From 26ba4c11aaceab82cf539716869427f1e28b5cc2 Mon Sep 17 00:00:00 2001 From: Khalid Shakir Date: Wed, 22 Oct 2014 17:37:37 +0800 Subject: [PATCH] Minor fixups for previous commit once tests (only runnable at Broad) were run. Fixed off by one error in size calculation IntervalUtils.scatterContigIntervals(). In test for fewer files than intervals, adjusted expected intervals. In test for more files than intervals, adjusted expected exception. --- .../gatk/utils/interval/IntervalUtils.java | 2 +- .../gatk/utils/interval/IntervalUtilsUnitTest.java | 12 ++++++------ 2 files changed, 7 insertions(+), 7 deletions(-) diff --git a/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/utils/interval/IntervalUtils.java b/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/utils/interval/IntervalUtils.java index faeebbf30..7fffb12e2 100644 --- a/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/utils/interval/IntervalUtils.java +++ b/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/utils/interval/IntervalUtils.java @@ -371,7 +371,7 @@ public class IntervalUtils { long totalBases = 0; for(GenomeLoc loc : locs) - totalBases += loc.getStop() - loc.getStart(); + totalBases += loc.size(); long idealBasesPerPart = totalBases / scatterParts.size(); if(idealBasesPerPart == 0) diff --git a/public/gatk-tools-public/src/test/java/org/broadinstitute/gatk/utils/interval/IntervalUtilsUnitTest.java b/public/gatk-tools-public/src/test/java/org/broadinstitute/gatk/utils/interval/IntervalUtilsUnitTest.java index d21424bc3..e9846da21 100644 --- a/public/gatk-tools-public/src/test/java/org/broadinstitute/gatk/utils/interval/IntervalUtilsUnitTest.java +++ b/public/gatk-tools-public/src/test/java/org/broadinstitute/gatk/utils/interval/IntervalUtilsUnitTest.java @@ -671,17 +671,17 @@ public class IntervalUtilsUnitTest extends BaseTest { List locs2 = IntervalUtils.parseIntervalArguments(hg18GenomeLocParser, Arrays.asList(files.get(1).toString())); List locs3 = IntervalUtils.parseIntervalArguments(hg18GenomeLocParser, Arrays.asList(files.get(2).toString())); - Assert.assertEquals(locs1.size(), 1); + Assert.assertEquals(locs1.size(), 2); Assert.assertEquals(locs2.size(), 1); - Assert.assertEquals(locs3.size(), 2); + Assert.assertEquals(locs3.size(), 1); Assert.assertEquals(locs1.get(0), chr1); - Assert.assertEquals(locs2.get(0), chr2); - Assert.assertEquals(locs3.get(0), chr3); - Assert.assertEquals(locs3.get(1), chr4); + Assert.assertEquals(locs1.get(1), chr2); + Assert.assertEquals(locs2.get(0), chr3); + Assert.assertEquals(locs3.get(0), chr4); } - @Test(expectedExceptions=UserException.BadArgumentValue.class) + @Test(expectedExceptions=UserException.BadInput.class) public void testScatterContigIntervalsMoreFiles() { List files = testFiles("contig_more.", 3, ".intervals"); IntervalUtils.scatterContigIntervals(hg18Header, getLocs("chr1", "chr2"), files);