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Added functionality of outputting sorted GATKReport Tables 

- Added an optional argument to BaseRecalibrator to produce sorted GATKReport Tables
- Modified BSQR Integration Tests to include the optional argument. Tests now produce sorted tables
This commit is contained in:
Tad Jordan 2012-12-14 12:12:10 -05:00
parent b0cb513793
commit b491c177ff
11 changed files with 156 additions and 60 deletions
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37
protected/java/test/org/broadinstitute/sting/gatk/walkers/bqsr/BQSRIntegrationTest.java
View File

@ -38,7 +38,8 @@ public class BQSRIntegrationTest extends WalkerTest {
args +
" -knownSites " + (reference.equals(b36KGReference) ? b36dbSNP129 : hg18dbSNP132) +
" --allow_potentially_misencoded_quality_scores" + // TODO -- remove me when we get new SOLiD bams
" -o %s";
" -o %s" +
" -sortAllCols";
}
@Override
@ -52,21 +53,21 @@ public class BQSRIntegrationTest extends WalkerTest {
String HiSeqBam = privateTestDir + "HiSeq.1mb.1RG.bam";
String HiSeqInterval = "chr1:10,000,000-10,100,000";
return new Object[][]{
{new BQSRTest(hg18Reference, HiSeqBam, HiSeqInterval, "", "4fd3c9ad97e6ac58cba644a76564c9f7")},
{new BQSRTest(hg18Reference, HiSeqBam, HiSeqInterval, " --no_standard_covs -cov ContextCovariate", "2620f734cce20f70ce13afd880e46e5c")},
{new BQSRTest(hg18Reference, HiSeqBam, HiSeqInterval, " --no_standard_covs -cov CycleCovariate", "5eb3b94e767da19a4c037ee132e4b19a")},
{new BQSRTest(hg18Reference, HiSeqBam, HiSeqInterval, " --indels_context_size 4", "ab261d291b107a3da7897759c0e4fa89")},
{new BQSRTest(hg18Reference, HiSeqBam, HiSeqInterval, " --low_quality_tail 5", "292303f649fbb19dc05d4a0197a49eeb")},
{new BQSRTest(hg18Reference, HiSeqBam, HiSeqInterval, " --quantizing_levels 6", "8ced9d1094493f17fb1876b818a64541")},
{new BQSRTest(hg18Reference, HiSeqBam, HiSeqInterval, " --mismatches_context_size 4", "abb838131e403d39820dbd66932d1ed0")},
{new BQSRTest(b36KGReference, validationDataLocation + "NA12892.SLX.SRP000031.2009_06.selected.1Mb.1RG.bam", "1:10,000,000-10,200,000", "", "f70d8b5358bc2f76696f14b7a807ede0")},
{new BQSRTest(b36KGReference, validationDataLocation + "NA19240.chr1.BFAST.SOLID.bam", "1:10,000,000-10,200,000", "", "4c0f63e06830681560a1e9f9aad9fe98")},
{new BQSRTest(b36KGReference, validationDataLocation + "NA12873.454.SRP000031.2009_06.chr1.10_20mb.1RG.bam", "1:10,000,000-10,200,000", "", "8f62aa0e75770204c98d8299793cc53c")},
{new BQSRTest(b36KGReference, validationDataLocation + "originalQuals.1kg.chr1.1-1K.1RG.bam", "1:1-1,000", " -OQ", "03c29a0c1d21f72b12daf51cec111599")},
{new BQSRTest(b36KGReference, validationDataLocation + "NA19240.chr1.BFAST.SOLID.bam", "1:10,000,000-20,000,000", " --solid_recal_mode REMOVE_REF_BIAS", "7080b2cad02ec6e67ebc766b2dccebf8")},
{new BQSRTest(b36KGReference, privateTestDir + "NA19240.chr1.BFAST.SOLID.hasCSNoCall.bam", "1:50,000-80,000", " --solid_nocall_strategy LEAVE_READ_UNRECALIBRATED", "30e76055c16843b6e33e5b9bd8ced57c")},
{new BQSRTest(b36KGReference, validationDataLocation + "NA12892.SLX.SRP000031.2009_06.selected.1Mb.1RG.bam", "1:10,000,000-10,200,000", " -knownSites:anyNameABCD,VCF " + privateTestDir + "vcfexample3.vcf", "f70d8b5358bc2f76696f14b7a807ede0")},
