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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
This commit is contained in:
hanna 2009-12-28 23:42:46 +00:00
parent b5e5e27225
commit 4617052b3c
2 changed files with 16 additions and 38 deletions
Show Stats Download Patch File Download Diff File Expand all files Collapse all files

6
build.xml
View File

@ -279,12 +279,14 @@
<property name="test.classes" value="${build.dir}/testclasses"/> <property name="test.classes" value="${build.dir}/testclasses"/>
<property name="test.output" value="${dist.dir}/test"/> <property name="test.output" value="${dist.dir}/test"/>
<property name="test.sources" value="java/test"/> <property name="test.sources" value="java/test"/>
<!-- provide a ceiling on the memory that unit/integration tests can consume. -->
<property name="test.maxmemory" value="2g"/>
<!-- TEST --> <!-- TEST -->
<target name="test" depends="test.compile,agent" description="Run unit tests"> <target name="test" depends="test.compile,agent" description="Run unit tests">
<mkdir dir="${report}"/> <mkdir dir="${report}"/>
<echo message="Sting: Running test cases!"/> <echo message="Sting: Running test cases!"/>
<junit printsummary="yes" showoutput="yes" clonevm="yes" haltonfailure="${halt}" failureProperty="test.failure"> <junit printsummary="yes" showoutput="yes" maxmemory="${test.maxmemory}" clonevm="yes" haltonfailure="${halt}" failureProperty="test.failure">
<jvmarg value="-javaagent:${build.dir}/TestAgent.jar"/> <jvmarg value="-javaagent:${build.dir}/TestAgent.jar"/>
<formatter type="${testOutput}" usefile="${usefile}" /> <formatter type="${testOutput}" usefile="${usefile}" />
<classpath> <classpath>
@ -309,7 +311,7 @@
description="Run the long integration unit tests"> description="Run the long integration unit tests">
<mkdir dir="${report}"/> <mkdir dir="${report}"/>
<echo message="Sting: Running integration test cases!"/> <echo message="Sting: Running integration test cases!"/>
<junit printsummary="yes" showoutput="yes" clonevm="yes" haltonfailure="${halt}" failureProperty="test.failure"> <junit printsummary="yes" showoutput="yes" maxmemory="${test.maxmemory}" clonevm="yes" haltonfailure="${halt}" failureProperty="test.failure">
<formatter type="${testOutput}" usefile="${usefile}" /> <formatter type="${testOutput}" usefile="${usefile}" />
<classpath> <classpath>
<path refid="runtime.dependencies"/> <path refid="runtime.dependencies"/>

48
java/test/org/broadinstitute/sting/utils/fasta/IndexedFastaSequenceFileTest.java
View File

