.broadinstitute.sting.gatk.walkers.bqsr; +package org.broadinstitute.sting.utils.recalibration.covariates; +import org.broadinstitute.sting.utils.recalibration.ReadCovariates; +import org.broadinstitute.sting.gatk.walkers.bqsr.RecalibrationArgumentCollection; import org.broadinstitute.sting.utils.exceptions.UserException; import org.broadinstitute.sting.utils.sam.GATKSAMRecord; diff --git a/public/java/src/org/broadinstitute/sting/gatk/walkers/bqsr/ContextCovariate.java b/public/java/src/org/broadinstitute/sting/utils/recalibration/covariates/ContextCovariate.java similarity index 98% rename from public/java/src/org/broadinstitute/sting/gatk/walkers/bqsr/ContextCovariate.java rename to public/java/src/org/broadinstitute/sting/utils/recalibration/covariates/ContextCovariate.java index 5fe8809fb..4c20284d9 100644 --- a/public/java/src/org/broadinstitute/sting/gatk/walkers/bqsr/ContextCovariate.java +++ b/public/java/src/org/broadinstitute/sting/utils/recalibration/covariates/ContextCovariate.java @@ -23,8 +23,10 @@ * THE USE OR OTHER DEALINGS IN THE SOFTWARE. */ -package org.broadinstitute.sting.gatk.walkers.bqsr; +package org.broadinstitute.sting.utils.recalibration.covariates; +import org.broadinstitute.sting.utils.recalibration.ReadCovariates; +import org.broadinstitute.sting.gatk.walkers.bqsr.RecalibrationArgumentCollection; import org.broadinstitute.sting.utils.BaseUtils; import org.broadinstitute.sting.utils.clipping.ClippingRepresentation; import org.broadinstitute.sting.utils.clipping.ReadClipper; diff --git a/public/java/src/org/broadinstitute/sting/gatk/walkers/bqsr/Covariate.java b/public/java/src/org/broadinstitute/sting/utils/recalibration/covariates/Covariate.java similarity index 94% rename from public/java/src/org/broadinstitute/sting/gatk/walkers/bqsr/Covariate.java rename to public/java/src/org/broadinstitute/sting/utils/recalibration/covariates/Covariate.java index 1ad5346fa..c613135bb 100755 --- a/public/java/src/org/broadinstitute/sting/gatk/walkers/bqsr/Covariate.java +++ b/public/java/src/org/broadinstitute/sting/utils/recalibration/covariates/Covariate.java @@ -1,5 +1,7 @@ -package org.broadinstitute.sting.gatk.walkers.bqsr; +package org.broadinstitute.sting.utils.recalibration.covariates; +import org.broadinstitute.sting.utils.recalibration.ReadCovariates; +import org.broadinstitute.sting.gatk.walkers.bqsr.RecalibrationArgumentCollection; import org.broadinstitute.sting.utils.sam.GATKSAMRecord; /* @@ -89,8 +91,3 @@ public interface Covariate { public int maximumKeyValue(); } -interface RequiredCovariate extends Covariate {} - -interface StandardCovariate extends Covariate {} - -interface ExperimentalCovariate extends Covariate {} diff --git a/public/java/src/org/broadinstitute/sting/gatk/walkers/bqsr/CycleCovariate.java b/public/java/src/org/broadinstitute/sting/utils/recalibration/covariates/CycleCovariate.java similarity index 97% rename from public/java/src/org/broadinstitute/sting/gatk/walkers/bqsr/CycleCovariate.java rename to public/java/src/org/broadinstitute/sting/utils/recalibration/covariates/CycleCovariate.java index f0ff8f2bd..4f15419c7 100755 --- a/public/java/src/org/broadinstitute/sting/gatk/walkers/bqsr/CycleCovariate.java +++ b/public/java/src/org/broadinstitute/sting/utils/recalibration/covariates/CycleCovariate.java @@ -1,5 +1,7 @@ -package org.broadinstitute.sting.gatk.walkers.bqsr; +package org.broadinstitute.sting.utils.recalibration.covariates; +import org.broadinstitute.sting.utils.recalibration.ReadCovariates; +import org.broadinstitute.sting.gatk.walkers.bqsr.RecalibrationArgumentCollection; import org.broadinstitute.sting.utils.BaseUtils; import org.broadinstitute.sting.utils.NGSPlatform; import org.broadinstitute.sting.utils.exceptions.UserException; diff --git a/public/java/src/org/broadinstitute/sting/utils/recalibration/covariates/ExperimentalCovariate.java b/public/java/src/org/broadinstitute/sting/utils/recalibration/covariates/ExperimentalCovariate.java new file mode 100644 index 000000000..72df2a410 --- /dev/null +++ b/public/java/src/org/broadinstitute/sting/utils/recalibration/covariates/ExperimentalCovariate.java @@ -0,0 +1,30 @@ +package org.broadinstitute.sting.utils.recalibration.covariates; + +/** + * [Short one sentence description of this walker] + *

