diff --git a/public/java/src/org/broadinstitute/sting/gatk/datasources/sample/PropertyDefinition.java b/public/java/src/org/broadinstitute/sting/gatk/datasources/sample/PropertyDefinition.java
deleted file mode 100644
index 433e0af40..000000000
--- a/public/java/src/org/broadinstitute/sting/gatk/datasources/sample/PropertyDefinition.java
+++ /dev/null
@@ -1,30 +0,0 @@
-package org.broadinstitute.sting.gatk.datasources.sample;
-
-/**
- * Created by IntelliJ IDEA.
- * User: brett
- * Date: Aug 12, 2010
- * Time: 2:09:16 PM
- */
-public class PropertyDefinition {
-
-    String property;
-
-    String[] values;
-
-    public String getProperty() {
-        return property;
-    }
-
-    public void setProperty(String property) {
-        this.property = property;
-    }
-
-    public String[] getValues() {
-        return values;
-    }
-
-    public void setValues(String[] values) {
-        this.values = values;
-    }
-}
\ No newline at end of file
diff --git a/public/java/src/org/broadinstitute/sting/gatk/datasources/sample/SampleAlias.java b/public/java/src/org/broadinstitute/sting/gatk/datasources/sample/SampleAlias.java
deleted file mode 100644
index ce749cb83..000000000
--- a/public/java/src/org/broadinstitute/sting/gatk/datasources/sample/SampleAlias.java
+++ /dev/null
@@ -1,31 +0,0 @@
-package org.broadinstitute.sting.gatk.datasources.sample;
-
-/**
- * Created by IntelliJ IDEA.
- * User: brett
- * Date: Aug 13, 2010
- * Time: 5:13:46 PM
- */
-public class SampleAlias {
-
-    String mainId;
-
-    String[] otherIds;
-
-    public String getMainId() {
-        return mainId;
-    }
-
-    public void setMainId(String mainId) {
-        this.mainId = mainId;
-    }
-
-    public String[] getOtherIds() {
-        return otherIds;
-    }
-
-    public void setOtherIds(String[] otherIds) {
-        this.otherIds = otherIds;
-    }
-
-}
diff --git a/public/java/src/org/broadinstitute/sting/gatk/datasources/sample/SampleFileParser.java b/public/java/src/org/broadinstitute/sting/gatk/datasources/sample/SampleFileParser.java
deleted file mode 100644
index a362af663..000000000
--- a/public/java/src/org/broadinstitute/sting/gatk/datasources/sample/SampleFileParser.java
+++ /dev/null
@@ -1,65 +0,0 @@
-package org.broadinstitute.sting.gatk.datasources.sample;
-
-/**
- * Created by IntelliJ IDEA.
- * User: brett
- * Date: Aug 12, 2010
- * Time: 1:30:44 PM
- */
-public class SampleFileParser {
-
-    private SampleAlias[] sampleAliases;
-
-    private String[] allowedProperties;
-
-    private String[] allowedRelationships;
-
-    private PropertyDefinition[] propertyDefinitions;
-
-    private SampleParser[] samples;
-
-    public PropertyDefinition[] getPropertyDefinitions() {
-        return propertyDefinitions;
-    }
-
-    public void setPropertyDefinitions(PropertyDefinition[] propertyDefinitions) {
-        this.propertyDefinitions = propertyDefinitions;
-    }
-
-    public SampleFileParser() {
-
-    }
-
-    public String[] getAllowedProperties() {
-        return allowedProperties;
-    }
-
-    public void setAllowedProperties(String[] allowedProperties) {
-        this.allowedProperties = allowedProperties;
-    }
-
-    public SampleParser[] getSamples() {
-        return samples;
-    }
-
-    public void setSamples(SampleParser[] samples) {
-        this.samples = samples;
-    }
-
-    public String[] getAllowedRelationships() {
-        return allowedRelationships;
-    }
-
-    public void setAllowedRelationships(String[] allowedRelationships) {
-        this.allowedRelationships = allowedRelationships;
-    }
-
-    public SampleAlias[] getSampleAliases() {
-        return sampleAliases;
-    }
-
-    public void setSampleAliases(SampleAlias[] sampleAliases) {
-        this.sampleAliases = sampleAliases;
-    }
-
-}
\ No newline at end of file
diff --git a/public/java/src/org/broadinstitute/sting/gatk/datasources/sample/SampleParser.java b/public/java/src/org/broadinstitute/sting/gatk/datasources/sample/SampleParser.java
deleted file mode 100644
index f5e07ca29..000000000
--- a/public/java/src/org/broadinstitute/sting/gatk/datasources/sample/SampleParser.java
+++ /dev/null
@@ -1,43 +0,0 @@
-package org.broadinstitute.sting.gatk.datasources.sample;
-
-import java.util.HashMap;
-
-/**
- * Created by IntelliJ IDEA.
- * User: brett
- * Date: Aug 13, 2010
- * Time: 2:09:43 PM
- */
-public class SampleParser {
-
-    private String id;
-
-    private HashMap<String, Object> properties;
-
-    private HashMap<String, String> relationships;
-
-    public String getId() {
-        return id;
-    }
-
-    public void setId(String id) {
-        this.id = id;
-    }
-
-    public HashMap<String, Object> getProperties() {
-        return properties;
-    }
-
-    public void setProperties(HashMap<String, Object> properties) {
-        this.properties = properties;
-    }
-
-    public HashMap<String, String> getRelationships() {
-        return relationships;
-    }
-
-    public void setRelationships(HashMap<String, String> relationships) {
-        this.relationships = relationships;
-    }
-
-}