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Small change for Matt -- output partition types in lexicographic order. 

git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@4365 348d0f76-0448-11de-a6fe-93d51630548a
This commit is contained in:
chartl 2010-09-28 20:08:03 +00:00
parent 7ad87d328d
commit 862c94c8ce
4 changed files with 30 additions and 7 deletions
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15
java/src/org/broadinstitute/sting/gatk/walkers/coverage/DepthOfCoverageWalker.java
View File

@ -148,15 +148,18 @@ public class DepthOfCoverageWalker extends LocusWalker<Map<DoCOutputType.Partiti
PrintStream out = getCorrectStream(null, DoCOutputType.Aggregation.locus, DoCOutputType.FileType.summary);
out.printf("%s\t%s","Locus","Total_Depth");
for (DoCOutputType.Partition type : partitionTypes ) {
// mhanna 22 Aug 2010 - Deliberately force this header replacement to make sure integration tests pass.
// TODO: Update integration tests and get rid of this.
String typeName = (type == DoCOutputType.Partition.readgroup ? "read_group" : type.toString());
out.printf("\t%s_%s","Average_Depth",typeName);
out.printf("\t%s_%s","Average_Depth",type.toString());
}
// get all the samples
HashSet<String> allSamples = getSamplesFromToolKit(partitionTypes);
ArrayList<String> allSampleList = new ArrayList<String>(allSamples.size());
for ( String s : allSamples ) {
allSampleList.add(s);
}
Collections.sort(allSampleList);
for ( String s : allSamples) {
for ( String s : allSampleList) {
out.printf("\t%s_%s","Depth_for",s);
if ( printBaseCounts ) {
out.printf("\t%s_%s",s,"base_counts");
@ -258,6 +261,7 @@ public class DepthOfCoverageWalker extends LocusWalker<Map<DoCOutputType.Partiti
public CoveragePartitioner reduce(Map<DoCOutputType.Partition,Map<String,int[]>> thisMap, CoveragePartitioner prevReduce) {
if ( ! omitDepthOutput ) {
//checkOrder(prevReduce); // tests prevReduce.getIdentifiersByType().get(t) against the initialized header order
printDepths(getCorrectStream(null, DoCOutputType.Aggregation.locus, DoCOutputType.FileType.summary),thisMap,prevReduce.getIdentifiersByType());
// this is an additional iteration through thisMap, plus dealing with IO, so should be much slower without
// turning on omit
@ -757,6 +761,7 @@ public class DepthOfCoverageWalker extends LocusWalker<Map<DoCOutputType.Partiti
}
private void checkOrder(CoveragePartitioner ag) {
// make sure the ordering stored at initialize() is propagated along reduce
for (DoCOutputType.Partition t : partitionTypes ) {
List<String> order = orderCheck.get(t);
List<String> namesInAg = ag.getIdentifiersByType().get(t);

3
java/src/org/broadinstitute/sting/utils/classloader/PackageUtils.java
View File

@ -77,6 +77,9 @@ public class PackageUtils {
for( Class<? extends T> type: allTypes ) {
if( JVMUtils.isConcrete(type) )
concreteTypes.add(type);
else {
System.out.printf("%s %s %s%n","Class",type.getSimpleName()," is not concrete. Skipping.");
}
}
return concreteTypes;

15
java/test/org/broadinstitute/sting/gatk/walkers/coverage/DepthOfCoverageB36IntegrationTest.java
View File

@ -72,4 +72,19 @@ public class DepthOfCoverageB36IntegrationTest extends WalkerTest {
execute("testMapQ0Only",spec);
}
@Test
public void testLotsOfSamples() {
File baseOutputFile = this.createTempFile("testManySamples",".tmp");
this.setOutputFileLocation(baseOutputFile);
String[] intervals = {"1:1105290-1105295"};
String[] bams = {"/humgen/gsa-hpprojects/GATK/data/Validation_Data/pilot3.CEU+TSI.5loci.bam"};
String cmd = buildRootCmd(b36KGReference, new ArrayList<String>(Arrays.asList(bams)), new ArrayList<String>(Arrays.asList(intervals)));
WalkerTestSpec spec = new WalkerTestSpec(cmd,0,new ArrayList<String>());
spec.addAuxFile("c9561b52344536d2b06ab97b0bb1a234",baseOutputFile);
execute("testLotsOfSamples",spec);
}
}

4
java/test/org/broadinstitute/sting/gatk/walkers/coverage/DepthOfCoverageIntegrationTest.java
View File

@ -55,7 +55,7 @@ public class DepthOfCoverageIntegrationTest extends WalkerTest {
WalkerTestSpec spec = new WalkerTestSpec(cmd,0, new ArrayList<String>());
// now add the expected files that get generated
spec.addAuxFile("494c174ea0773bda98297a0cbdc188eb", baseOutputFile);
spec.addAuxFile("423571e4c05e7934322172654ac6dbb7", baseOutputFile);
spec.addAuxFile("9df5e7e07efeb34926c94a724714c219", createTempFileFromBase(baseOutputFile.getAbsolutePath()+".library_cumulative_coverage_counts"));
spec.addAuxFile("b9a7748e5aec4dc06daed893c901c00d", createTempFileFromBase(baseOutputFile.getAbsolutePath()+".library_cumulative_coverage_proportions"));
spec.addAuxFile("9cd395f47b329b9dd00ad024fcac9929", createTempFileFromBase(baseOutputFile.getAbsolutePath()+".library_interval_statistics"));
@ -89,7 +89,7 @@ public class DepthOfCoverageIntegrationTest extends WalkerTest {
String cmd = buildRootCmd(hg18Reference,new ArrayList<String>(Arrays.asList(bams)),new ArrayList<String>(Arrays.asList(intervals))) + " -mmq 0 -mbq 5 --maxBaseQuality 4 -dels -baseCounts -pt readgroup -pt sample -pt library --outputFormat csv";
WalkerTestSpec spec = new WalkerTestSpec(cmd,0, new ArrayList<String>());
spec.addAuxFile("d570c27d82a80ebd2852e9d34aff4e87",baseOutputFile);
spec.addAuxFile("6ccd7d8970ba98cb95fe41636a070c1c",baseOutputFile);
spec.addAuxFile("0ee40f3e5091536c14e077b77557083a",createTempFileFromBase(baseOutputFile.getAbsolutePath()+".library_interval_summary"));
execute("testNoCoverageDueToFiltering",spec);