{new BQSRTest(b36KGReference, validationDataLocation + "NA12892.SLX.SRP000031.2009_06.selected.1Mb.1RG.bam", "1:10,000,000-10,200,000", " -knownSites:bed " + validationDataLocation + "bqsrKnownTest.bed", "5e657fd6a44dcdc7674b6e5a2de5dc83")},
{new BQSRTest(hg18Reference, HiSeqBam, HiSeqInterval, "", "2f250fecb930e0dfe0f63fe0fed3960b")},
{new BQSRTest(hg18Reference, HiSeqBam, HiSeqInterval, " --no_standard_covs -cov ContextCovariate", "26c8d7226139a040557b1d3b1c8792f0")},
{new BQSRTest(hg18Reference, HiSeqBam, HiSeqInterval, " --no_standard_covs -cov CycleCovariate", "9b43a1839cb6ea03aec1d96f15ca8efb")},
{new BQSRTest(hg18Reference, HiSeqBam, HiSeqInterval, " --indels_context_size 4", "3159a9d136c45e4a65d46a23dc8fd3b5")},
{new BQSRTest(hg18Reference, HiSeqBam, HiSeqInterval, " --low_quality_tail 5", "bb7262829effbbdbc8d88dd36f480368")},
{new BQSRTest(hg18Reference, HiSeqBam, HiSeqInterval, " --quantizing_levels 6", "fbb002fa2b9197c4b555852dccc11562")},
{new BQSRTest(hg18Reference, HiSeqBam, HiSeqInterval, " --mismatches_context_size 4", "7392acb71131a60a527ca32715fc59be")},
{new BQSRTest(b36KGReference, validationDataLocation + "NA12892.SLX.SRP000031.2009_06.selected.1Mb.1RG.bam", "1:10,000,000-10,200,000", "", "49d4383896a90795d94138db1410a7df")},
{new BQSRTest(b36KGReference, validationDataLocation + "NA19240.chr1.BFAST.SOLID.bam", "1:10,000,000-10,200,000", "", "427448eff98cf194cc7217c0b1401e79")},
{new BQSRTest(b36KGReference, validationDataLocation + "NA12873.454.SRP000031.2009_06.chr1.10_20mb.1RG.bam", "1:10,000,000-10,200,000", "", "50cd1a10b6ecb3d09f90f1e4a66da95d")},
{new BQSRTest(b36KGReference, validationDataLocation + "originalQuals.1kg.chr1.1-1K.1RG.bam", "1:1-1,000", " -OQ", "1dc71561c9d0fb56f9876cb5043c5376")},
{new BQSRTest(b36KGReference, validationDataLocation + "NA19240.chr1.BFAST.SOLID.bam", "1:10,000,000-20,000,000", " --solid_recal_mode REMOVE_REF_BIAS", "13e8f032e76340b114847c90af0a1f8a")},
{new BQSRTest(b36KGReference, privateTestDir + "NA19240.chr1.BFAST.SOLID.hasCSNoCall.bam", "1:50,000-80,000", " --solid_nocall_strategy LEAVE_READ_UNRECALIBRATED", "03f58ae4f9d203034e895a3636fc108f")},
{new BQSRTest(b36KGReference, validationDataLocation + "NA12892.SLX.SRP000031.2009_06.selected.1Mb.1RG.bam", "1:10,000,000-10,200,000", " -knownSites:anyNameABCD,VCF " + privateTestDir + "vcfexample3.vcf", "49d4383896a90795d94138db1410a7df")},
{new BQSRTest(b36KGReference, validationDataLocation + "NA12892.SLX.SRP000031.2009_06.selected.1Mb.1RG.bam", "1:10,000,000-10,200,000", " -knownSites:bed " + validationDataLocation + "bqsrKnownTest.bed", "2db2ef8c2d63e167663d70340182f49a")},
};
}
@ -100,6 +101,7 @@ public class BQSRIntegrationTest extends WalkerTest {
" -knownSites " + b36dbSNP129 +
" -L 1:10,000,000-10,200,000" +
" -o /dev/null" +
" -sortAllCols" +
" --plot_pdf_file /dev/null" +
" --intermediate_csv_file %s",
Arrays.asList("d1c38a3418979400630e2bca1140689c"));
@ -114,7 +116,8 @@ public class BQSRIntegrationTest extends WalkerTest {
" -I " + privateTestDir + "NA19240.chr1.BFAST.SOLID.hasCSNoCall.bam" +
" -L 1:50,000-80,000" +
" --allow_potentially_misencoded_quality_scores" + // TODO -- remove me when we get new SOLiD bams
" -o %s",
" -o %s" +
" -sortAllCols",
1, // just one output file
UserException.class);
executeTest("testBQSRFailWithSolidNoCall", spec);

