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fix a crash in the event that the input file has no read groups! 

git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@714 348d0f76-0448-11de-a6fe-93d51630548a
This commit is contained in:
jmaguire 2009-05-14 19:27:41 +00:00
parent d8c1b010f1
commit 641afc4e76
1 changed files with 12 additions and 8 deletions
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20
java/src/org/broadinstitute/sting/playground/gatk/walkers/SingleSampleGenotyper.java
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@ -13,7 +13,7 @@ import org.broadinstitute.sting.utils.BaseUtils;
import org.broadinstitute.sting.utils.MathUtils;
import org.broadinstitute.sting.utils.QualityUtils;
import net.sf.samtools.SAMRecord;
import net.sf.samtools.*;
import java.io.*;
import java.util.*;
@ -46,8 +46,8 @@ public class SingleSampleGenotyper extends LocusWalker<AlleleFrequencyEstimate,
{
try
{
metrics = new AlleleMetrics(metricsFileName, lodThreshold);
sample_name = null;
metrics = new AlleleMetrics(metricsFileName, lodThreshold);
calls_file = new PrintStream(callsFileName);
}
catch (Exception e)
@ -66,12 +66,16 @@ public class SingleSampleGenotyper extends LocusWalker<AlleleFrequencyEstimate,
{
SAMRecord read = context.getReads().get(0);
String RG = (String)(read.getAttribute("RG"));
String local_sample_name = read.getHeader().getReadGroup(RG).getSample();
if (sample_name == null) { sample_name = local_sample_name; }
else
{
if (! sample_name.equals(local_sample_name)) { System.out.printf("SAMPLE NAME MIXUP: %s vs. %s\n", sample_name, local_sample_name); }
assert(sample_name.equals(local_sample_name));
SAMReadGroupRecord read_group_record = read.getHeader().getReadGroup(RG);
if (read_group_record != null)
{
String local_sample_name = read.getHeader().getReadGroup(RG).getSample();
if (sample_name == null) { sample_name = local_sample_name; }
else
{
if (! sample_name.equals(local_sample_name)) { System.out.printf("SAMPLE NAME MIXUP: %s vs. %s\n", sample_name, local_sample_name); }
assert(sample_name.equals(local_sample_name));
}
}
}