compatible with invalid read
diff --git a/genomix/genomix-data/src/main/java/edu/uci/ics/genomix/type/KmerBytesWritable.java b/genomix/genomix-data/src/main/java/edu/uci/ics/genomix/type/KmerBytesWritable.java
index e901de6..fd4c252 100644
--- a/genomix/genomix-data/src/main/java/edu/uci/ics/genomix/type/KmerBytesWritable.java
+++ b/genomix/genomix-data/src/main/java/edu/uci/ics/genomix/type/KmerBytesWritable.java
@@ -123,7 +123,7 @@
byte l = 0;
int bytecount = 0;
int bcount = this.size - 1;
- for (int i = start; i < start + kmerlength; i++) {
+ for (int i = start; i < start + kmerlength && i < array.length; i++) {
byte code = GeneCode.getCodeFromSymbol(array[i]);
l |= (byte) (code << bytecount);
bytecount += 2;
@@ -151,7 +151,7 @@
byte l = 0;
int bytecount = 0;
int bcount = size - 1;
- for (int i = start + kmerlength - 1; i >= 0; i--) {
+ for (int i = start + kmerlength - 1; i >= 0 && i < array.length; i--) {
byte code = GeneCode.getCodeFromSymbol(array[i]);
l |= (byte) (code << bytecount);
bytecount += 2;
diff --git a/genomix/genomix-data/src/main/java/edu/uci/ics/genomix/type/VKmerBytesWritable.java b/genomix/genomix-data/src/main/java/edu/uci/ics/genomix/type/VKmerBytesWritable.java
index b958ec6..abedad6 100644
--- a/genomix/genomix-data/src/main/java/edu/uci/ics/genomix/type/VKmerBytesWritable.java
+++ b/genomix/genomix-data/src/main/java/edu/uci/ics/genomix/type/VKmerBytesWritable.java
@@ -38,18 +38,18 @@
super(other);
}
- public void setSize(int size) {
+ protected void setSize(int size) {
if (size > getCapacity()) {
setCapacity((size * 3 / 2));
}
this.size = size;
}
- public int getCapacity() {
+ protected int getCapacity() {
return bytes.length;
}
- public void setCapacity(int new_cap) {
+ protected void setCapacity(int new_cap) {
if (new_cap != getCapacity()) {
byte[] new_data = new byte[new_cap];
if (new_cap < size) {
diff --git a/genomix/genomix-hyracks/src/main/java/edu/uci/ics/genomix/dataflow/ReadsKeyValueParserFactory.java b/genomix/genomix-hyracks/src/main/java/edu/uci/ics/genomix/dataflow/ReadsKeyValueParserFactory.java
index 4f5b4da..409b434 100644
--- a/genomix/genomix-hyracks/src/main/java/edu/uci/ics/genomix/dataflow/ReadsKeyValueParserFactory.java
+++ b/genomix/genomix-hyracks/src/main/java/edu/uci/ics/genomix/dataflow/ReadsKeyValueParserFactory.java
@@ -1,157 +1,160 @@
-/*
- * Copyright 2009-2012 by The Regents of the University of California
- * Licensed under the Apache License, Version 2.0 (the "License");
- * you may not use this file except in compliance with the License.
- * you may obtain a copy of the License from
- *
- * http://www.apache.org/licenses/LICENSE-2.0
- *
- * Unless required by applicable law or agreed to in writing, software
- * distributed under the License is distributed on an "AS IS" BASIS,
- * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
- * See the License for the specific language governing permissions and
- * limitations under the License.
