From eeddf0d08ef2007834be50eb10e063632bb15709 Mon Sep 17 00:00:00 2001
From: ebanks <ebanks@348d0f76-0448-11de-a6fe-93d51630548a>
Date: Fri, 18 Dec 2009 18:51:21 +0000
Subject: [PATCH] Adding sample utils for convenience methods to pull out
 samples from e.g. SAMFileHeader or Genotype objects

git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2405 348d0f76-0448-11de-a6fe-93d51630548a
---
 .../sting/utils/SampleUtils.java              | 54 +++++++++++++++++++
 1 file changed, 54 insertions(+)
 create mode 100755 java/src/org/broadinstitute/sting/utils/SampleUtils.java

diff --git a/java/src/org/broadinstitute/sting/utils/SampleUtils.java b/java/src/org/broadinstitute/sting/utils/SampleUtils.java
new file mode 100755
index 000000000..8f68f209b
--- /dev/null
+++ b/java/src/org/broadinstitute/sting/utils/SampleUtils.java
@@ -0,0 +1,54 @@
+package org.broadinstitute.sting.utils;
+
+import net.sf.samtools.SAMReadGroupRecord;
+import net.sf.samtools.SAMFileHeader;
+
+import java.util.*;
+
+import org.broadinstitute.sting.utils.genotype.Genotype;
+import org.broadinstitute.sting.utils.genotype.SampleBacked;
+
+
+/**
+ * SampleUtils is a static class (no instantiation allowed!) with some utility methods for getting samples
+ * quality scores.
+ *
+ * @author ebanks
+ */
+public class SampleUtils {
+    /**
+     * Private constructor.  No instantiating this class!
+     */
+    private SampleUtils() {}
+
+    /**
+     * Pull out the samples from a SAMFileHeader;
+     * note that we use a TreeSet so that they are sorted
+     *
+     * @param header  the sam file header
+     * @return list of strings representing the sample names
+     */
+    public static Set<String> getSAMFileSamples(SAMFileHeader header) {
+        // get all of the unique sample names
+        Set<String> samples = new TreeSet<String>();
+        List<SAMReadGroupRecord> readGroups = header.getReadGroups();
+        for ( SAMReadGroupRecord readGroup : readGroups )
+            samples.add(readGroup.getSample());
+        return samples;
+    }
+
+    /**
+     * get the samples names from genotype objects if they are backed by samples
+     *
+     * @param genotypes the genotype list
+     * @return list of strings representing the sample names
+     */
+    public static List<String> getGenotypeSamples(List<Genotype> genotypes) {
+        List<String> samples = new ArrayList<String>();
+        for ( Genotype genotype : genotypes ) {
+            if ( genotype instanceof SampleBacked )
+                samples.add(((SampleBacked)genotype).getSampleName());
+        }
+        return samples;
+    }
+}
\ No newline at end of file