finish mapKmerToReadID
diff --git a/genomix/genomix-data/.classpath b/genomix/genomix-data/.classpath
index 6e26406..e43402f 100644
--- a/genomix/genomix-data/.classpath
+++ b/genomix/genomix-data/.classpath
@@ -1,10 +1,36 @@
<?xml version="1.0" encoding="UTF-8"?>
<classpath>
- <classpathentry kind="src" output="target/classes" path="src/main/java"/>
- <classpathentry excluding="**" kind="src" output="target/classes" path="src/main/resources"/>
- <classpathentry kind="src" output="target/test-classes" path="src/test/java"/>
- <classpathentry excluding="**" kind="src" output="target/test-classes" path="src/test/resources"/>
- <classpathentry kind="con" path="org.eclipse.jdt.launching.JRE_CONTAINER/org.eclipse.jdt.internal.debug.ui.launcher.StandardVMType/JavaSE-1.7"/>
- <classpathentry kind="con" path="org.eclipse.m2e.MAVEN2_CLASSPATH_CONTAINER"/>
+ <classpathentry kind="src" output="target/classes" path="src/main/java">
+ <attributes>
+ <attribute name="optional" value="true"/>
+ <attribute name="maven.pomderived" value="true"/>
+ </attributes>
+ </classpathentry>
+ <classpathentry excluding="**" kind="src" output="target/classes" path="src/main/resources">
+ <attributes>
+ <attribute name="maven.pomderived" value="true"/>
+ </attributes>
+ </classpathentry>
+ <classpathentry kind="src" output="target/test-classes" path="src/test/java">
+ <attributes>
+ <attribute name="optional" value="true"/>
+ <attribute name="maven.pomderived" value="true"/>
+ </attributes>
+ </classpathentry>
+ <classpathentry excluding="**" kind="src" output="target/test-classes" path="src/test/resources">
+ <attributes>
+ <attribute name="maven.pomderived" value="true"/>
+ </attributes>
+ </classpathentry>
+ <classpathentry kind="con" path="org.eclipse.jdt.launching.JRE_CONTAINER/org.eclipse.jdt.internal.debug.ui.launcher.StandardVMType/JavaSE-1.7">
+ <attributes>
+ <attribute name="maven.pomderived" value="true"/>
+ </attributes>
+ </classpathentry>
+ <classpathentry kind="con" path="org.eclipse.m2e.MAVEN2_CLASSPATH_CONTAINER">
+ <attributes>
+ <attribute name="maven.pomderived" value="true"/>
+ </attributes>
+ </classpathentry>
<classpathentry kind="output" path="target/classes"/>
</classpath>
diff --git a/genomix/genomix-data/src/main/java/edu/uci/ics/genomix/type/Position.java b/genomix/genomix-data/src/main/java/edu/uci/ics/genomix/type/Position.java
new file mode 100644
index 0000000..0dc24a5
--- /dev/null
+++ b/genomix/genomix-data/src/main/java/edu/uci/ics/genomix/type/Position.java
@@ -0,0 +1,45 @@
+package edu.uci.ics.genomix.type;
+
+import java.io.DataInput;
+import java.io.DataOutput;
+import java.io.IOException;
+
+import org.apache.hadoop.io.Writable;
+
+public class Position implements Writable {
+ public int readID;
+ public byte posInRead;
+
+ public Position() {
+ readID = 0;
+ posInRead = 0;
+ }
+
+ public Position(int readID, byte posInRead) {
+ this.readID = readID;
+ this.posInRead = posInRead;
+ }
+
+ public Position(final Position pos) {
+ this.readID = pos.readID;
+ this.posInRead = pos.posInRead;
+ }
+
+ public void set(int readID, byte posInRead) {
+ this.readID = readID;
+ this.posInRead = posInRead;
+ }
+
+ @Override
+ public void readFields(DataInput in) throws IOException {
+ readID = in.readInt();
+ posInRead = in.readByte();
+ }
+
+ @Override
+ public void write(DataOutput out) throws IOException {
+ out.writeInt(readID);
+ out.writeByte(posInRead);
+ }
+
+}