- */
-
-package edu.uci.ics.genomix.dataflow;
-
-import java.nio.ByteBuffer;
-import java.util.regex.Matcher;
-import java.util.regex.Pattern;
-
-import org.apache.hadoop.io.LongWritable;
-import org.apache.hadoop.io.Text;
-
-import edu.uci.ics.genomix.data.std.accessors.ByteSerializerDeserializer;
-import edu.uci.ics.genomix.type.GeneCode;
-import edu.uci.ics.genomix.type.KmerBytesWritable;
-import edu.uci.ics.hyracks.api.comm.IFrameWriter;
-import edu.uci.ics.hyracks.api.context.IHyracksTaskContext;
-import edu.uci.ics.hyracks.api.exceptions.HyracksDataException;
-import edu.uci.ics.hyracks.dataflow.common.comm.io.ArrayTupleBuilder;
-import edu.uci.ics.hyracks.dataflow.common.comm.io.FrameTupleAppender;
-import edu.uci.ics.hyracks.dataflow.common.comm.util.FrameUtils;
-import edu.uci.ics.hyracks.hdfs.api.IKeyValueParser;
-import edu.uci.ics.hyracks.hdfs.api.IKeyValueParserFactory;
-
-;
-
-public class ReadsKeyValueParserFactory implements IKeyValueParserFactory<LongWritable, Text> {
- private static final long serialVersionUID = 1L;
-
- private KmerBytesWritable kmer;
- private boolean bReversed;
-
- public ReadsKeyValueParserFactory(int k, boolean bGenerateReversed) {
- bReversed = bGenerateReversed;
- kmer = new KmerBytesWritable(k);
- }
-
- @Override
- public IKeyValueParser<LongWritable, Text> createKeyValueParser(final IHyracksTaskContext ctx) {
- final ArrayTupleBuilder tupleBuilder = new ArrayTupleBuilder(2);
- final ByteBuffer outputBuffer = ctx.allocateFrame();
- final FrameTupleAppender outputAppender = new FrameTupleAppender(ctx.getFrameSize());
- outputAppender.reset(outputBuffer, true);
-
- return new IKeyValueParser<LongWritable, Text>() {
-
- @Override
- public void parse(LongWritable key, Text value, IFrameWriter writer) throws HyracksDataException {
- String geneLine = value.toString(); // Read the Real Gene Line
- Pattern genePattern = Pattern.compile("[AGCT]+");
- Matcher geneMatcher = genePattern.matcher(geneLine);
- boolean isValid = geneMatcher.matches();
- if (isValid) {
- SplitReads(geneLine.getBytes(), writer);
- }
- }
-
- private void SplitReads(byte[] array, IFrameWriter writer) {
- /** first kmer */
- int k = kmer.getKmerLength();
- kmer.setByRead(array, 0);
- byte pre = 0;
- byte next = GeneCode.getAdjBit(array[k]);
- InsertToFrame(kmer, pre, next, writer);
-
- /** middle kmer */
- for (int i = k; i < array.length - 1; i++) {
- pre = GeneCode.getBitMapFromGeneCode(kmer.shiftKmerWithNextChar(array[i]));
- next = GeneCode.getAdjBit(array[i + 1]);
- InsertToFrame(kmer, pre, next, writer);
- }
-
- /** last kmer */
- pre = GeneCode.getBitMapFromGeneCode(kmer.shiftKmerWithNextChar(array[array.length - 1]));
- next = 0;
- InsertToFrame(kmer, pre, next, writer);
-
- if (bReversed) {
- /** first kmer */
- kmer.setByReadReverse(array, 0);
- next = 0;
- pre = GeneCode.getAdjBit(array[k]);
- InsertToFrame(kmer, pre, next, writer);
- /** middle kmer */
- for (int i = k; i < array.length - 1; i++) {
- next = GeneCode.getBitMapFromGeneCode(kmer.shiftKmerWithPreChar(array[i]));
- pre = GeneCode.getAdjBit(array[i + 1]);
- InsertToFrame(kmer, pre, next, writer);
- }
- /** last kmer */
- next = GeneCode.getBitMapFromGeneCode(kmer.shiftKmerWithPreChar(array[array.length - 1]));
- pre = 0;
- InsertToFrame(kmer, pre, next, writer);
- }
- }
-
- /**
- * At this graph building phase, we assume the kmer length are all
- * the same Thus we didn't output those Kmer length
- *
- * @param kmer
- * :input kmer
- * @param pre
- * : pre neighbor code
- * @param next
- * : next neighbor code
- * @param writer
- * : output writer
- */
- private void InsertToFrame(KmerBytesWritable kmer, byte pre, byte next, IFrameWriter writer) {
- try {
- byte adj = GeneCode.mergePreNextAdj(pre, next);
- tupleBuilder.reset();
- tupleBuilder.addField(kmer.getBytes(), 0, kmer.getLength());
- tupleBuilder.addField(ByteSerializerDeserializer.INSTANCE, adj);
-
- if (!outputAppender.append(tupleBuilder.getFieldEndOffsets(), tupleBuilder.getByteArray(), 0,
- tupleBuilder.getSize())) {
- FrameUtils.flushFrame(outputBuffer, writer);
- outputAppender.reset(outputBuffer, true);
- if (!outputAppender.append(tupleBuilder.getFieldEndOffsets(), tupleBuilder.getByteArray(), 0,
- tupleBuilder.getSize())) {
- throw new IllegalStateException(
- "Failed to copy an record into a frame: the record size is too large.");
- }
- }
- } catch (Exception e) {
- throw new IllegalStateException(e);
- }
- }
-
- @Override
- public void open(IFrameWriter writer) throws HyracksDataException {
- // TODO Auto-generated method stub
-
- }
-
- @Override
- public void close(IFrameWriter writer) throws HyracksDataException {
- FrameUtils.flushFrame(outputBuffer, writer);
- }
- };
- }
-
+/*
+ * Copyright 2009-2012 by The Regents of the University of California
+ * Licensed under the Apache License, Version 2.0 (the "License");
+ * you may not use this file except in compliance with the License.
