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Removed sorting by row from walkers

This commit is contained in:
Tad Jordan 2013-01-04 11:52:04 -05:00
parent 810e2da1d4
commit fe06912a87
4 changed files with 5 additions and 5 deletions
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2
public/java/src/org/broadinstitute/sting/gatk/walkers/diagnostics/ErrorRatePerCycle.java
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@ -124,7 +124,7 @@ public class ErrorRatePerCycle extends LocusWalker<Integer, Integer> {
public void initialize() { public void initialize() {
report = new GATKReport(); report = new GATKReport();
report.addTable(reportName, reportDescription, 6, GATKReportTable.TableSortingWay.SORT_BY_ROW); report.addTable(reportName, reportDescription, 6);
table = report.getTable(reportName); table = report.getTable(reportName);
table.addColumn("readgroup"); table.addColumn("readgroup");
table.addColumn("cycle"); table.addColumn("cycle");

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

4
public/java/src/org/broadinstitute/sting/utils/recalibration/QuantizationInfo.java
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@ -67,9 +67,9 @@ public class QuantizationInfo {
return quantizationLevels; return quantizationLevels;
} }
public GATKReportTable generateReportTable(boolean sortBycols) { public GATKReportTable generateReportTable(boolean sortByCols) {
GATKReportTable quantizedTable; GATKReportTable quantizedTable;
if(sortBycols) { if(sortByCols) {
quantizedTable = new GATKReportTable(RecalUtils.QUANTIZED_REPORT_TABLE_TITLE, "Quality quantization map", 3, GATKReportTable.TableSortingWay.SORT_BY_COLUMN); quantizedTable = new GATKReportTable(RecalUtils.QUANTIZED_REPORT_TABLE_TITLE, "Quality quantization map", 3, GATKReportTable.TableSortingWay.SORT_BY_COLUMN);
} else { } else {
quantizedTable = new GATKReportTable(RecalUtils.QUANTIZED_REPORT_TABLE_TITLE, "Quality quantization map", 3); quantizedTable = new GATKReportTable(RecalUtils.QUANTIZED_REPORT_TABLE_TITLE, "Quality quantization map", 3);

2
public/java/test/org/broadinstitute/sting/gatk/report/GATKReportUnitTest.java
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@ -105,7 +105,7 @@ public class GATKReportUnitTest extends BaseTest {
private boolean isSorted(GATKReportTable table) { private boolean isSorted(GATKReportTable table) {
boolean result = true; boolean result = true;
File testingSortingTableFile = new File("myFile.txt"); File testingSortingTableFile = new File("testSortingFile.txt");
try { try {
// Connect print stream to the output stream // Connect print stream to the output stream