From 4617052b3c93a5e053a0fe491a8f8f60046ba1e0 Mon Sep 17 00:00:00 2001 From: hanna Date: Mon, 28 Dec 2009 23:42:46 +0000 Subject: [PATCH] For Alec, and others at the Broad who want to run our unit/integration tests off of gsa1/gsa2: put a ceiling on the amount of memory that integration tests can use. Reduce the memory footprint of the fasta reader test. git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2457 348d0f76-0448-11de-a6fe-93d51630548a --- build.xml | 6 ++- .../fasta/IndexedFastaSequenceFileTest.java | 48 +++++-------------- 2 files changed, 16 insertions(+), 38 deletions(-) diff --git a/build.xml b/build.xml index 7aa77f491..35ddb091f 100644 --- a/build.xml +++ b/build.xml @@ -279,12 +279,14 @@ + + - + @@ -309,7 +311,7 @@ description="Run the long integration unit tests"> - + diff --git a/java/test/org/broadinstitute/sting/utils/fasta/IndexedFastaSequenceFileTest.java b/java/test/org/broadinstitute/sting/utils/fasta/IndexedFastaSequenceFileTest.java index 012353e10..5f4a31df5 100755 --- a/java/test/org/broadinstitute/sting/utils/fasta/IndexedFastaSequenceFileTest.java +++ b/java/test/org/broadinstitute/sting/utils/fasta/IndexedFastaSequenceFileTest.java @@ -56,9 +56,7 @@ public class IndexedFastaSequenceFileTest extends BaseTest { Assert.assertEquals("Sequence contig is not correct", sequence.getName(), "chrM"); Assert.assertEquals("Sequence contig index is not correct", sequence.getContigIndex(), 0); - Assert.assertEquals( "First n bases of chrM are incorrect", - firstBasesOfChrM, - StringUtil.bytesToString( sequence.getBases() ) ); + Assert.assertArrayEquals( "First n bases of chrM are incorrect",StringUtil.stringToBytes(firstBasesOfChrM),sequence.getBases()); System.err.printf("testFirstSequence runtime: %dms%n", (endTime - startTime)) ; } @@ -71,9 +69,7 @@ public class IndexedFastaSequenceFileTest extends BaseTest { Assert.assertEquals("Sequence contig is not correct", sequence.getName(), "chrM"); Assert.assertEquals("Sequence contig index is not correct", sequence.getContigIndex(), 0); - Assert.assertEquals( "First n bases of chrM are incorrect", - extendedBasesOfChrM, - StringUtil.bytesToString(sequence.getBases()) ); + Assert.assertArrayEquals( "First n bases of chrM are incorrect",StringUtil.stringToBytes(extendedBasesOfChrM),sequence.getBases()); System.err.printf("testFirstSequenceExtended runtime: %dms%n", (endTime - startTime)) ; } @@ -91,9 +87,7 @@ public class IndexedFastaSequenceFileTest extends BaseTest { Assert.assertEquals("Sequence contig is not correct", sequence.getName(), "chrM"); Assert.assertEquals("Sequence contig index is not correct", sequence.getContigIndex(), 0); - Assert.assertEquals( "First n bases of chrM are incorrect", - truncated, - StringUtil.bytesToString( sequence.getBases() ) ); + Assert.assertArrayEquals( "First n bases of chrM are incorrect",StringUtil.stringToBytes(truncated),sequence.getBases()); System.err.printf("testReadStartingInCenterOfFirstLine runtime: %dms%n", (endTime - startTime)) ; } @@ -111,9 +105,7 @@ public class IndexedFastaSequenceFileTest extends BaseTest { Assert.assertEquals("Sequence contig is not correct", sequence.getName(), "chrM"); Assert.assertEquals("Sequence contig index is not correct", sequence.getContigIndex(), 0); - Assert.assertEquals( "First n bases of chrM are incorrect", - truncated, - StringUtil.bytesToString( sequence.getBases() ) ); + Assert.assertArrayEquals( "First n bases of chrM are incorrect",StringUtil.stringToBytes(truncated),sequence.getBases()); System.err.printf("testReadStartingInCenterOfMiddleLine runtime: %dms%n", (endTime - startTime)) ; } @@ -129,9 +121,7 @@ public class IndexedFastaSequenceFileTest extends BaseTest { Assert.assertEquals("Sequence contig is not correct", sequence.getName(), "chrM"); Assert.assertEquals("Sequence contig index is not correct", sequence.getContigIndex(), 0); - Assert.assertEquals("chrM is incorrect", - StringUtil.bytesToString(expectedSequence.getBases()), - StringUtil.bytesToString(sequence.getBases()) ); + Assert.assertArrayEquals("chrM is incorrect",expectedSequence.getBases(),sequence.getBases()); System.err.printf("testFirstCompleteContigRead runtime: %dms%n", (endTime - startTime)) ; } @@ -173,9 +163,7 @@ public class IndexedFastaSequenceFileTest extends BaseTest { Assert.assertEquals("Sequence contig is not correct", sequence.getName(), "chrY"); Assert.assertEquals("Sequence contig index is not correct", sequence.getContigIndex(), 24); - Assert.assertEquals("chrY is incorrect", - StringUtil.bytesToString(expectedSequence.getBases()), - StringUtil.bytesToString(sequence.getBases()) ); + Assert.assertArrayEquals("chrY is incorrect",expectedSequence.getBases(),sequence.getBases()); System.err.printf("testMiddleCompleteContigRead runtime: %dms%n", (endTime - startTime)) ; } @@ -193,9 +181,7 @@ public class IndexedFastaSequenceFileTest extends BaseTest { Assert.assertEquals("Sequence contig is not correct", sequence.getName(), "chrX_random"); Assert.assertEquals("Sequence contig index is not correct", sequence.getContigIndex(), 44); - Assert.assertEquals("chrX_random is incorrect", - StringUtil.bytesToString(expectedSequence.getBases()), - StringUtil.bytesToString(sequence.getBases()) ); + Assert.assertArrayEquals("chrX_random is incorrect",expectedSequence.getBases(),sequence.getBases()); System.err.printf("testLastCompleteContigRead runtime: %dms%n", (endTime - startTime)) ; } @@ -209,9 +195,7 @@ public class IndexedFastaSequenceFileTest extends BaseTest { Assert.assertEquals("Sequence contig is not correct", sequence.getName(), "chr1"); Assert.assertEquals("Sequence contig index is not correct", sequence.getContigIndex(), 1); - Assert.assertEquals( "First n bases of chr1 are incorrect", - firstBasesOfChr1, - StringUtil.bytesToString( sequence.getBases() ) ); + Assert.assertArrayEquals( "First n bases of chr1 are incorrect",StringUtil.stringToBytes(firstBasesOfChr1),sequence.getBases()); System.err.printf("testFirstOfChr1 runtime: %dms%n", (endTime - startTime)) ; } @@ -224,9 +208,7 @@ public class IndexedFastaSequenceFileTest extends BaseTest { Assert.assertEquals("Sequence contig is not correct", sequence.getName(), "chr8"); Assert.assertEquals("Sequence contig index is not correct", sequence.getContigIndex(), 8); - Assert.assertEquals( "First n bases of chr8 are incorrect", - firstBasesOfChr8, - StringUtil.bytesToString( sequence.getBases() ) ); + Assert.assertArrayEquals( "First n bases of chr8 are incorrect",StringUtil.stringToBytes(firstBasesOfChr8),sequence.getBases()); System.err.printf("testFirstOfChr8 runtime: %dms%n", (endTime - startTime)) ; } @@ -242,9 +224,7 @@ public class IndexedFastaSequenceFileTest extends BaseTest { Assert.assertEquals("Sequence contig is not correct", sequence.getName(), "chrM"); Assert.assertEquals("Sequence contig index is not correct", sequence.getContigIndex(), 0); - Assert.assertEquals("chrM is incorrect", - StringUtil.bytesToString(expectedSequence.getBases()), - StringUtil.bytesToString(sequence.getBases()) ); + Assert.assertArrayEquals("chrM is incorrect",expectedSequence.getBases(),sequence.getBases()); System.err.printf("testFirstElementOfIterator runtime: %dms%n", (endTime - startTime)) ; } @@ -264,9 +244,7 @@ public class IndexedFastaSequenceFileTest extends BaseTest { Assert.assertEquals("Sequence contig is not correct", "chr1", sequence.getName()); Assert.assertEquals("Sequence contig index is not correct", 1, sequence.getContigIndex()); Assert.assertEquals("Sequence size is not correct", expectedSequence.length(), sequence.length()); - Assert.assertEquals("chr1 is incorrect", - StringUtil.bytesToString(expectedSequence.getBases()), - StringUtil.bytesToString(sequence.getBases()) ); + Assert.assertArrayEquals("chr1 is incorrect",expectedSequence.getBases(),sequence.getBases()); System.err.printf("testNextElementOfIterator runtime: %dms%n", (endTime - startTime)) ; } @@ -287,9 +265,7 @@ public class IndexedFastaSequenceFileTest extends BaseTest { Assert.assertEquals("Sequence contig is not correct", "chrM", sequence.getName()); Assert.assertEquals("Sequence contig index is not correct", 0, sequence.getContigIndex()); Assert.assertEquals("Sequence size is not correct", expectedSequence.length(), sequence.length()); - Assert.assertEquals("chrM is incorrect", - StringUtil.bytesToString(expectedSequence.getBases()), - StringUtil.bytesToString(sequence.getBases()) ); + Assert.assertArrayEquals("chrM is incorrect", expectedSequence.getBases(),sequence.getBases()); System.err.printf("testReset runtime: %dms%n", (endTime - startTime)) ; }