+ *

+ * [Functionality of this walker] + *

+ *

+ *

Input

+ *

+ * [Input description] + *

+ *

+ *

Output

+ *

+ * [Output description] + *

+ *

+ *

Examples

+ * 
+ *    java
+ *      -jar GenomeAnalysisTK.jar
+ *      -T $WalkerName
+ *
+ * + * @author Your Name + * @since Date created + */ +public interface ExperimentalCovariate extends Covariate {} diff --git a/public/java/src/org/broadinstitute/sting/gatk/walkers/bqsr/QualityScoreCovariate.java b/public/java/src/org/broadinstitute/sting/utils/recalibration/covariates/QualityScoreCovariate.java similarity index 92% rename from public/java/src/org/broadinstitute/sting/gatk/walkers/bqsr/QualityScoreCovariate.java rename to public/java/src/org/broadinstitute/sting/utils/recalibration/covariates/QualityScoreCovariate.java index dd7060ff8..3ef8ee931 100755 --- a/public/java/src/org/broadinstitute/sting/gatk/walkers/bqsr/QualityScoreCovariate.java +++ b/public/java/src/org/broadinstitute/sting/utils/recalibration/covariates/QualityScoreCovariate.java @@ -1,5 +1,7 @@ -package org.broadinstitute.sting.gatk.walkers.bqsr; +package org.broadinstitute.sting.utils.recalibration.covariates; +import org.broadinstitute.sting.utils.recalibration.ReadCovariates; +import org.broadinstitute.sting.gatk.walkers.bqsr.RecalibrationArgumentCollection; import org.broadinstitute.sting.utils.QualityUtils; import org.broadinstitute.sting.utils.sam.GATKSAMRecord; diff --git a/public/java/src/org/broadinstitute/sting/gatk/walkers/bqsr/ReadGroupCovariate.java b/public/java/src/org/broadinstitute/sting/utils/recalibration/covariates/ReadGroupCovariate.java similarity index 94% rename from public/java/src/org/broadinstitute/sting/gatk/walkers/bqsr/ReadGroupCovariate.java rename to public/java/src/org/broadinstitute/sting/utils/recalibration/covariates/ReadGroupCovariate.java index f04d27b7a..85568dac9 100755 --- a/public/java/src/org/broadinstitute/sting/gatk/walkers/bqsr/ReadGroupCovariate.java +++ b/public/java/src/org/broadinstitute/sting/utils/recalibration/covariates/ReadGroupCovariate.java @@ -1,5 +1,7 @@ -package org.broadinstitute.sting.gatk.walkers.bqsr; +package org.broadinstitute.sting.utils.recalibration.covariates; +import org.broadinstitute.sting.utils.recalibration.ReadCovariates; +import org.broadinstitute.sting.gatk.walkers.bqsr.RecalibrationArgumentCollection; import org.broadinstitute.sting.utils.sam.GATKSAMReadGroupRecord; import org.broadinstitute.sting.utils.sam.GATKSAMRecord; diff --git a/public/java/src/org/broadinstitute/sting/utils/recalibration/covariates/RequiredCovariate.java b/public/java/src/org/broadinstitute/sting/utils/recalibration/covariates/RequiredCovariate.java new file mode 100644 index 000000000..50755dbcf --- /dev/null +++ b/public/java/src/org/broadinstitute/sting/utils/recalibration/covariates/RequiredCovariate.java @@ -0,0 +1,30 @@ +package org.broadinstitute.sting.utils.recalibration.covariates; + +/** + * [Short one sentence description of this walker] + *

