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More CRAM Encoding tests + updates #1203

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merged 9 commits into from
Nov 6, 2018
Merged

More CRAM Encoding tests + updates #1203

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7bd259b
Remove incorrect Beta Code link
jmthibault79 Oct 22, 2018
8bbda87
rename Huffman*Encoding to CanonicalHuffman*Encoding
jmthibault79 Oct 23, 2018
d06de29
External*CodecTests
jmthibault79 Oct 19, 2018
05a77d7
make ITF8/LTF8 consts pkg-priv
jmthibault79 Oct 29, 2018
50d42e1
ITF8/LTF8: rewrap IOException as RuntimeIOException
jmthibault79 Oct 29, 2018
5fbd2ce
RuntimeEOFException
jmthibault79 Oct 29, 2018
a058888
final all the things
jmthibault79 Oct 29, 2018
4cafed7
rm throws IOException
jmthibault79 Oct 31, 2018
2a1ecbf
MAX_BYTES
jmthibault79 Oct 31, 2018
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10 changes: 5 additions & 5 deletions src/main/java/htsjdk/samtools/cram/build/CompressionHeaderFactory.java
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Original file line number Diff line number Diff line change
Expand Up @@ -23,7 +23,7 @@
import htsjdk.samtools.cram.encoding.ExternalByteEncoding;
import htsjdk.samtools.cram.encoding.ExternalCompressor;
import htsjdk.samtools.cram.encoding.ExternalIntegerEncoding;
import htsjdk.samtools.cram.encoding.huffman.codec.HuffmanIntegerEncoding;
import htsjdk.samtools.cram.encoding.huffman.codec.CanonicalHuffmanIntegerEncoding;
import htsjdk.samtools.cram.encoding.rans.RANS;
import htsjdk.samtools.cram.encoding.readfeatures.ReadFeature;
import htsjdk.samtools.cram.encoding.readfeatures.Substitution;
Expand Down Expand Up @@ -422,21 +422,21 @@ private EncodingDetails buildEncodingForTag(final List<CramCompressionRecord> re
case 'c':
case 'C':
details.params = ByteArrayLenEncoding.toParam(
HuffmanIntegerEncoding.toParam(new int[] { 1 }, new int[] { 0 }),
CanonicalHuffmanIntegerEncoding.toParam(new int[] { 1 }, new int[] { 0 }),
ExternalByteEncoding.toParam(tagID));
return details;
case 'I':
case 'i':
case 'f':
details.params = ByteArrayLenEncoding.toParam(
HuffmanIntegerEncoding.toParam(new int[] { 4 }, new int[] { 0 }),
CanonicalHuffmanIntegerEncoding.toParam(new int[] { 4 }, new int[] { 0 }),
ExternalByteEncoding.toParam(tagID));
return details;

case 's':
case 'S':
details.params = ByteArrayLenEncoding.toParam(
HuffmanIntegerEncoding.toParam(new int[] { 2 }, new int[] { 0 }),
CanonicalHuffmanIntegerEncoding.toParam(new int[] { 2 }, new int[] { 0 }),
ExternalByteEncoding.toParam(tagID));
return details;
case 'Z':
Expand All @@ -445,7 +445,7 @@ private EncodingDetails buildEncodingForTag(final List<CramCompressionRecord> re
final boolean singleSize = stats.min == stats.max;
if (singleSize) {
details.params = ByteArrayLenEncoding.toParam(
HuffmanIntegerEncoding.toParam(new int[] { stats.min }, new int[] { 0 }),
CanonicalHuffmanIntegerEncoding.toParam(new int[] { stats.min }, new int[] { 0 }),
ExternalByteEncoding.toParam(tagID));
return details;
}
Expand Down
8 changes: 4 additions & 4 deletions src/main/java/htsjdk/samtools/cram/encoding/EncodingFactory.java
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Expand Up @@ -17,8 +17,8 @@
*/
package htsjdk.samtools.cram.encoding;

import htsjdk.samtools.cram.encoding.huffman.codec.HuffmanByteEncoding;
import htsjdk.samtools.cram.encoding.huffman.codec.HuffmanIntegerEncoding;
import htsjdk.samtools.cram.encoding.huffman.codec.CanonicalHuffmanByteEncoding;
import htsjdk.samtools.cram.encoding.huffman.codec.CanonicalHuffmanIntegerEncoding;
import htsjdk.samtools.cram.structure.EncodingID;

/**
Expand All @@ -45,7 +45,7 @@ public <T> Encoding<T> createEncoding(final DataSeriesType valueType,
case EXTERNAL:
return (Encoding<T>) new ExternalByteEncoding();
case HUFFMAN:
return (Encoding<T>) new HuffmanByteEncoding();
return (Encoding<T>) new CanonicalHuffmanByteEncoding();
case NULL:
return new NullEncoding<T>();

