-
Notifications
You must be signed in to change notification settings - Fork 5
Commit
This commit does not belong to any branch on this repository, and may belong to a fork outside of the repository.
adding sam record and variant context converters, work in progress
- Loading branch information
Showing
23 changed files
with
1,924 additions
and
7 deletions.
There are no files selected for viewing
This file contains bidirectional Unicode text that may be interpreted or compiled differently than what appears below. To review, open the file in an editor that reveals hidden Unicode characters.
Learn more about bidirectional Unicode characters
This file contains bidirectional Unicode text that may be interpreted or compiled differently than what appears below. To review, open the file in an editor that reveals hidden Unicode characters.
Learn more about bidirectional Unicode characters
299 changes: 299 additions & 0 deletions
299
convert-htsjdk/src/main/java/org/bdgenomics/convert/htsjdk/AlignmentRecordToSamRecord.java
This file contains bidirectional Unicode text that may be interpreted or compiled differently than what appears below. To review, open the file in an editor that reveals hidden Unicode characters.
Learn more about bidirectional Unicode characters
| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -0,0 +1,299 @@ | ||
| /** | ||
| * Licensed to Big Data Genomics (BDG) under one | ||
| * or more contributor license agreements. See the NOTICE file | ||
| * distributed with this work for additional information | ||
| * regarding copyright ownership. The BDG licenses this file | ||
| * to you 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 at | ||
| * | ||
| * 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 org.bdgenomics.convert.htsjdk; | ||
|
|
||
| import java.util.regex.Matcher; | ||
| import java.util.regex.Pattern; | ||
|
|
||
| import com.google.inject.Inject; | ||
|
|
||
| import com.google.inject.assistedinject.Assisted; | ||
|
|
||
| import htsjdk.samtools.SAMFileHeader; | ||
| import htsjdk.samtools.SAMReadGroupRecord; | ||
| import htsjdk.samtools.SAMRecord; | ||
| import htsjdk.samtools.SAMUtils; | ||
|
|
||
| import org.bdgenomics.convert.AbstractConverter; | ||
| import org.bdgenomics.convert.ConversionException; | ||
| import org.bdgenomics.convert.ConversionStringency; | ||
|
|
||
| import org.bdgenomics.formats.avro.AlignmentRecord; | ||
|
|
||
| import org.slf4j.Logger; | ||
|
|
||
| /** | ||
| * Convert AlignmentRecord to htsjdk SAMRecord. | ||
| */ | ||
| public final class AlignmentRecordToSamRecord extends AbstractConverter<AlignmentRecord, SAMRecord> { | ||
|
|
||
| /** Regex to capture attributes. */ | ||
| private static final Pattern ATTRIBUTE = Pattern.compile("([^:]{2,4}):([AifZHB]):(.*)"); | ||
|
|
||
| /** Regex to capture array attribute types. */ | ||
| private static final Pattern ARRAY_ATTRIBUTE = Pattern.compile("([cCiIsSf]{1},)(.*)"); | ||
|
|
||
| /** Header. */ | ||
| private final SAMFileHeader header; | ||
|
|
||
|
|
||
| /** | ||
| * Create a new AlignmentRecord to htsjdk SAMRecord converter with the specified header. | ||
| * | ||
| * @param header header, must not be null | ||
| */ | ||
| @Inject | ||
| public AlignmentRecordToSamRecord(@Assisted final SAMFileHeader header) { | ||
| super(AlignmentRecord.class, SAMRecord.class); | ||
|
|
||
| checkNotNull(header); | ||
| this.header = header; | ||
| } | ||
|
|
||
|
|
||
| @Override | ||
| public SAMRecord convert(final AlignmentRecord alignmentRecord, | ||
| final ConversionStringency stringency, | ||
| final Logger logger) throws ConversionException { | ||
|
|
||
| if (alignmentRecord == null) { | ||
| warnOrThrow(alignmentRecord, "must not be null", null, stringency, logger); | ||
| return null; | ||
| } | ||
|
|
||
| SAMRecord builder = new SAMRecord(header); | ||
| builder.setReadName(alignmentRecord.getReadName()); | ||
| builder.setReadString(alignmentRecord.getSequence()); | ||
|
|
||
| if (alignmentRecord.getQuality() == null) { | ||
| builder.setBaseQualityString("*"); | ||
| } | ||
| else { | ||
| builder.setBaseQualityString(alignmentRecord.getQuality()); | ||
| } | ||
|
|
||
| String readGroupId = alignmentRecord.getReadGroupId(); | ||
| if (readGroupId != null) { | ||
| builder.setAttribute("RG", readGroupId); | ||
|
|
||
| SAMReadGroupRecord readGroup = header.getReadGroup(readGroupId); | ||
