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Quick patch to fix the sample code. It wasn't actually initializing the sample data source, so I added a call to initializeSampleDataSource() in GenomeAnalysisEngine. I think there was just an error resolving the versions of GenomeAnalysisEngine 

Also added a new error message that I thought would be helpful...



git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@4301 348d0f76-0448-11de-a6fe-93d51630548a
This commit is contained in:
bthomas 2010-09-17 14:05:26 +00:00
parent a10b2a00a5
commit bc12055fcf
3 changed files with 28 additions and 11 deletions
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2
java/src/org/broadinstitute/sting/gatk/GenomeAnalysisEngine.java
View File

@ -381,6 +381,8 @@ public class GenomeAnalysisEngine {
validateSuppliedReferenceAgainstWalker(my_walker, argCollection);
referenceDataSource = openReferenceSequenceFile(argCollection.referenceFile);
initializeSampleDataSource();
if (argCollection.DBSNPFile != null) bindConvenienceRods(DbSNPHelper.STANDARD_DBSNP_TRACK_NAME, "dbsnp", argCollection.DBSNPFile);
RMDTrackBuilder manager = new RMDTrackBuilder();

15
java/src/org/broadinstitute/sting/gatk/datasources/sample/SampleDataSource.java
View File

@ -121,7 +121,7 @@ public class SampleDataSource {
try {
parser = (SampleFileParser) yaml.load(reader);
}
catch (Exception e) { // TODO: should we have more granular exception here?
catch (Exception e) {
throw new StingException("There was a syntactic error with the YAML in sample file " + sampleFile.getAbsolutePath(), e);
}
@ -149,6 +149,7 @@ public class SampleDataSource {
// loop through each sample in the file - a SampleParser stores an object that will become a Sample
for (SampleParser sampleParser : parser.getSamples()) {
try {
// step 1: add the sample if it doesn't already exist
Sample sample = getSampleById(sampleParser.getId());
if (sample == null) {
@ -219,6 +220,10 @@ public class SampleDataSource {
saveRelationship(sample, relationship, relativeId);
}
}
} catch (Exception e) {
throw new StingException("An error occurred while loading this sample from the sample file: " +
sampleParser.getId(), e);
}
}
}
@ -326,9 +331,13 @@ public class SampleDataSource {
else if (value != null) {
throw new StingException("'gender' property must be male, female, or unknown.");
}
value = null;
}
sample.setProperty(key, value);
try {
sample.setProperty(key, value);
}
catch (Exception e) {
throw new StingException("Could not save property " + key, e);
}
}
/**

22
java/src/org/broadinstitute/sting/playground/sample/CountLociByPopulationWalker.java
View File

@ -3,6 +3,7 @@ package org.broadinstitute.sting.playground.sample;
import net.sf.samtools.SAMRecord;
import org.broadinstitute.sting.gatk.contexts.AlignmentContext;
import org.broadinstitute.sting.gatk.contexts.ReferenceContext;
import org.broadinstitute.sting.gatk.datasources.sample.Sample;
import org.broadinstitute.sting.gatk.refdata.RefMetaDataTracker;
import org.broadinstitute.sting.gatk.walkers.LocusWalker;
import org.broadinstitute.sting.gatk.walkers.TreeReducible;
@ -11,27 +12,32 @@ import java.util.ArrayList;
import java.util.HashMap;
/**
* Walks over the input data set, calculating the total number of covered loci for diagnostic purposes.
* Simplest example of a locus walker.
* Extends locus walker to print how many reads there are at each locus, by population
*/
public class CountLociByPopulationWalker extends LocusWalker<Integer, Long> implements TreeReducible<Long> {
public Integer map(RefMetaDataTracker tracker, ReferenceContext ref, AlignmentContext context) {
// in this HashMap, we'll keep count of how many
HashMap<String, Integer> count = new HashMap<String, Integer>();
ArrayList<SAMRecord> reads = (ArrayList) context.getBasePileup().getReads();
for (SAMRecord read : reads) {
String population = getToolkit().getSampleByRead(read).getPopulation();
if (!count.containsKey(population)) {
count.put(population, 1);
// get the sample
Sample sample = getToolkit().getSampleByRead(read);
if (sample == null)
return 1;
if (!count.containsKey(sample.getPopulation())) {
count.put(sample.getPopulation(), 1);
}
count.put(population, count.get(population) + 1);
count.put(sample.getPopulation(), count.get(sample.getPopulation()) + 1);
}
System.out.println("\n\n\n***** LOCUS: " + ref.toString() + " *****");
System.out.println("\n\n\n***** LOCUS: " + ref.getLocus().toString() + " *****");
for (String population : count.keySet()) {
System.out.println(String.format("%s | %d\n", population, count.get(population)));
System.out.println(String.format("%s | %d", population, count.get(population)));
}
return 1;