7
public/java/src/org/broadinstitute/sting/gatk/report/GATKReport.java
View File

@ -117,7 +117,7 @@ public class GATKReport {
* @param numColumns the number of columns in this table
*/
public void addTable(final String tableName, final String tableDescription, final int numColumns) {
addTable(tableName, tableDescription, numColumns, false);
addTable(tableName, tableDescription, numColumns, false, false);
}
/**
@ -127,9 +127,10 @@ public class GATKReport {
* @param tableDescription the description of the table
* @param numColumns the number of columns in this table
* @param sortByRowID whether to sort the rows by the row ID
* @param sortByAllColumns whether to sort the rows by all columns starting from leftmost column
*/
public void addTable(final String tableName, final String tableDescription, final int numColumns, final boolean sortByRowID) {
GATKReportTable table = new GATKReportTable(tableName, tableDescription, numColumns, sortByRowID);
public void addTable(final String tableName, final String tableDescription, final int numColumns, final boolean sortByRowID, final boolean sortByAllColumns) {
GATKReportTable table = new GATKReportTable(tableName, tableDescription, numColumns, sortByRowID, sortByAllColumns);
tables.put(tableName, table);
}

121
public/java/src/org/broadinstitute/sting/gatk/report/GATKReportTable.java
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@ -47,6 +47,7 @@ public class GATKReportTable {
private final String tableDescription;
private final boolean sortByRowID;
private final boolean sortByAllColumns;
private List<Object[]> underlyingData;
private final List<GATKReportColumn> columnInfo;
@ -108,6 +109,9 @@ public class GATKReportTable {
// when reading from a file, we do not re-sort the rows
sortByRowID = false;
// when reading from a file, we do not re-sort the rows
sortByAllColumns = false;
// initialize the data
final int nColumns = Integer.parseInt(tableData[TableDataHeaderFields.COLS.index()]);
final int nRows = Integer.parseInt(tableData[TableDataHeaderFields.ROWS.index()]);
@ -177,7 +181,7 @@ public class GATKReportTable {
* @param numColumns the number of columns in this table
*/
public GATKReportTable(final String tableName, final String tableDescription, final int numColumns) {
this(tableName, tableDescription, numColumns, true);
this(tableName, tableDescription, numColumns, true, false);
}
/**
@ -187,8 +191,9 @@ public class GATKReportTable {
* @param tableDescription the description of the table
* @param numColumns the number of columns in this table
* @param sortByRowID whether to sort rows by the row ID (instead of the order in which they were added)
* @param sortByAllColumns whether to sort rows by all columns (instead of the order in which they were added)
*/
public GATKReportTable(final String tableName, final String tableDescription, final int numColumns, final boolean sortByRowID) {
public GATKReportTable(final String tableName, final String tableDescription, final int numColumns, final boolean sortByRowID, final boolean sortByAllColumns) {
if ( !isValidName(tableName) ) {
throw new ReviewedStingException("Attempted to set a GATKReportTable name of '" + tableName + "'. GATKReportTable names must be purely alphanumeric - no spaces or special characters are allowed.");
}
@ -200,6 +205,7 @@ public class GATKReportTable {
this.tableName = tableName;
this.tableDescription = tableDescription;
this.sortByRowID = sortByRowID;
this.sortByAllColumns = sortByAllColumns;
underlyingData = new ArrayList<Object[]>(INITITAL_ARRAY_SIZE);
columnInfo = new ArrayList<GATKReportColumn>(numColumns);
@ -212,7 +218,7 @@ public class GATKReportTable {
* @param tableToCopy
*/
public GATKReportTable(final GATKReportTable tableToCopy, final boolean copyData) {
this(tableToCopy.getTableName(), tableToCopy.getTableDescription(), tableToCopy.getNumColumns(), tableToCopy.sortByRowID);
this(tableToCopy.getTableName(), tableToCopy.getTableDescription(), tableToCopy.getNumColumns(), tableToCopy.sortByRowID, tableToCopy.sortByAllColumns);
for ( final GATKReportColumn column : tableToCopy.getColumnInfo() )
addColumn(column.getColumnName(), column.getFormat());
if ( copyData )
@ -559,30 +565,62 @@ public class GATKReportTable {
needsPadding = true;
