Added the base test case, fixed the rest of the test cases to follow suit. Added more verbose output to ant for junit tests.
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@403 348d0f76-0448-11de-a6fe-93d51630548a
This commit is contained in:
aaron
parent
961dbbd4ef
commit
4b3578e1de
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@ -199,7 +199,7 @@
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<target name="test.compile" depends="compile">
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<echo message="Sting: Compiling test cases!"/>
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<mkdir dir="${test.classes}"/>
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<javac destdir="${test.classes}" debug="on" optimize="on">
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<javac destdir="${test.classes}" debug="true" optimize="on">
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<src path="${test.sources}"/>
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<classpath>
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<path refid="external.dependencies"/>
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@ -214,9 +214,8 @@
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<target name="test" depends="test.compile" description="Run unit tests">
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<mkdir dir="${report}"/>
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<echo message="Sting: Running test cases!"/>
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<junit printsummary="yes" showoutput="yes" clonevm="yes" haltonfailure="yes">
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<formatter type="plain"/>
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<junit printsummary="yes" showoutput="yes" clonevm="yes" haltonfailure="yes" failureProperty="test.failure">
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<formatter type="brief" usefile="false" />
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<classpath>
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<path refid="external.dependencies"/>
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<pathelement location="build"/>
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@ -227,9 +226,11 @@
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<batchtest fork="yes" todir="${report}">
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<fileset dir="${test.classes}">
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<include name="**/*.class"/>
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<exclude name="**/BaseTest.class"/>
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</fileset>
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</batchtest>
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</junit>
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<fail message="test failed" if="test.failure" />
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</target>
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@ -4,6 +4,7 @@ import static junit.framework.Assert.assertEquals;
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import static junit.framework.Assert.fail;
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import net.sf.samtools.SAMSequenceDictionary;
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import net.sf.samtools.SAMSequenceRecord;
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import org.broadinstitute.sting.BaseTest;
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import org.broadinstitute.sting.utils.FastaSequenceFile2;
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import org.broadinstitute.sting.utils.GenomeLoc;
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import org.junit.*;
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@ -37,7 +38,7 @@ import java.util.ArrayList;
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* <p/>
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* A descriptions should go here. Blame aaron if it's missing.
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*/
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public class ShardStrategyFactoryTest {
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public class ShardStrategyFactoryTest extends BaseTest {
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private static FastaSequenceFile2 seq;
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@ -47,7 +48,7 @@ public class ShardStrategyFactoryTest {
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*/
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@BeforeClass
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public static void doBeforeAnyTests() {
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seq = new FastaSequenceFile2(new File("/seq/references/Homo_sapiens_assembly18/v0/Homo_sapiens_assembly18.fasta"));
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seq = new FastaSequenceFile2(new File(seqLocation + "/references/Homo_sapiens_assembly18/v0/Homo_sapiens_assembly18.fasta"));
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}
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/**
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@ -117,17 +118,17 @@ public class ShardStrategyFactoryTest {
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int size = 10000;
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int location = 1;
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GenomeLoc.setupRefContigOrdering(dic);
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System.err.println("done to sleep");
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logger.debug("done to sleep");
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// keep track of the number of genome locs we build
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int genomeLocs = 0;
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ArrayList<GenomeLoc> locations = new ArrayList<GenomeLoc>();
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System.err.println("done to sleep2");
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logger.debug("done to sleep2");
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try {
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while (location + size < stop) {
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System.err.println("s = " + s.getSequenceName() + " " + location + " " + size);
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logger.debug("s = " + s.getSequenceName() + " " + location + " " + size);
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// lets make up some fake locations
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GenomeLoc gl = new GenomeLoc(s.getSequenceName(), location, location + size - 1);
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System.err.println("loc = " + location);
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logger.debug("loc = " + location);
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// let's move the location up, with a size space
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location += (size * 2);
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@ -141,18 +142,18 @@ public class ShardStrategyFactoryTest {
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} catch (Exception e) {
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e.printStackTrace();
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}
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System.err.println("Location count = " + genomeLocs);