+ * you may obtain a copy of the License from
+ *
+ * http://www.apache.org/licenses/LICENSE-2.0
+ *
+ * Unless required by applicable law or agreed to in writing, software
+ * distributed under the License is distributed on an "AS IS" BASIS,
+ * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+ * See the License for the specific language governing permissions and
+ * limitations under the License.
+ */
+
+package edu.uci.ics.genomix.dataflow;
+
+import java.nio.ByteBuffer;
+import java.util.regex.Matcher;
+import java.util.regex.Pattern;
+
+import org.apache.hadoop.io.LongWritable;
+import org.apache.hadoop.io.Text;
+
+import edu.uci.ics.genomix.data.std.accessors.ByteSerializerDeserializer;
+import edu.uci.ics.genomix.type.GeneCode;
+import edu.uci.ics.genomix.type.KmerBytesWritable;
+import edu.uci.ics.hyracks.api.comm.IFrameWriter;
+import edu.uci.ics.hyracks.api.context.IHyracksTaskContext;
+import edu.uci.ics.hyracks.api.exceptions.HyracksDataException;
+import edu.uci.ics.hyracks.dataflow.common.comm.io.ArrayTupleBuilder;
+import edu.uci.ics.hyracks.dataflow.common.comm.io.FrameTupleAppender;
+import edu.uci.ics.hyracks.dataflow.common.comm.util.FrameUtils;
+import edu.uci.ics.hyracks.hdfs.api.IKeyValueParser;
+import edu.uci.ics.hyracks.hdfs.api.IKeyValueParserFactory;
+
+;
+
+public class ReadsKeyValueParserFactory implements IKeyValueParserFactory<LongWritable, Text> {
+ private static final long serialVersionUID = 1L;
+
+ private KmerBytesWritable kmer;
+ private boolean bReversed;
+
+ public ReadsKeyValueParserFactory(int k, boolean bGenerateReversed) {
+ bReversed = bGenerateReversed;
+ kmer = new KmerBytesWritable(k);
+ }
+
+ @Override
+ public IKeyValueParser<LongWritable, Text> createKeyValueParser(final IHyracksTaskContext ctx) {
+ final ArrayTupleBuilder tupleBuilder = new ArrayTupleBuilder(2);
+ final ByteBuffer outputBuffer = ctx.allocateFrame();
+ final FrameTupleAppender outputAppender = new FrameTupleAppender(ctx.getFrameSize());
+ outputAppender.reset(outputBuffer, true);
+
+ return new IKeyValueParser<LongWritable, Text>() {
+
+ @Override
+ public void parse(LongWritable key, Text value, IFrameWriter writer) throws HyracksDataException {
+ String geneLine = value.toString(); // Read the Real Gene Line
+ Pattern genePattern = Pattern.compile("[AGCT]+");
+ Matcher geneMatcher = genePattern.matcher(geneLine);
+ boolean isValid = geneMatcher.matches();
+ if (isValid) {
+ SplitReads(geneLine.getBytes(), writer);
+ }
+ }
+
+ private void SplitReads(byte[] array, IFrameWriter writer) {
+ /** first kmer */
+ int k = kmer.getKmerLength();
+ if (k >= array.length){
+ return;
+ }
+ kmer.setByRead(array, 0);
+ byte pre = 0;
+ byte next = GeneCode.getAdjBit(array[k]);
+ InsertToFrame(kmer, pre, next, writer);
+
+ /** middle kmer */