out.printf(column.getColumnFormat().getNameFormat(), column.getColumnName());
}
out.println();
}
out.println();
// write the table body
if ( sortByRowID ) {
// make sure that there are exactly the correct number of ID mappings
if ( rowIdToIndex.size() != underlyingData.size() )
throw new ReviewedStingException("There isn't a 1-to-1 mapping from row ID to index; this can happen when rows are not created consistently");
// write the table body
if ( sortByAllColumns ) {
Collections.sort(underlyingData, new Comparator<Object[]>() {
//INVARIANT the two arrays are of the same length and corresponding elements are of the same type
@Override
public int compare(Object[] objectArr1, Object[] objectArr2) {
final int EQUAL = 0;
final TreeMap<Object, Integer> sortedMap;
try {
sortedMap = new TreeMap<Object, Integer>(rowIdToIndex);
} catch (ClassCastException e) {
throw new ReviewedStingException("Unable to sort the rows based on the row IDs because the ID Objects are of different types");
}
for ( final Map.Entry<Object, Integer> rowKey : sortedMap.entrySet() )
writeRow(out, underlyingData.get(rowKey.getValue()));
} else {
for ( final Object[] row : underlyingData )
writeRow(out, row);
}
int result = EQUAL;
out.println();
}
int l = objectArr1.length;
for (int x = 0; x < l; x++) {
if (objectArr1[x] instanceof Integer) {
result = ((Integer)objectArr1[x]).compareTo((Integer)objectArr2[x]);
if( result != EQUAL) {
return result;
}
} else if (objectArr1[x] instanceof Double) {
result = ((Double)objectArr1[x]).compareTo((Double)objectArr2[x]);
if( result != EQUAL) {
return result;
}
} else { // default uses String comparison
result = objectArr1[x].toString().compareTo(objectArr2[x].toString());
if( result != EQUAL) {
return result;
}
}
}
return result;
}
});
for ( final Object[] row : underlyingData )
writeRow(out, row);
} else if ( sortByRowID ) {
// make sure that there are exactly the correct number of ID mappings
if ( rowIdToIndex.size() != underlyingData.size() )
throw new ReviewedStingException("There isn't a 1-to-1 mapping from row ID to index; this can happen when rows are not created consistently");
final TreeMap<Object, Integer> sortedMap;
try {
sortedMap = new TreeMap<Object, Integer>(rowIdToIndex);
} catch (ClassCastException e) {
throw new ReviewedStingException("Unable to sort the rows based on the row IDs because the ID Objects are of different types");
}
for ( final Map.Entry<Object, Integer> rowKey : sortedMap.entrySet() )
writeRow(out, underlyingData.get(rowKey.getValue()));
} else {
for ( final Object[] row : underlyingData )
writeRow(out, row);
}
out.println();
}
private void writeRow(final PrintStream out, final Object[] row) {
boolean needsPadding = false;
@ -697,8 +735,41 @@ public class GATKReportTable {
}
private List<Object[]> getOrderedRows() {
if ( !sortByRowID )
if ( sortByAllColumns ) {
Collections.sort(underlyingData, new Comparator<Object[]>() {
//INVARIANT the two arrays are of the same length and corresponding elements are of the same type
@Override
public int compare(Object[] objectArr1, Object[] objectArr2) {
final int EQUAL = 0;
int result = EQUAL;
int l = objectArr1.length;
for (int x = 0; x < l; x++) {
if (objectArr1[x] instanceof Integer) {
result = ((Integer)objectArr1[x]).compareTo((Integer)objectArr2[x]);
if( result != EQUAL) {
return result;
}
} else if (objectArr1[x] instanceof Double) {
result = ((Double)objectArr1[x]).compareTo((Double)objectArr2[x]);
if( result != EQUAL) {
return result;
}
} else { // default uses String comparison
result = objectArr1[x].toString().compareTo(objectArr2[x].toString());
if( result != EQUAL) {
return result;
}
}
}
return result;
}
});
return underlyingData;
} else if ( !sortByRowID ) {
return underlyingData;
}
final TreeMap<Object, Integer> sortedMap;
try {

2
public/java/src/org/broadinstitute/sting/gatk/walkers/bqsr/BaseRecalibrator.java
View File

@ -481,6 +481,6 @@ public class BaseRecalibrator extends ReadWalker<Long, Long> implements NanoSche
}
private void generateReport() {
RecalUtils.outputRecalibrationReport(RAC, quantizationInfo, recalibrationTables, requestedCovariates);
RecalUtils.outputRecalibrationReport(RAC, quantizationInfo, recalibrationTables, requestedCovariates, RAC.SORT_BY_ALL_COLUMNS);
}
}

