From fe06912a87c2a55f3f22b5760855afc9d4987afe Mon Sep 17 00:00:00 2001 From: Tad Jordan Date: Fri, 4 Jan 2013 11:52:04 -0500 Subject: [PATCH] Removed sorting by row from walkers --- .../sting/gatk/walkers/diagnostics/ErrorRatePerCycle.java | 2 +- .../gatk/walkers/varianteval/VariantEvalReportWriter.java | 2 +- .../sting/utils/recalibration/QuantizationInfo.java | 4 ++-- .../broadinstitute/sting/gatk/report/GATKReportUnitTest.java | 2 +- 4 files changed, 5 insertions(+), 5 deletions(-) diff --git a/public/java/src/org/broadinstitute/sting/gatk/walkers/diagnostics/ErrorRatePerCycle.java b/public/java/src/org/broadinstitute/sting/gatk/walkers/diagnostics/ErrorRatePerCycle.java index 5972322f8..98e581e21 100755 --- a/public/java/src/org/broadinstitute/sting/gatk/walkers/diagnostics/ErrorRatePerCycle.java +++ b/public/java/src/org/broadinstitute/sting/gatk/walkers/diagnostics/ErrorRatePerCycle.java @@ -124,7 +124,7 @@ public class ErrorRatePerCycle extends LocusWalker { public void initialize() { report = new GATKReport(); - report.addTable(reportName, reportDescription, 6, GATKReportTable.TableSortingWay.SORT_BY_ROW); + report.addTable(reportName, reportDescription, 6); table = report.getTable(reportName); table.addColumn("readgroup"); table.addColumn("cycle"); diff --git a/public/java/src/org/broadinstitute/sting/gatk/walkers/varianteval/VariantEvalReportWriter.java b/public/java/src/org/broadinstitute/sting/gatk/walkers/varianteval/VariantEvalReportWriter.java index 6dad128fe..91efd1ffd 100644 --- a/public/java/src/org/broadinstitute/sting/gatk/walkers/varianteval/VariantEvalReportWriter.java +++ b/public/java/src/org/broadinstitute/sting/gatk/walkers/varianteval/VariantEvalReportWriter.java @@ -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()), 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 final GATKReportTable table = report.getTable(tableName); diff --git a/public/java/src/org/broadinstitute/sting/utils/recalibration/QuantizationInfo.java b/public/java/src/org/broadinstitute/sting/utils/recalibration/QuantizationInfo.java index fc942499c..5cf16dc9f 100644 --- a/public/java/src/org/broadinstitute/sting/utils/recalibration/QuantizationInfo.java +++ b/public/java/src/org/broadinstitute/sting/utils/recalibration/QuantizationInfo.java @@ -67,9 +67,9 @@ public class QuantizationInfo { return quantizationLevels; } - public GATKReportTable generateReportTable(boolean sortBycols) { + public GATKReportTable generateReportTable(boolean sortByCols) { GATKReportTable quantizedTable; - if(sortBycols) { + if(sortByCols) { quantizedTable = new GATKReportTable(RecalUtils.QUANTIZED_REPORT_TABLE_TITLE, "Quality quantization map", 3, GATKReportTable.TableSortingWay.SORT_BY_COLUMN); } else { quantizedTable = new GATKReportTable(RecalUtils.QUANTIZED_REPORT_TABLE_TITLE, "Quality quantization map", 3); diff --git a/public/java/test/org/broadinstitute/sting/gatk/report/GATKReportUnitTest.java b/public/java/test/org/broadinstitute/sting/gatk/report/GATKReportUnitTest.java index 40d8d8ff9..0637e9a25 100644 --- a/public/java/test/org/broadinstitute/sting/gatk/report/GATKReportUnitTest.java +++ b/public/java/test/org/broadinstitute/sting/gatk/report/GATKReportUnitTest.java @@ -105,7 +105,7 @@ public class GATKReportUnitTest extends BaseTest { private boolean isSorted(GATKReportTable table) { boolean result = true; - File testingSortingTableFile = new File("myFile.txt"); + File testingSortingTableFile = new File("testSortingFile.txt"); try { // Connect print stream to the output stream