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logger.debug("Location count = " + genomeLocs);
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ShardStrategy strategy = ShardStrategyFactory.shatter(ShardStrategyFactory.SHATTER_STRATEGY.LINEAR, seq.getSequenceDictionary(), 5000, locations);
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int shardCount = 0;
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try {
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for (Shard sh : strategy) {
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GenomeLoc l = sh.getGenomeLoc();
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System.err.println("Shard start: " + l.getStart() + " stop " + l.getStop() + " contig " + l.getContig());
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logger.debug("Shard start: " + l.getStart() + " stop " + l.getStop() + " contig " + l.getContig());
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shardCount++;
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}
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System.err.println("Shard count = " + shardCount);
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logger.debug("Shard count = " + shardCount);
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assertEquals(shardCount, genomeLocs * 2);
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} catch (Exception e) {
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@ -2,6 +2,7 @@ package org.broadinstitute.sting.gatk.dataSources.simpleDataSources;
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import static junit.framework.Assert.fail;
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import net.sf.samtools.SAMRecord;
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import org.broadinstitute.sting.BaseTest;
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import org.broadinstitute.sting.gatk.dataSources.shards.Shard;
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import org.broadinstitute.sting.gatk.dataSources.shards.ShardStrategy;
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import org.broadinstitute.sting.gatk.dataSources.shards.ShardStrategyFactory;
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@ -42,7 +43,7 @@ import java.util.List;
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* <p/>
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* A descriptions should go here. Blame aaron if it's missing.
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*/
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public class SAMBAMDataSourceTest {
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public class SAMBAMDataSourceTest extends BaseTest {
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private List<String> fl;
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private FastaSequenceFile2 seq;
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@ -57,7 +58,7 @@ public class SAMBAMDataSourceTest {
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fl = new ArrayList<String>();
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// sequence
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seq = new FastaSequenceFile2(new File("/seq/references/Homo_sapiens_assembly18/v0/Homo_sapiens_assembly18.fasta"));
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seq = new FastaSequenceFile2(new File(seqLocation + "/references/Homo_sapiens_assembly18/v0/Homo_sapiens_assembly18.fasta"));
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GenomeLoc.setupRefContigOrdering(seq.getSequenceDictionary());
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}
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@ -81,7 +82,7 @@ public class SAMBAMDataSourceTest {
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int count = 0;
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// setup the data
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fl.add("/humgen/gsa-scr1/aaron/stink/NA12892.bam");
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fl.add(oneKGLocation + "/pilot3/sams/NA12892.bam");
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try {
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@ -90,8 +91,8 @@ public class SAMBAMDataSourceTest {
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int readCount = 0;
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count++;
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System.out.println("Start : " + sh.getGenomeLoc().getStart() + " stop : " + sh.getGenomeLoc().getStop() + " contig " + sh.getGenomeLoc().getContig());
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System.out.println("count = " + count);
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logger.debug("Start : " + sh.getGenomeLoc().getStart() + " stop : " + sh.getGenomeLoc().getStop() + " contig " + sh.getGenomeLoc().getContig());
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logger.debug("count = " + count);
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MergingSamRecordIterator2 datum = data.seek(sh.getGenomeLoc());
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// for the first couple of shards make sure we can see the reads
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@ -118,7 +119,7 @@ public class SAMBAMDataSourceTest {
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// setup the test files
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fl.add("/seq/dirseq/analysis/cancer_exome/sams/TCGA-06-0188.aligned.duplicates_marked.bam");
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fl.add(seqLocation + "/dirseq/analysis/cancer_exome/sams/TCGA-06-0188.aligned.duplicates_marked.bam");
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ArrayList<Integer> readcountPerShard = new ArrayList<Integer>();
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ArrayList<Integer> readcountPerShard2 = new ArrayList<Integer>();
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@ -143,7 +144,7 @@ public class SAMBAMDataSourceTest {
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}
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readcountPerShard.add(readCount);
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System.out.println("read count = " + readCount);
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logger.debug("read count = " + readCount);
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datum.close();
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}
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}
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@ -155,13 +156,13 @@ public class SAMBAMDataSourceTest {
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// setup the data and the counter before our second run
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fl.clear();
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fl.add("/seq/dirseq/analysis/cancer_exome/sams/TCGA-06-0188-01A-01W.aligned.duplicates_marked.bam");
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fl.add("/seq/dirseq/analysis/cancer_exome/sams/TCGA-06-0188-10B-01W.aligned.duplicates_marked.bam");
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fl.add(seqLocation + "/dirseq/analysis/cancer_exome/sams/TCGA-06-0188-01A-01W.aligned.duplicates_marked.bam");
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fl.add(seqLocation + "/dirseq/analysis/cancer_exome/sams/TCGA-06-0188-10B-01W.aligned.duplicates_marked.bam");
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count = 0;
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// the sharding strat.