12
public/java/src/org/broadinstitute/sting/gatk/walkers/bqsr/RecalibrationArgumentCollection.java
View File

@ -180,6 +180,11 @@ public class RecalibrationArgumentCollection {
@Argument(fullName = "binary_tag_name", shortName = "bintag", required = false, doc = "the binary tag covariate name if using it")
public String BINARY_TAG_NAME = null;
/*
* whether GATK report tables should have rows in sorted order, starting from leftmost column
*/
@Argument(fullName = "sort_by_all_columns", shortName = "sortAllCols", doc = "Sort the rows in the tables of reports", required = false)
public Boolean SORT_BY_ALL_COLUMNS = false;
/////////////////////////////
// Debugging-only Arguments
@ -200,7 +205,12 @@ public class RecalibrationArgumentCollection {
public File existingRecalibrationReport = null;
public GATKReportTable generateReportTable(final String covariateNames) {
GATKReportTable argumentsTable = new GATKReportTable("Arguments", "Recalibration argument collection values used in this run", 2);
GATKReportTable argumentsTable;
if(SORT_BY_ALL_COLUMNS) {
argumentsTable = new GATKReportTable("Arguments", "Recalibration argument collection values used in this run", 2, false, true);
} else {
argumentsTable = new GATKReportTable("Arguments", "Recalibration argument collection values used in this run", 2);
}
argumentsTable.addColumn("Argument");
argumentsTable.addColumn(RecalUtils.ARGUMENT_VALUE_COLUMN_NAME);
argumentsTable.addRowID("covariate", true);

2
public/java/src/org/broadinstitute/sting/gatk/walkers/diagnostics/ErrorRatePerCycle.java
View File

@ -124,7 +124,7 @@ public class ErrorRatePerCycle extends LocusWalker<Integer, Integer> {
public void initialize() {
report = new GATKReport();
report.addTable(reportName, reportDescription, 6, true);
report.addTable(reportName, reportDescription, 6, true, false);
table = report.getTable(reportName);
table.addColumn("readgroup");
table.addColumn("cycle");

2
public/java/src/org/broadinstitute/sting/gatk/walkers/varianteval/VariantEvalReportWriter.java
View File

@ -162,7 +162,7 @@ public class VariantEvalReportWriter {
// create the table
final String tableName = ve.getSimpleName();
final String tableDesc = ve.getClass().getAnnotation(Analysis.class).description();
report.addTable(tableName, tableDesc, 1 + stratifiers.size() + (scanner.hasMoltenField() ? 2 : datamap.size()), true);
report.addTable(tableName, tableDesc, 1 + stratifiers.size() + (scanner.hasMoltenField() ? 2 : datamap.size()), true, false);
// grab the table, and add the columns we need to it
final GATKReportTable table = report.getTable(tableName);

9
public/java/src/org/broadinstitute/sting/utils/recalibration/QuantizationInfo.java
View File

@ -67,8 +67,13 @@ public class QuantizationInfo {
return quantizationLevels;
}
public GATKReportTable generateReportTable() {
GATKReportTable quantizedTable = new GATKReportTable(RecalUtils.QUANTIZED_REPORT_TABLE_TITLE, "Quality quantization map", 3);
public GATKReportTable generateReportTable(boolean sortBycols) {
GATKReportTable quantizedTable;
if(sortBycols) {
quantizedTable = new GATKReportTable(RecalUtils.QUANTIZED_REPORT_TABLE_TITLE, "Quality quantization map", 3, false, true);
} else {
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);

17
public/java/src/org/broadinstitute/sting/utils/recalibration/RecalUtils.java
View File