+ *

+ * [Functionality of this walker] + *

+ *

+ *

Input

+ *

+ * [Input description] + *

+ *

+ *

Output

+ *

+ * [Output description] + *

+ *

+ *

Examples

+ * 
+ *    java
+ *      -jar GenomeAnalysisTK.jar
+ *      -T $WalkerName
+ *
+ * + * @author Your Name + * @since Date created + */ +public interface RequiredCovariate extends Covariate {} diff --git a/public/java/src/org/broadinstitute/sting/utils/recalibration/covariates/StandardCovariate.java b/public/java/src/org/broadinstitute/sting/utils/recalibration/covariates/StandardCovariate.java new file mode 100644 index 000000000..444954f25 --- /dev/null +++ b/public/java/src/org/broadinstitute/sting/utils/recalibration/covariates/StandardCovariate.java @@ -0,0 +1,30 @@ +package org.broadinstitute.sting.utils.recalibration.covariates; + +/** + * [Short one sentence description of this walker] + *

+ *

+ * [Functionality of this walker] + *

+ *

+ *

Input

+ *

+ * [Input description] + *

+ *

+ *

Output

+ *

+ * [Output description] + *

+ *

+ *

Examples

+ * 
+ *    java
+ *      -jar GenomeAnalysisTK.jar
+ *      -T $WalkerName
+ *
+ * + * @author Your Name + * @since Date created + */ +public interface StandardCovariate extends Covariate {} diff --git a/public/java/src/org/broadinstitute/sting/utils/sam/GATKSAMRecord.java b/public/java/src/org/broadinstitute/sting/utils/sam/GATKSAMRecord.java index 659615cf4..c9b3a2df8 100755 --- a/public/java/src/org/broadinstitute/sting/utils/sam/GATKSAMRecord.java +++ b/public/java/src/org/broadinstitute/sting/utils/sam/GATKSAMRecord.java @@ -25,7 +25,7 @@ package org.broadinstitute.sting.utils.sam; import net.sf.samtools.*; -import org.broadinstitute.sting.gatk.walkers.bqsr.EventType; +import org.broadinstitute.sting.utils.recalibration.EventType; import org.broadinstitute.sting.utils.NGSPlatform; import org.broadinstitute.sting.utils.exceptions.ReviewedStingException; diff --git a/public/java/test/org/broadinstitute/sting/gatk/walkers/bqsr/BQSRGathererUnitTest.java b/public/java/test/org/broadinstitute/sting/gatk/walkers/bqsr/BQSRGathererUnitTest.java index 8e9f2533f..f1ffbe80f 100644 --- a/public/java/test/org/broadinstitute/sting/gatk/walkers/bqsr/BQSRGathererUnitTest.java +++ b/public/java/test/org/broadinstitute/sting/gatk/walkers/bqsr/BQSRGathererUnitTest.java @@ -2,6 +2,7 @@ package org.broadinstitute.sting.gatk.walkers.bqsr; import org.broadinstitute.sting.gatk.report.GATKReport; import org.broadinstitute.sting.gatk.report.GATKReportTable; +import org.broadinstitute.sting.utils.recalibration.RecalUtils; import org.testng.Assert; import org.testng.annotations.Test; @@ -33,15 +34,15 @@ public class BQSRGathererUnitTest { for (GATKReportTable originalTable : originalReport.getTables()) { GATKReportTable calculatedTable = calculatedReport.getTable(originalTable.getTableName()); List columnsToTest = new LinkedList(); - columnsToTest.add(RecalDataManager.NUMBER_OBSERVATIONS_COLUMN_NAME); - columnsToTest.add(RecalDataManager.NUMBER_ERRORS_COLUMN_NAME); - if (originalTable.getTableName().equals(RecalDataManager.ARGUMENT_REPORT_TABLE_TITLE)) { // these tables must be IDENTICAL - columnsToTest.add(RecalDataManager.ARGUMENT_VALUE_COLUMN_NAME); + columnsToTest.add(RecalUtils.NUMBER_OBSERVATIONS_COLUMN_NAME); + columnsToTest.add(RecalUtils.NUMBER_ERRORS_COLUMN_NAME); + if (originalTable.getTableName().equals(RecalUtils.ARGUMENT_REPORT_TABLE_TITLE)) { // these tables must be IDENTICAL + columnsToTest.add(RecalUtils.ARGUMENT_VALUE_COLUMN_NAME); testTablesWithColumnsAndFactor(originalTable, calculatedTable, columnsToTest, 1); } - else if (originalTable.getTableName().equals(RecalDataManager.QUANTIZED_REPORT_TABLE_TITLE)) { - columnsToTest.add(RecalDataManager.QUANTIZED_COUNT_COLUMN_NAME); + else if (originalTable.getTableName().equals(RecalUtils.QUANTIZED_REPORT_TABLE_TITLE)) { + columnsToTest.add(RecalUtils.QUANTIZED_COUNT_COLUMN_NAME); testTablesWithColumnsAndFactor(originalTable, calculatedTable, columnsToTest, 2); } diff --git a/public/java/test/org/broadinstitute/sting/gatk/walkers/bqsr/ContextCovariateUnitTest.java b/public/java/test/org/broadinstitute/sting/utils/recalibration/ContextCovariateUnitTest.java similarity index 89% rename from public/java/test/org/broadinstitute/sting/gatk/walkers/bqsr/ContextCovariateUnitTest.java rename to public/java/test/org/broadinstitute/sting/utils/recalibration/ContextCovariateUnitTest.java index 553b7e237..2556448ad 100644 --- a/public/java/test/org/broadinstitute/sting/gatk/walkers/bqsr/ContextCovariateUnitTest.java +++ b/public/java/test/org/broadinstitute/sting/utils/recalibration/ContextCovariateUnitTest.java @@ -1,5 +1,8 @@ -package org.broadinstitute.sting.gatk.walkers.bqsr; +package org.broadinstitute.sting.utils.recalibration; +import org.broadinstitute.sting.gatk.walkers.bqsr.RecalibrationArgumentCollection; +import org.broadinstitute.sting.utils.recalibration.covariates.ContextCovariate; +import org.broadinstitute.sting.utils.recalibration.covariates.Covariate; import org.broadinstitute.sting.utils.clipping.ClippingRepresentation; import org.broadinstitute.sting.utils.clipping.ReadClipper; import org.broadinstitute.sting.utils.sam.GATKSAMRecord; diff --git a/public/java/test/org/broadinstitute/sting/gatk/walkers/bqsr/CycleCovariateUnitTest.java b/public/java/test/org/broadinstitute/sting/utils/recalibration/CycleCovariateUnitTest.java similarity index 90% rename from public/java/test/org/broadinstitute/sting/gatk/walkers/bqsr/CycleCovariateUnitTest.java rename to public/java/test/org/broadinstitute/sting/utils/recalibration/CycleCovariateUnitTest.java index 3fa1e916d..c3d93b2cb 100644 --- a/public/java/test/org/broadinstitute/sting/gatk/walkers/bqsr/CycleCovariateUnitTest.java +++ b/public/java/test/org/broadinstitute/sting/utils/recalibration/CycleCovariateUnitTest.java @@ -1,5 +1,7 @@ -package org.broadinstitute.sting.gatk.walkers.bqsr; +package org.broadinstitute.sting.utils.recalibration; +import org.broadinstitute.sting.gatk.walkers.bqsr.RecalibrationArgumentCollection; +import org.broadinstitute.sting.utils.recalibration.covariates.CycleCovariate; import org.broadinstitute.sting.utils.sam.GATKSAMReadGroupRecord; import org.broadinstitute.sting.utils.sam.GATKSAMRecord; import org.broadinstitute.sting.utils.sam.ReadUtils; diff --git a/public/java/test/org/broadinstitute/sting/gatk/walkers/bqsr/ReadCovariatesUnitTest.java b/public/java/test/org/broadinstitute/sting/utils/recalibration/ReadCovariatesUnitTest.java similarity index 92% rename from public/java/test/org/broadinstitute/sting/gatk/walkers/bqsr/ReadCovariatesUnitTest.java rename to public/java/test/org/broadinstitute/sting/utils/recalibration/ReadCovariatesUnitTest.java index 37994cf12..dac26cb53 100644 --- a/public/java/test/org/broadinstitute/sting/gatk/walkers/bqsr/ReadCovariatesUnitTest.java +++ b/public/java/test/org/broadinstitute/sting/utils/recalibration/ReadCovariatesUnitTest.java @@ -1,5 +1,7 @@ -package org.broadinstitute.sting.gatk.walkers.bqsr; +package org.broadinstitute.sting.utils.recalibration; +import org.broadinstitute.sting.gatk.walkers.bqsr.RecalibrationArgumentCollection; +import org.broadinstitute.sting.utils.recalibration.covariates.