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strat = ShardStrategyFactory.shatter(ShardStrategyFactory.SHATTER_STRATEGY.LINEAR, seq.getSequenceDictionary(), 100000);
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System.err.println("Pile two:");
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logger.debug("Pile two:");
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try {
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SAMBAMDataSource data = new SAMBAMDataSource(fl);
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for (Shard sh : strat) {
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@ -180,7 +181,7 @@ public class SAMBAMDataSourceTest {
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}
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readcountPerShard2.add(readCount);
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System.out.println("read count = " + readCount);
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logger.debug("read count = " + readCount);
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datum.close();
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}
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}
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@ -1,12 +1,11 @@
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package org.broadinstitute.sting.utils;
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import org.junit.*;
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import org.apache.log4j.BasicConfigurator;
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import java.io.File;
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import edu.mit.broad.picard.reference.ReferenceSequence;
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import net.sf.samtools.util.StringUtil;
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import org.broadinstitute.sting.BaseTest;
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import org.junit.*;
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import java.io.File;
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/**
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* Created by IntelliJ IDEA.
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@ -14,9 +13,9 @@ import net.sf.samtools.util.StringUtil;
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* Date: Apr 11, 2009
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* Time: 2:32:52 PM
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*/
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public class FastaSequenceFile2Test {
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public class FastaSequenceFile2Test extends BaseTest {
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private final String sequenceFileName = "/seq/references/Homo_sapiens_assembly18/v0/Homo_sapiens_assembly18.fasta";
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private static String sequenceFileName;
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private FastaSequenceFile2 sequenceFile = null;
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private final String firstBasesOfChrM = "GATCACAGGTCTATCACCCT";
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@ -25,7 +24,7 @@ public class FastaSequenceFile2Test {
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@BeforeClass
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public static void initialize() {
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BasicConfigurator.configure();
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sequenceFileName = seqLocation + "/references/Homo_sapiens_assembly18/v0/Homo_sapiens_assembly18.fasta";
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}
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@Before
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@ -116,6 +115,7 @@ public class FastaSequenceFile2Test {
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try {
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startTime = System.currentTimeMillis();
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boolean success = sequenceFile.seekToContig("absent");
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}
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finally {
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endTime = System.currentTimeMillis();
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@ -7,6 +7,7 @@ package org.broadinstitute.sting.utils.cmdLine;
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import org.junit.*;
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import static org.junit.Assert.*;
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import org.apache.commons.cli.ParseException;
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import org.broadinstitute.sting.BaseTest;
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/**
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* The ArgumentParserTest test class. In JUnit 4, you don't have to extent the
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@ -24,7 +25,7 @@ import org.apache.commons.cli.ParseException;
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* <p/>
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* You should use the methods like
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*/
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public class ArgumentParserTest {
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public class ArgumentParserTest extends BaseTest {
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// our argument parser
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private ArgumentParser m_parser = null;
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