+ for (int i = k; i < array.length - 1; i++) {
+ pre = GeneCode.getBitMapFromGeneCode(kmer.shiftKmerWithNextChar(array[i]));
+ next = GeneCode.getAdjBit(array[i + 1]);
+ InsertToFrame(kmer, pre, next, writer);
+ }
+
+ /** last kmer */
+ pre = GeneCode.getBitMapFromGeneCode(kmer.shiftKmerWithNextChar(array[array.length - 1]));
+ next = 0;
+ InsertToFrame(kmer, pre, next, writer);
+
+ if (bReversed) {
+ /** first kmer */
+ kmer.setByReadReverse(array, 0);
+ next = 0;
+ pre = GeneCode.getAdjBit(array[k]);
+ InsertToFrame(kmer, pre, next, writer);
+ /** middle kmer */
+ for (int i = k; i < array.length - 1; i++) {
+ next = GeneCode.getBitMapFromGeneCode(kmer.shiftKmerWithPreChar(array[i]));
+ pre = GeneCode.getAdjBit(array[i + 1]);
+ InsertToFrame(kmer, pre, next, writer);
+ }
+ /** last kmer */
+ next = GeneCode.getBitMapFromGeneCode(kmer.shiftKmerWithPreChar(array[array.length - 1]));
+ pre = 0;
+ InsertToFrame(kmer, pre, next, writer);
+ }
+ }
+
+ /**
+ * At this graph building phase, we assume the kmer length are all
+ * the same Thus we didn't output those Kmer length
+ *
+ * @param kmer
+ * :input kmer
+ * @param pre
+ * : pre neighbor code
+ * @param next
+ * : next neighbor code
+ * @param writer
+ * : output writer
+ */
+ private void InsertToFrame(KmerBytesWritable kmer, byte pre, byte next, IFrameWriter writer) {
+ try {
+ byte adj = GeneCode.mergePreNextAdj(pre, next);
+ tupleBuilder.reset();
+ tupleBuilder.addField(kmer.getBytes(), 0, kmer.getLength());
+ tupleBuilder.addField(ByteSerializerDeserializer.INSTANCE, adj);
+
+ if (!outputAppender.append(tupleBuilder.getFieldEndOffsets(), tupleBuilder.getByteArray(), 0,
+ tupleBuilder.getSize())) {
+ FrameUtils.flushFrame(outputBuffer, writer);
+ outputAppender.reset(outputBuffer, true);
+ if (!outputAppender.append(tupleBuilder.getFieldEndOffsets(), tupleBuilder.getByteArray(), 0,
+ tupleBuilder.getSize())) {
+ throw new IllegalStateException(
+ "Failed to copy an record into a frame: the record size is too large.");
+ }
+ }
+ } catch (Exception e) {
+ throw new IllegalStateException(e);
+ }
+ }
+
+ @Override
+ public void open(IFrameWriter writer) throws HyracksDataException {
+ // TODO Auto-generated method stub
+
+ }
+
+ @Override
+ public void close(IFrameWriter writer) throws HyracksDataException {
+ FrameUtils.flushFrame(outputBuffer, writer);
+ }
+ };
+ }
+
}
\ No newline at end of file
diff --git a/genomix/genomix-hyracks/src/test/resources/data/webmap/text.txt b/genomix/genomix-hyracks/src/test/resources/data/webmap/text.txt
index f5a05a8..9874fc2 100755
--- a/genomix/genomix-hyracks/src/test/resources/data/webmap/text.txt
+++ b/genomix/genomix-hyracks/src/test/resources/data/webmap/text.txt
@@ -5,4 +5,4 @@
EDBDB?BEEEDGGEGGGDGGGA>DG@GGD;GD@DG@F?<B<BFFD?
AATAGAAG
AATAGAAG
-AATAGAAG
+AATAGAAG
\ No newline at end of file