*; import org.broadinstitute.sting.utils.sam.GATKSAMReadGroupRecord; import org.broadinstitute.sting.utils.sam.GATKSAMRecord; import org.broadinstitute.sting.utils.sam.ReadUtils; @@ -41,7 +43,7 @@ public class ReadCovariatesUnitTest { requestedCovariates[2] = coCov; requestedCovariates[3] = cyCov; - ReadCovariates rc = RecalDataManager.computeCovariates(read, requestedCovariates); + ReadCovariates rc = RecalUtils.computeCovariates(read, requestedCovariates); // check that the length is correct Assert.assertEquals(rc.getMismatchesKeySet().length, length); diff --git a/public/java/test/org/broadinstitute/sting/gatk/walkers/bqsr/ReadGroupCovariateUnitTest.java b/public/java/test/org/broadinstitute/sting/utils/recalibration/ReadGroupCovariateUnitTest.java similarity index 88% rename from public/java/test/org/broadinstitute/sting/gatk/walkers/bqsr/ReadGroupCovariateUnitTest.java rename to public/java/test/org/broadinstitute/sting/utils/recalibration/ReadGroupCovariateUnitTest.java index a83508353..78a74d259 100644 --- a/public/java/test/org/broadinstitute/sting/gatk/walkers/bqsr/ReadGroupCovariateUnitTest.java +++ b/public/java/test/org/broadinstitute/sting/utils/recalibration/ReadGroupCovariateUnitTest.java @@ -1,5 +1,7 @@ -package org.broadinstitute.sting.gatk.walkers.bqsr; +package org.broadinstitute.sting.utils.recalibration; +import org.broadinstitute.sting.gatk.walkers.bqsr.RecalibrationArgumentCollection; +import org.broadinstitute.sting.utils.recalibration.covariates.ReadGroupCovariate; import org.broadinstitute.sting.utils.sam.GATKSAMReadGroupRecord; import org.broadinstitute.sting.utils.sam.GATKSAMRecord; import org.broadinstitute.sting.utils.sam.ReadUtils; diff --git a/public/java/test/org/broadinstitute/sting/gatk/walkers/bqsr/RecalibrationReportUnitTest.java b/public/java/test/org/broadinstitute/sting/utils/recalibration/RecalibrationReportUnitTest.java similarity index 95% rename from public/java/test/org/broadinstitute/sting/gatk/walkers/bqsr/RecalibrationReportUnitTest.java rename to public/java/test/org/broadinstitute/sting/utils/recalibration/RecalibrationReportUnitTest.java index e4a77c016..387cc94d6 100644 --- a/public/java/test/org/broadinstitute/sting/gatk/walkers/bqsr/RecalibrationReportUnitTest.java +++ b/public/java/test/org/broadinstitute/sting/utils/recalibration/RecalibrationReportUnitTest.java @@ -1,9 +1,10 @@ -package org.broadinstitute.sting.gatk.walkers.bqsr; +package org.broadinstitute.sting.utils.recalibration; +import org.broadinstitute.sting.gatk.walkers.bqsr.RecalibrationArgumentCollection; +import org.broadinstitute.sting.utils.recalibration.covariates.*; import org.broadinstitute.sting.utils.QualityUtils; import org.broadinstitute.sting.utils.collections.NestedIntegerArray; import org.broadinstitute.sting.utils.exceptions.ReviewedStingException; -import org.broadinstitute.sting.utils.recalibration.RecalibrationTables; import org.broadinstitute.sting.utils.sam.GATKSAMReadGroupRecord; import org.broadinstitute.sting.utils.sam.GATKSAMRecord; import org.broadinstitute.sting.utils.sam.ReadUtils; @@ -72,7 +73,7 @@ public class RecalibrationReportUnitTest { final int expectedKeys = expectedNumberOfKeys(4, length, RAC.INDELS_CONTEXT_SIZE, RAC.MISMATCHES_CONTEXT_SIZE); int nKeys = 0; // keep track of how many keys were produced - final ReadCovariates rc = RecalDataManager.computeCovariates(read, requestedCovariates); + final ReadCovariates rc = RecalUtils.computeCovariates(read, requestedCovariates); final RecalibrationTables recalibrationTables = new RecalibrationTables(requestedCovariates); final NestedIntegerArray rgTable = recalibrationTables.getTable(RecalibrationTables.TableType.READ_GROUP_TABLE);