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Small CRAM refactor: common ExternalEncoding Abstract Base Class #1346

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merged 2 commits into from
May 15, 2019
Merged

Small CRAM refactor: common ExternalEncoding Abstract Base Class #1346

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e4c5c07
ExternalEncodings inherit from ExternalEncoding
jmthibault79 Mar 8, 2019
676b5a8
CompressionHeaderFactory refactor: these methods are not datatype-spe…
jmthibault79 Mar 8, 2019
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90 changes: 37 additions & 53 deletions src/main/java/htsjdk/samtools/cram/build/CompressionHeaderFactory.java
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Expand Up @@ -21,10 +21,7 @@
import htsjdk.samtools.cram.compression.ExternalCompressor;
import htsjdk.samtools.cram.encoding.*;
import htsjdk.samtools.cram.encoding.core.CanonicalHuffmanIntegerEncoding;
import htsjdk.samtools.cram.encoding.external.ByteArrayStopEncoding;
import htsjdk.samtools.cram.encoding.external.ExternalByteArrayEncoding;
import htsjdk.samtools.cram.encoding.external.ExternalByteEncoding;
import htsjdk.samtools.cram.encoding.external.ExternalIntegerEncoding;
import htsjdk.samtools.cram.encoding.external.*;
import htsjdk.samtools.cram.compression.rans.RANS;
import htsjdk.samtools.cram.encoding.readfeatures.ReadFeature;
import htsjdk.samtools.cram.encoding.readfeatures.Substitution;
Expand Down Expand Up @@ -80,36 +77,36 @@ public CompressionHeader build(final List<CramCompressionRecord> records, Substi

final CompressionHeaderBuilder builder = new CompressionHeaderBuilder(coordinateSorted);

builder.addExternalIntegerRansOrderZeroEncoding(DataSeries.AP_AlignmentPositionOffset);
builder.addExternalByteRansOrderOneEncoding(DataSeries.BA_Base);
builder.addExternalRansOrderZeroEncoding(DataSeries.AP_AlignmentPositionOffset);
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The typed versions (Byte, Integer, etc.) actually all did the same thing because their encoding parameters are identical. The Codecs differ, but that's not relevant here.

builder.addExternalRansOrderOneEncoding(DataSeries.BA_Base);
// BB is not used
builder.addExternalIntegerRansOrderOneEncoding(DataSeries.BF_BitFlags);
builder.addExternalByteGzipEncoding(DataSeries.BS_BaseSubstitutionCode);
builder.addExternalIntegerRansOrderOneEncoding(DataSeries.CF_CompressionBitFlags);
builder.addExternalIntegerGzipEncoding(DataSeries.DL_DeletionLength);
builder.addExternalByteGzipEncoding(DataSeries.FC_FeatureCode);
builder.addExternalIntegerGzipEncoding(DataSeries.FN_NumberOfReadFeatures);
builder.addExternalIntegerGzipEncoding(DataSeries.FP_FeaturePosition);
builder.addExternalIntegerGzipEncoding(DataSeries.HC_HardClip);
builder.addExternalRansOrderOneEncoding(DataSeries.BF_BitFlags);
builder.addExternalGzipEncoding(DataSeries.BS_BaseSubstitutionCode);
builder.addExternalRansOrderOneEncoding(DataSeries.CF_CompressionBitFlags);
builder.addExternalGzipEncoding(DataSeries.DL_DeletionLength);
builder.addExternalGzipEncoding(DataSeries.FC_FeatureCode);
builder.addExternalGzipEncoding(DataSeries.FN_NumberOfReadFeatures);
builder.addExternalGzipEncoding(DataSeries.FP_FeaturePosition);
builder.addExternalGzipEncoding(DataSeries.HC_HardClip);
builder.addExternalByteArrayStopTabGzipEncoding(DataSeries.IN_Insertion);
builder.addExternalIntegerGzipEncoding(DataSeries.MF_MateBitFlags);
builder.addExternalIntegerGzipEncoding(DataSeries.MQ_MappingQualityScore);
builder.addExternalIntegerGzipEncoding(DataSeries.NF_RecordsToNextFragment);
builder.addExternalIntegerGzipEncoding(DataSeries.NP_NextFragmentAlignmentStart);
builder.addExternalIntegerRansOrderOneEncoding(DataSeries.NS_NextFragmentReferenceSequenceID);
builder.addExternalIntegerGzipEncoding(DataSeries.PD_padding);
builder.addExternalGzipEncoding(DataSeries.MF_MateBitFlags);
builder.addExternalGzipEncoding(DataSeries.MQ_MappingQualityScore);
builder.addExternalGzipEncoding(DataSeries.NF_RecordsToNextFragment);
builder.addExternalGzipEncoding(DataSeries.NP_NextFragmentAlignmentStart);
builder.addExternalRansOrderOneEncoding(DataSeries.NS_NextFragmentReferenceSequenceID);
builder.addExternalGzipEncoding(DataSeries.PD_padding);
// QQ is not used
builder.addExternalByteRansOrderOneEncoding(DataSeries.QS_QualityScore);
builder.addExternalIntegerRansOrderOneEncoding(DataSeries.RG_ReadGroup);
builder.addExternalIntegerRansOrderZeroEncoding(DataSeries.RI_RefId);
builder.addExternalIntegerRansOrderOneEncoding(DataSeries.RL_ReadLength);
builder.addExternalRansOrderOneEncoding(DataSeries.QS_QualityScore);
builder.addExternalRansOrderOneEncoding(DataSeries.RG_ReadGroup);
builder.addExternalRansOrderZeroEncoding(DataSeries.RI_RefId);
builder.addExternalRansOrderOneEncoding(DataSeries.RL_ReadLength);
builder.addExternalByteArrayStopTabGzipEncoding(DataSeries.RN_ReadName);
builder.addExternalIntegerGzipEncoding(DataSeries.RS_RefSkip);
builder.addExternalGzipEncoding(DataSeries.RS_RefSkip);
builder.addExternalByteArrayStopTabGzipEncoding(DataSeries.SC_SoftClip);
builder.addExternalIntegerGzipEncoding(DataSeries.TC_TagCount);
builder.addExternalIntegerEncoding(DataSeries.TL_TagIdList, ExternalCompressor.createGZIP());
builder.addExternalIntegerGzipEncoding(DataSeries.TN_TagNameAndType);
builder.addExternalIntegerRansOrderOneEncoding(DataSeries.TS_InsertSize);
builder.addExternalGzipEncoding(DataSeries.TC_TagCount);
builder.addExternalGzipEncoding(DataSeries.TL_TagIdList);
builder.addExternalGzipEncoding(DataSeries.TN_TagNameAndType);
builder.addExternalRansOrderOneEncoding(DataSeries.TS_InsertSize);