@ -56,9 +56,7 @@ public class IndexedFastaSequenceFileTest extends BaseTest {
Assert.assertEquals("Sequence contig is not correct", sequence.getName(), "chrM"); Assert.assertEquals("Sequence contig is not correct", sequence.getName(), "chrM");
Assert.assertEquals("Sequence contig index is not correct", sequence.getContigIndex(), 0); Assert.assertEquals("Sequence contig index is not correct", sequence.getContigIndex(), 0);
Assert.assertEquals( "First n bases of chrM are incorrect", Assert.assertArrayEquals( "First n bases of chrM are incorrect",StringUtil.stringToBytes(firstBasesOfChrM),sequence.getBases());
firstBasesOfChrM,
StringUtil.bytesToString( sequence.getBases() ) );
System.err.printf("testFirstSequence runtime: %dms%n", (endTime - startTime)) ; 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 is not correct", sequence.getName(), "chrM");
Assert.assertEquals("Sequence contig index is not correct", sequence.getContigIndex(), 0); Assert.assertEquals("Sequence contig index is not correct", sequence.getContigIndex(), 0);
Assert.assertEquals( "First n bases of chrM are incorrect", Assert.assertArrayEquals( "First n bases of chrM are incorrect",StringUtil.stringToBytes(extendedBasesOfChrM),sequence.getBases());
extendedBasesOfChrM,
StringUtil.bytesToString(sequence.getBases()) );
System.err.printf("testFirstSequenceExtended runtime: %dms%n", (endTime - startTime)) ; 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 is not correct", sequence.getName(), "chrM");
Assert.assertEquals("Sequence contig index is not correct", sequence.getContigIndex(), 0); Assert.assertEquals("Sequence contig index is not correct", sequence.getContigIndex(), 0);
Assert.assertEquals( "First n bases of chrM are incorrect", Assert.assertArrayEquals( "First n bases of chrM are incorrect",StringUtil.stringToBytes(truncated),sequence.getBases());
truncated,
StringUtil.bytesToString( sequence.getBases() ) );
System.err.printf("testReadStartingInCenterOfFirstLine runtime: %dms%n", (endTime - startTime)) ; 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 is not correct", sequence.getName(), "chrM");
Assert.assertEquals("Sequence contig index is not correct", sequence.getContigIndex(), 0); Assert.assertEquals("Sequence contig index is not correct", sequence.getContigIndex(), 0);
Assert.assertEquals( "First n bases of chrM are incorrect", Assert.assertArrayEquals( "First n bases of chrM are incorrect",StringUtil.stringToBytes(truncated),sequence.getBases());
truncated,
StringUtil.bytesToString( sequence.getBases() ) );
System.err.printf("testReadStartingInCenterOfMiddleLine runtime: %dms%n", (endTime - startTime)) ; 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 is not correct", sequence.getName(), "chrM");
Assert.assertEquals("Sequence contig index is not correct", sequence.getContigIndex(), 0); Assert.assertEquals("Sequence contig index is not correct", sequence.getContigIndex(), 0);
Assert.assertEquals("chrM is incorrect", Assert.assertArrayEquals("chrM is incorrect",expectedSequence.getBases(),sequence.getBases());
StringUtil.bytesToString(expectedSequence.getBases()),
StringUtil.bytesToString(sequence.getBases()) );
System.err.printf("testFirstCompleteContigRead runtime: %dms%n", (endTime - startTime)) ; 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 is not correct", sequence.getName(), "chrY");
Assert.assertEquals("Sequence contig index is not correct", sequence.getContigIndex(), 24); Assert.assertEquals("Sequence contig index is not correct", sequence.getContigIndex(), 24);
Assert.assertEquals("chrY is incorrect", Assert.assertArrayEquals("chrY is incorrect",expectedSequence.getBases(),sequence.getBases());
StringUtil.bytesToString(expectedSequence.getBases()),
StringUtil.bytesToString(sequence.getBases()) );
System.err.printf("testMiddleCompleteContigRead runtime: %dms%n", (endTime - startTime)) ; 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 is not correct", sequence.getName(), "chrX_random");
Assert.assertEquals("Sequence contig index is not correct", sequence.getContigIndex(), 44); Assert.assertEquals("Sequence contig index is not correct", sequence.getContigIndex(), 44);
Assert.assertEquals("chrX_random is incorrect", Assert.assertArrayEquals("chrX_random is incorrect",expectedSequence.getBases(),sequence.getBases());
StringUtil.bytesToString(expectedSequence.getBases()),
StringUtil.bytesToString(sequence.getBases()) );
System.err.printf("testLastCompleteContigRead runtime: %dms%n", (endTime - startTime)) ; 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 is not correct", sequence.getName(), "chr1");
Assert.assertEquals("Sequence contig index is not correct", sequence.getContigIndex(), 1); Assert.assertEquals("Sequence contig index is not correct", sequence.getContigIndex(), 1);
Assert.assertEquals( "First n bases of chr1 are incorrect", Assert.assertArrayEquals( "First n bases of chr1 are incorrect",StringUtil.stringToBytes(firstBasesOfChr1),sequence.getBases());
firstBasesOfChr1,
StringUtil.bytesToString( sequence.getBases() ) );
System.err.printf("testFirstOfChr1 runtime: %dms%n", (endTime - startTime)) ; 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 is not correct", sequence.getName(), "chr8");
Assert.assertEquals("Sequence contig index is not correct", sequence.getContigIndex(), 8); Assert.assertEquals("Sequence contig index is not correct", sequence.getContigIndex(), 8);
Assert.assertEquals( "First n bases of chr8 are incorrect", Assert.assertArrayEquals( "First n bases of chr8 are incorrect",StringUtil.stringToBytes(firstBasesOfChr8),sequence.getBases());
firstBasesOfChr8,
StringUtil.bytesToString( sequence.getBases() ) );
System.err.printf("testFirstOfChr8 runtime: %dms%n", (endTime - startTime)) ; 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 is not correct", sequence.getName(), "chrM");
Assert.assertEquals("Sequence contig index is not correct", sequence.getContigIndex(), 0); Assert.assertEquals("Sequence contig index is not correct", sequence.getContigIndex(), 0);
Assert.assertEquals("chrM is incorrect", Assert.assertArrayEquals("chrM is incorrect",expectedSequence.getBases(),sequence.getBases());
StringUtil.bytesToString(expectedSequence.getBases()),
StringUtil.bytesToString(sequence.getBases()) );
System.err.printf("testFirstElementOfIterator runtime: %dms%n", (endTime - startTime)) ; 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 is not correct", "chr1", sequence.getName());
Assert.assertEquals("Sequence contig index is not correct", 1, sequence.getContigIndex()); Assert.assertEquals("Sequence contig index is not correct", 1, sequence.getContigIndex());
Assert.assertEquals("Sequence size is not correct", expectedSequence.length(), sequence.length()); Assert.assertEquals("Sequence size is not correct", expectedSequence.length(), sequence.length());
Assert.assertEquals("chr1 is incorrect", Assert.assertArrayEquals("chr1 is incorrect",expectedSequence.getBases(),sequence.getBases());
StringUtil.bytesToString(expectedSequence.getBases()),
StringUtil.bytesToString(sequence.getBases()) );
System.err.printf("testNextElementOfIterator runtime: %dms%n", (endTime - startTime)) ; 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 is not correct", "chrM", sequence.getName());
Assert.assertEquals("Sequence contig index is not correct", 0, sequence.getContigIndex()); Assert.assertEquals("Sequence contig index is not correct", 0, sequence.getContigIndex());
Assert.assertEquals("Sequence size is not correct", expectedSequence.length(), sequence.length()); Assert.assertEquals("Sequence size is not correct", expectedSequence.length(), sequence.length());
Assert.assertEquals("chrM is incorrect", Assert.assertArrayEquals("chrM is incorrect", expectedSequence.getBases(),sequence.getBases());
StringUtil.bytesToString(expectedSequence.getBases()),
StringUtil.bytesToString(sequence.getBases()) );
System.err.printf("testReset runtime: %dms%n", (endTime - startTime)) ; System.err.printf("testReset runtime: %dms%n", (endTime - startTime)) ;
} }