Expand All @@ -58,7 +58,7 @@ public <T> Encoding<T> createEncoding(final DataSeriesType valueType,
case INT:
switch (id) {
case HUFFMAN:
return (Encoding<T>) new HuffmanIntegerEncoding();
return (Encoding<T>) new CanonicalHuffmanIntegerEncoding();
case NULL:
return new NullEncoding<T>();
case EXTERNAL:
Expand Down
7 changes: 1 addition & 6 deletions src/main/java/htsjdk/samtools/cram/encoding/ExternalIntegerCodec.java
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Expand Up @@ -61,12 +61,7 @@ public long write(final BitOutputStream bitOutputStream, final Integer value) th

@Override
public long numberOfBits(final Integer value) {
try {
return ITF8.writeUnsignedITF8(value, nullOutputStream);
} catch (final IOException e) {
// this should never happened but still:
throw new RuntimeException(e);
}
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Yay thanks.

return ITF8.writeUnsignedITF8(value, nullOutputStream);
}

@Override
Expand Down
6 changes: 3 additions & 3 deletions ...ng/huffman/codec/HuffmanByteEncoding.java → ...n/codec/CanonicalHuffmanByteEncoding.java
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Expand Up @@ -28,13 +28,13 @@
import java.nio.ByteBuffer;
import java.util.Map;

public class HuffmanByteEncoding implements Encoding<Byte> {
public class CanonicalHuffmanByteEncoding implements Encoding<Byte> {
private static final EncodingID ENCODING_ID = EncodingID.HUFFMAN;
private int[] bitLengths;
private byte[] values;
private ByteBuffer buf = ByteBuffer.allocate(1024);

public HuffmanByteEncoding() {
public CanonicalHuffmanByteEncoding() {
}

@Override
Expand Down Expand Up @@ -82,7 +82,7 @@ public BitCodec<Byte> buildCodec(final Map<Integer, InputStream> inputMap,
}

public static EncodingParams toParam(final byte[] bfValues, final int[] bfBitLens) {
final HuffmanByteEncoding e = new HuffmanByteEncoding();
final CanonicalHuffmanByteEncoding e = new CanonicalHuffmanByteEncoding();
e.values = bfValues;
e.bitLengths = bfBitLens;
return new EncodingParams(ENCODING_ID, e.toByteArray());
Expand Down
10 changes: 5 additions & 5 deletions ...huffman/codec/HuffmanIntegerEncoding.java → ...odec/CanonicalHuffmanIntegerEncoding.java
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Expand Up @@ -29,13 +29,13 @@
import java.util.Arrays;
import java.util.Map;

public class HuffmanIntegerEncoding implements Encoding<Integer> {
public class CanonicalHuffmanIntegerEncoding implements Encoding<Integer> {
private static final EncodingID ENCODING_ID = EncodingID.HUFFMAN;
private int[] bitLengths;
private int[] values;
private final ByteBuffer buf = ByteBuffer.allocate(1024 * 10);

public HuffmanIntegerEncoding() {
public CanonicalHuffmanIntegerEncoding() {
}

@Override
Expand Down Expand Up @@ -82,16 +82,16 @@ public BitCodec<Integer> buildCodec(final Map<Integer, InputStream> inputMap,
}

public static EncodingParams toParam(final int[] bfValues, final int[] bfBitLens) {
final HuffmanIntegerEncoding e = new HuffmanIntegerEncoding();
final CanonicalHuffmanIntegerEncoding e = new CanonicalHuffmanIntegerEncoding();
e.values = bfValues;
e.bitLengths = bfBitLens;
return new EncodingParams(ENCODING_ID, e.toByteArray());
}

@Override
public boolean equals(final Object obj) {
if (obj instanceof HuffmanIntegerEncoding) {
final HuffmanIntegerEncoding foe = (HuffmanIntegerEncoding) obj;
if (obj instanceof CanonicalHuffmanIntegerEncoding) {
final CanonicalHuffmanIntegerEncoding foe = (CanonicalHuffmanIntegerEncoding) obj;
return Arrays.equals(bitLengths, foe.bitLengths) && Arrays.equals(values, foe.values);

}
Expand Down
4 changes: 2 additions & 2 deletions src/main/java/htsjdk/samtools/cram/io/CramIntArray.java
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Expand Up @@ -15,7 +15,7 @@ public class CramIntArray {
* @return array of integers from the input stream
* @throws IOException as per java IO contract
*/
public static int[] array(final InputStream inputStream) throws IOException {
public static int[] array(final InputStream inputStream) {
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Javadoc @throws can be removed for these now.

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good catch, thanks

final int size = ITF8.readUnsignedITF8(inputStream);
final int[] array = new int[size];
for (int i = 0; i < size; i++)
Expand All @@ -32,7 +32,7 @@ public static int[] array(final InputStream inputStream) throws IOException {
* @return the number of bits written out
* @throws IOException as per java IO contract
*/
public static int write(final int[] array, final OutputStream outputStream) throws IOException {
public static int write(final int[] array, final OutputStream outputStream) {
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Same as above.

int length = ITF8.writeUnsignedITF8(array.length, outputStream);
for (final int intValue : array) length += ITF8.writeUnsignedITF8(intValue, outputStream);

Expand Down
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