new GenomixMapper
diff --git a/genomix/genomix-hadoop/src/main/java/edu/uci/ics/genomix/graphbuilding/GenomixMapper.java b/genomix/genomix-hadoop/src/main/java/edu/uci/ics/genomix/graphbuilding/GenomixMapper.java
index b9b9aec..3fb3425 100755
--- a/genomix/genomix-hadoop/src/main/java/edu/uci/ics/genomix/graphbuilding/GenomixMapper.java
+++ b/genomix/genomix-hadoop/src/main/java/edu/uci/ics/genomix/graphbuilding/GenomixMapper.java
@@ -38,14 +38,9 @@
public class GenomixMapper extends MapReduceBase implements
Mapper<LongWritable, Text, KmerBytesWritable, KmerCountValue> {
- public class CurrenByte {
- public byte curByte;
- public byte preMarker;
- }
-
public static int KMER_SIZE;
- public KmerCountValue outputAdjList;
- public KmerBytesWritable outputKmer;
+ public KmerCountValue outputAdjList;
+ public KmerBytesWritable outputKmer;
@Override
public void configure(JobConf job) {
@@ -79,7 +74,7 @@
/** first kmer */
byte count = 1;
byte[] array = geneLine.getBytes();
- outputKmer.setByRead( array, 0);
+ outputKmer.setByRead(array, 0);
byte pre = 0;
byte next = GeneCode.getAdjBit(array[KMER_SIZE]);
byte adj = GeneCode.mergePreNextAdj(pre, next);