builder.setTagIdDictionary(buildTagIdDictionary(records));

Expand Down Expand Up @@ -512,36 +509,23 @@ private void addExternalByteArrayStopTabGzipEncoding(final DataSeries dataSeries
ExternalCompressor.createGZIP());
}

private void addExternalIntegerEncoding(final DataSeries dataSeries, final ExternalCompressor compressor) {
addExternalEncoding(dataSeries,
new ExternalIntegerEncoding(dataSeries.getExternalBlockContentId()).toParam(),
compressor);
}

private void addExternalIntegerGzipEncoding(final DataSeries dataSeries) {
addExternalEncoding(dataSeries,
new ExternalIntegerEncoding(dataSeries.getExternalBlockContentId()).toParam(),
ExternalCompressor.createGZIP());
private void addExternalEncoding(final DataSeries dataSeries, final ExternalCompressor compressor) {
// we need a concrete type; the choice of Byte is arbitrary.
// params are equal for all External Encoding value types
final EncodingParams params = new ExternalByteEncoding(dataSeries.getExternalBlockContentId()).toParam();
addExternalEncoding(dataSeries, params, compressor);
}

private void addExternalByteGzipEncoding(final DataSeries dataSeries) {
addExternalEncoding(dataSeries,
new ExternalByteEncoding(dataSeries.getExternalBlockContentId()).toParam(),
ExternalCompressor.createGZIP());
}

private void addExternalByteRansOrderOneEncoding(final DataSeries dataSeries) {
addExternalEncoding(dataSeries,
new ExternalByteEncoding(dataSeries.getExternalBlockContentId()).toParam(),
ExternalCompressor.createRANS(RANS.ORDER.ONE));
private void addExternalGzipEncoding(final DataSeries dataSeries) {
addExternalEncoding(dataSeries, ExternalCompressor.createGZIP());
}

private void addExternalIntegerRansOrderOneEncoding(final DataSeries dataSeries) {
addExternalIntegerEncoding(dataSeries, ExternalCompressor.createRANS(RANS.ORDER.ONE));
private void addExternalRansOrderOneEncoding(final DataSeries dataSeries) {
addExternalEncoding(dataSeries, ExternalCompressor.createRANS(RANS.ORDER.ONE));
}

private void addExternalIntegerRansOrderZeroEncoding(final DataSeries dataSeries) {
addExternalIntegerEncoding(dataSeries, ExternalCompressor.createRANS(RANS.ORDER.ZERO));
private void addExternalRansOrderZeroEncoding(final DataSeries dataSeries) {
addExternalEncoding(dataSeries, ExternalCompressor.createRANS(RANS.ORDER.ZERO));
}

void addTagEncoding(final int tagId, final EncodingDetails encodingDetails) {
Expand Down
14 changes: 2 additions & 12 deletions src/main/java/htsjdk/samtools/cram/encoding/external/ExternalByteEncoding.java
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Expand Up @@ -18,34 +18,24 @@
package htsjdk.samtools.cram.encoding.external;

import htsjdk.samtools.cram.encoding.CRAMCodec;
import htsjdk.samtools.cram.encoding.CRAMEncoding;
import htsjdk.samtools.cram.io.BitInputStream;
import htsjdk.samtools.cram.io.BitOutputStream;
import htsjdk.samtools.cram.io.ITF8;
import htsjdk.samtools.cram.structure.EncodingID;

import java.io.ByteArrayInputStream;
import java.io.ByteArrayOutputStream;
import java.util.Map;

public class ExternalByteEncoding extends CRAMEncoding<Byte> {
private final int externalBlockContentId;

public class ExternalByteEncoding extends ExternalEncoding<Byte> {
public ExternalByteEncoding(final int externalBlockContentId) {
super(EncodingID.EXTERNAL);
this.externalBlockContentId = externalBlockContentId;
super(externalBlockContentId);
}

public static ExternalByteEncoding fromParams(byte[] params) {
final int contentId = ITF8.readUnsignedITF8(params);
return new ExternalByteEncoding(contentId);
}

