diff --git a/public/java/src/org/broadinstitute/sting/gatk/report/GATKReportColumn.java b/public/java/src/org/broadinstitute/sting/gatk/report/GATKReportColumn.java index 2db22679a..8b54442b0 100755 --- a/public/java/src/org/broadinstitute/sting/gatk/report/GATKReportColumn.java +++ b/public/java/src/org/broadinstitute/sting/gatk/report/GATKReportColumn.java @@ -132,6 +132,7 @@ public class GATKReportColumn extends LinkedHashMap { private static final Collection RIGHT_ALIGN_STRINGS = Arrays.asList( "null", "NA", + "unknown", String.valueOf(Double.POSITIVE_INFINITY), String.valueOf(Double.NEGATIVE_INFINITY), String.valueOf(Double.NaN)); @@ -144,7 +145,7 @@ public class GATKReportColumn extends LinkedHashMap { * @return true if the value is a right alignable */ protected static boolean isRightAlign(String value) { - return value == null || RIGHT_ALIGN_STRINGS.contains(value) || NumberUtils.isNumber(value); + return value == null || RIGHT_ALIGN_STRINGS.contains(value) || NumberUtils.isNumber(value.trim()); } /** @@ -213,7 +214,7 @@ public class GATKReportColumn extends LinkedHashMap { public Object put(Object key, Object value) { if (value != null) { String formatted = formatValue(value); - if (!formatted.equals("")) { + if (!formatted.equals("") && !formatted.equals("unknown")) { updateMaxWidth(formatted); updateFormat(formatted); } diff --git a/public/java/src/org/broadinstitute/sting/gatk/report/GATKReportTable.java b/public/java/src/org/broadinstitute/sting/gatk/report/GATKReportTable.java index 44d70ac4b..58002bd14 100755 --- a/public/java/src/org/broadinstitute/sting/gatk/report/GATKReportTable.java +++ b/public/java/src/org/broadinstitute/sting/gatk/report/GATKReportTable.java @@ -60,6 +60,8 @@ public class GATKReportTable { private static final String COULD_NOT_READ_DATA_LINE = "Could not read a data line of this table -- "; private static final String COULD_NOT_READ_EMPTY_LINE = "Could not read the last empty line of this table -- "; private static final String OLD_GATK_TABLE_VERSION = "We no longer support older versions of the GATK Tables"; + + private static final String NUMBER_CONVERSION_EXCEPTION = "String is a number but is not a long or a double: "; public GATKReportTable(BufferedReader reader, GATKReportVersion version) { int counter = 0; @@ -413,6 +415,8 @@ public class GATKReportTable { // This code below is bs. Why am do I have to conform to bad code // Below is some code to convert a string into its appropriate type. + + // I second Roger's rant! // If we got a string but the column is not a String type Object newValue = null; diff --git a/public/java/src/org/broadinstitute/sting/gatk/walkers/varianteval/stratifications/IntervalStratification.java b/public/java/src/org/broadinstitute/sting/gatk/walkers/varianteval/stratifications/IntervalStratification.java index d91422a7e..879e6066f 100644 --- a/public/java/src/org/broadinstitute/sting/gatk/walkers/varianteval/stratifications/IntervalStratification.java +++ b/public/java/src/org/broadinstitute/sting/gatk/walkers/varianteval/stratifications/IntervalStratification.java @@ -26,18 +26,17 @@ package org.broadinstitute.sting.gatk.walkers.varianteval.stratifications; import net.sf.picard.util.IntervalTree; import org.apache.log4j.Logger; -import org.broad.tribble.Feature; import org.broadinstitute.sting.gatk.contexts.ReferenceContext; import org.broadinstitute.sting.gatk.refdata.RefMetaDataTracker; -import org.broadinstitute.sting.gatk.walkers.annotator.SnpEff; import org.broadinstitute.sting.utils.GenomeLoc; -import org.broadinstitute.sting.utils.GenomeLocParser; -import org.broadinstitute.sting.utils.GenomeLocSortedSet; import org.broadinstitute.sting.utils.exceptions.UserException; import org.broadinstitute.sting.utils.interval.IntervalUtils; import org.broadinstitute.sting.utils.variantcontext.VariantContext; -import java.util.*; +import java.util.ArrayList; +import java.util.Arrays; +import java.util.List; +import java.util.Map; /** * Stratifies the variants by whether they overlap an interval in the set provided on the command line. 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 fe83dce22..dc6d1c512 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 @@ -2,10 +2,13 @@ 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.exceptions.ReviewedStingException; import org.testng.Assert; import org.testng.annotations.Test; import java.io.File; +import java.io.FileNotFoundException; +import java.io.PrintStream; import java.util.LinkedList; import java.util.List; @@ -18,6 +21,19 @@ public class BQSRGathererUnitTest { private static File recal = new File("public/testdata/exampleGRP.grp"); + @Test(enabled = true) + public void test(){ + PrintStream out; + try { + File f = new File("foo2.grp"); + out = new PrintStream(f); + } catch (FileNotFoundException e) { + throw new ReviewedStingException("f"); + } + GATKReport report = new GATKReport("foo.grp"); + report.print(out); + } + //todo -- this test doesnt work because the primary keys in different tables are not the same. Need to either implement "sort" for testing purposes on GATKReport or have a sophisticated comparison measure @Test(enabled = false) public void testCombineSimilarFiles() { diff --git a/public/java/test/org/broadinstitute/sting/gatk/walkers/varianteval/VariantEvalIntegrationTest.java b/public/java/test/org/broadinstitute/sting/gatk/walkers/varianteval/VariantEvalIntegrationTest.java index 610733d9c..128f11a31 100755 --- a/public/java/test/org/broadinstitute/sting/gatk/walkers/varianteval/VariantEvalIntegrationTest.java +++ b/public/java/test/org/broadinstitute/sting/gatk/walkers/varianteval/VariantEvalIntegrationTest.java @@ -439,7 +439,7 @@ public class VariantEvalIntegrationTest extends WalkerTest { buildCommandLine( "-T VariantEval", "-R " + b37KGReference, - "--dbsnp " + b37dbSNP132, + "--dbsnp " + "/humgen/gsa-hpprojects/GATK/data/Comparisons/Validated/dbSNP/dbsnp_132_b37.leftAligned.vcf", "--eval " + fundamentalTestSNPsVCF, "-noEV", "-EV CountVariants",