@ -257,11 +257,10 @@ public class RecalUtils {
}
}
private static List<GATKReportTable> generateReportTables(final RecalibrationTables recalibrationTables, final Covariate[] requestedCovariates) {
private static List<GATKReportTable> generateReportTables(final RecalibrationTables recalibrationTables, final Covariate[] requestedCovariates, boolean sortByCols) {
List<GATKReportTable> result = new LinkedList<GATKReportTable>();
int reportTableIndex = 0;
int rowIndex = 0;
final Map<Covariate, String> covariateNameMap = new HashMap<Covariate, String>(requestedCovariates.length);
for (final Covariate covariate : requestedCovariates)
covariateNameMap.put(covariate, parseCovariateName(covariate));
@ -287,7 +286,11 @@ public class RecalUtils {
final GATKReportTable reportTable;
if (tableIndex <= RecalibrationTables.TableType.OPTIONAL_COVARIATE_TABLES_START.index) {
reportTable = new GATKReportTable("RecalTable" + reportTableIndex++, "", columnNames.size());
if(sortByCols) {
reportTable = new GATKReportTable("RecalTable" + reportTableIndex++, "", columnNames.size(), false, true);
} else {
reportTable = new GATKReportTable("RecalTable" + reportTableIndex++, "", columnNames.size());
}
for (final Pair<String, String> columnName : columnNames)
reportTable.addColumn(columnName.getFirst(), columnName.getSecond());
rowIndex = 0; // reset the row index since we're starting with a new table
@ -334,8 +337,8 @@ public class RecalUtils {
return covariate.getClass().getSimpleName().split("Covariate")[0];
}
public static void outputRecalibrationReport(final RecalibrationArgumentCollection RAC, final QuantizationInfo quantizationInfo, final RecalibrationTables recalibrationTables, final Covariate[] requestedCovariates) {
outputRecalibrationReport(RAC.generateReportTable(covariateNames(requestedCovariates)), quantizationInfo.generateReportTable(), generateReportTables(recalibrationTables, requestedCovariates), RAC.RECAL_TABLE);
public static void outputRecalibrationReport(final RecalibrationArgumentCollection RAC, final QuantizationInfo quantizationInfo, final RecalibrationTables recalibrationTables, final Covariate[] requestedCovariates, boolean sortByCols) {
outputRecalibrationReport(RAC.generateReportTable(covariateNames(requestedCovariates)), quantizationInfo.generateReportTable(sortByCols), generateReportTables(recalibrationTables, requestedCovariates, sortByCols), RAC.RECAL_TABLE);
}
/**
@ -351,8 +354,8 @@ public class RecalUtils {
return Utils.join(",", names);
}
public static void outputRecalibrationReport(final GATKReportTable argumentTable, final QuantizationInfo quantizationInfo, final RecalibrationTables recalibrationTables, final Covariate[] requestedCovariates, final PrintStream outputFile) {
outputRecalibrationReport(argumentTable, quantizationInfo.generateReportTable(), generateReportTables(recalibrationTables, requestedCovariates), outputFile);
public static void outputRecalibrationReport(final GATKReportTable argumentTable, final QuantizationInfo quantizationInfo, final RecalibrationTables recalibrationTables, final Covariate[] requestedCovariates, final PrintStream outputFile, boolean sortByCols) {
outputRecalibrationReport(argumentTable, quantizationInfo.generateReportTable(sortByCols), generateReportTables(recalibrationTables, requestedCovariates, sortByCols), outputFile);
}
private static void outputRecalibrationReport(final GATKReportTable argumentTable, final GATKReportTable quantizationTable, final List<GATKReportTable> recalTables, final PrintStream outputFile) {

5
public/java/src/org/broadinstitute/sting/utils/recalibration/RecalibrationReport.java
View File

@ -304,6 +304,9 @@ public class RecalibrationReport {
else if (argument.equals("binary_tag_name"))
RAC.BINARY_TAG_NAME = (value == null) ? null : (String) value;
else if (argument.equals("sort_by_all_columns"))
RAC.SORT_BY_ALL_COLUMNS = Boolean.parseBoolean((String) value);
}
return RAC;
@ -318,7 +321,7 @@ public class RecalibrationReport {
}
public void output(PrintStream output) {
RecalUtils.outputRecalibrationReport(argumentTable, quantizationInfo, recalibrationTables, requestedCovariates, output);
RecalUtils.outputRecalibrationReport(argumentTable, quantizationInfo, recalibrationTables, requestedCovariates, output, RAC.SORT_BY_ALL_COLUMNS);
}
public RecalibrationArgumentCollection getRAC() {

2
public/java/test/org/broadinstitute/sting/gatk/report/GATKReportUnitTest.java
View File

@ -168,7 +168,7 @@ public class GATKReportUnitTest extends BaseTest {
table.set("RZ", "SomeFloat", 535646345.657453464576);
table.set("RZ", "TrueFalse", true);
report1.addTable("Table3", "blah", 1, true);
report1.addTable("Table3", "blah", 1, true, false);
report1.getTable("Table3").addColumn("a");
report1.getTable("Table3").addRowIDMapping("q", 2);
report1.getTable("Table3").addRowIDMapping("5", 3);