@Override
public byte[] toByteArray() {
return ITF8.writeUnsignedITF8(externalBlockContentId);
}

@Override
public CRAMCodec<Byte> buildCodec(final BitInputStream coreBlockInputStream,
final BitOutputStream coreBlockOutputStream,
Expand Down
19 changes: 19 additions & 0 deletions src/main/java/htsjdk/samtools/cram/encoding/external/ExternalEncoding.java
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@@ -0,0 +1,19 @@
package htsjdk.samtools.cram.encoding.external;

import htsjdk.samtools.cram.encoding.CRAMEncoding;
import htsjdk.samtools.cram.io.ITF8;
import htsjdk.samtools.cram.structure.EncodingID;

public abstract class ExternalEncoding<T> extends CRAMEncoding<T> {
protected final int externalBlockContentId;

ExternalEncoding(final int externalBlockContentId) {
super(EncodingID.EXTERNAL);
this.externalBlockContentId = externalBlockContentId;
}

@Override
public byte[] toByteArray() {
return ITF8.writeUnsignedITF8(externalBlockContentId);
}
}
14 changes: 2 additions & 12 deletions src/main/java/htsjdk/samtools/cram/encoding/external/ExternalIntegerEncoding.java
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Expand Up @@ -18,34 +18,24 @@
package htsjdk.samtools.cram.encoding.external;

import htsjdk.samtools.cram.encoding.CRAMCodec;
import htsjdk.samtools.cram.encoding.CRAMEncoding;
import htsjdk.samtools.cram.io.BitInputStream;
import htsjdk.samtools.cram.io.BitOutputStream;
import htsjdk.samtools.cram.io.ITF8;
import htsjdk.samtools.cram.structure.EncodingID;

import java.io.ByteArrayInputStream;
import java.io.ByteArrayOutputStream;
import java.util.Map;

public class ExternalIntegerEncoding extends CRAMEncoding<Integer> {
private final int externalBlockContentId;

public class ExternalIntegerEncoding extends ExternalEncoding<Integer> {
public ExternalIntegerEncoding(final int externalBlockContentId) {
super(EncodingID.EXTERNAL);
this.externalBlockContentId = externalBlockContentId;
super(externalBlockContentId);
}

public static ExternalIntegerEncoding fromParams(byte[] params) {
final int contentId = ITF8.readUnsignedITF8(params);
return new ExternalIntegerEncoding(contentId);
}

@Override
public byte[] toByteArray() {
return ITF8.writeUnsignedITF8(externalBlockContentId);
}

@Override
public CRAMCodec<Integer> buildCodec(final BitInputStream coreBlockInputStream,
final BitOutputStream coreBlockOutputStream,
Expand Down
16 changes: 3 additions & 13 deletions src/main/java/htsjdk/samtools/cram/encoding/external/ExternalLongEncoding.java
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Expand Up @@ -18,34 +18,24 @@
package htsjdk.samtools.cram.encoding.external;

import htsjdk.samtools.cram.encoding.CRAMCodec;
import htsjdk.samtools.cram.encoding.CRAMEncoding;
import htsjdk.samtools.cram.io.BitInputStream;
import htsjdk.samtools.cram.io.BitOutputStream;
import htsjdk.samtools.cram.io.ITF8;
import htsjdk.samtools.cram.structure.EncodingID;

import java.io.ByteArrayInputStream;
import java.io.ByteArrayOutputStream;
import java.util.Map;

public class ExternalLongEncoding extends CRAMEncoding<Long> {
private final int externalBlockContentId;

ExternalLongEncoding(final int externalBlockContentId) {
super(EncodingID.EXTERNAL);
this.externalBlockContentId = externalBlockContentId;
public class ExternalLongEncoding extends ExternalEncoding<Long> {
public ExternalLongEncoding(final int externalBlockContentId) {
super(externalBlockContentId);
}

public static ExternalLongEncoding fromParams(byte[] params) {
final int contentId = ITF8.readUnsignedITF8(params);
return new ExternalLongEncoding(contentId);
}

@Override
public byte[] toByteArray() {
return ITF8.writeUnsignedITF8(externalBlockContentId);
}

@Override
public CRAMCodec<Long> buildCodec(final BitInputStream coreBlockInputStream,
final BitOutputStream coreBlockOutputStream,
Expand Down