| if (readGroup != null && readGroup.getLibrary() != null) { | ||
| builder.setAttribute("LB", readGroup.getLibrary()); | ||
| } | ||
| if (readGroup != null && readGroup.getPlatformUnit() != null) { | ||
| builder.setAttribute("PU", readGroup.getPlatformUnit()); | ||
| } | ||
| } | ||
|
|
||
| if (alignmentRecord.getMateReferenceName() != null) { | ||
| builder.setMateReferenceName(alignmentRecord.getMateReferenceName()); | ||
| } | ||
| if (alignmentRecord.getMateAlignmentStart() != null) { | ||
| builder.setMateAlignmentStart(alignmentRecord.getMateAlignmentStart().intValue() + 1); | ||
| } | ||
| if (alignmentRecord.getInsertSize() != null) { | ||
| builder.setInferredInsertSize(alignmentRecord.getInsertSize().intValue()); | ||
| } | ||
|
|
||
| if (alignmentRecord.getReadPaired() != null) { | ||
| boolean readPaired = alignmentRecord.getReadPaired(); | ||
| builder.setReadPairedFlag(readPaired); | ||
|
|
||
| if (readPaired) { | ||
| if (alignmentRecord.getMateNegativeStrand() != null) { | ||
| builder.setMateNegativeStrandFlag(alignmentRecord.getMateNegativeStrand()); | ||
| } | ||
| if (alignmentRecord.getMateMapped() != null) { | ||
| builder.setMateUnmappedFlag(!alignmentRecord.getMateMapped()); | ||
| } | ||
| if (alignmentRecord.getProperPair() != null) { | ||
| builder.setProperPairFlag(alignmentRecord.getProperPair()); | ||
| } | ||
| if (alignmentRecord.getReadInFragment() != null) { | ||
| builder.setFirstOfPairFlag(alignmentRecord.getReadInFragment() == 0); | ||
| builder.setSecondOfPairFlag(alignmentRecord.getReadInFragment() == 1); | ||
| } | ||
| } | ||
| } | ||
|
|
||
| if (alignmentRecord.getDuplicateRead() != null) { | ||
| builder.setDuplicateReadFlag(alignmentRecord.getDuplicateRead()); | ||
| } | ||
|
|
||
| if (alignmentRecord.getReadMapped() != null) { | ||
| boolean readMapped = alignmentRecord.getReadMapped(); | ||
| builder.setReadUnmappedFlag(!readMapped); | ||
|
|
||
| if (alignmentRecord.getReadNegativeStrand() != null) { | ||
| builder.setReadNegativeStrandFlag(alignmentRecord.getReadNegativeStrand()); | ||
| } | ||
|
|
||
| if (readMapped) { | ||
| if (alignmentRecord.getReferenceName() == null) { | ||
| warnOrThrow(alignmentRecord, "referenceName must not be null if read aligned", null, stringency, logger); | ||
| } | ||
| else { | ||
| builder.setReferenceName(alignmentRecord.getReferenceName()); | ||
| } | ||
|
|
||
| if (alignmentRecord.getCigar() != null) { | ||
| builder.setCigarString(alignmentRecord.getCigar()); | ||
| } | ||
| if (alignmentRecord.getPrimaryAlignment() != null) { | ||
| builder.setNotPrimaryAlignmentFlag(!alignmentRecord.getPrimaryAlignment()); | ||
| } | ||
| if (alignmentRecord.getSupplementaryAlignment() != null) { | ||
| builder.setSupplementaryAlignmentFlag(alignmentRecord.getSupplementaryAlignment()); | ||
| } | ||
| if (alignmentRecord.getStart() != null) { | ||
| builder.setAlignmentStart(alignmentRecord.getStart().intValue() + 1); | ||
| } | ||
| if (alignmentRecord.getMappingQuality() != null) { | ||
| builder.setMappingQuality(alignmentRecord.getMappingQuality()); | ||
| } | ||
| } | ||
| else { | ||
| builder.setMappingQuality(0); | ||
| } | ||
| } | ||
|
|
||
| if (alignmentRecord.getFailedVendorQualityChecks() != null) { | ||
| builder.setReadFailsVendorQualityCheckFlag(alignmentRecord.getFailedVendorQualityChecks()); | ||
| } | ||
| if (alignmentRecord.getMismatchingPositions() != null) { | ||
| builder.setAttribute("MD", alignmentRecord.getMismatchingPositions()); | ||
| } | ||
| if (alignmentRecord.getOriginalQuality() != null) { | ||
| builder.setOriginalBaseQualities(SAMUtils.fastqToPhred(alignmentRecord.getOriginalQuality())); | ||
| } | ||
| if (alignmentRecord.getOriginalCigar() != null) { | ||
| builder.setAttribute("OC", alignmentRecord.getOriginalCigar()); | ||
| } | ||
| if (alignmentRecord.getOriginalStart() != null) { | ||
| builder.setAttribute("OP", alignmentRecord.getOriginalStart().intValue() + 1); | ||
| } | ||
|
|
||
| if (alignmentRecord.getAttributes() != null) { | ||
| String[] tokens = alignmentRecord.getAttributes().split("\t"); | ||
| for (String token : tokens) { | ||
| Matcher m = ATTRIBUTE.matcher(token); | ||
| if (m.matches()) { | ||
| String tagName = m.group(1); | ||
| String tagType = m.group(2); | ||
| String value = m.group(3); | ||
|
|
||
| if ("B".equals(tagType)) { | ||
| m = ARRAY_ATTRIBUTE.matcher(value); | ||
| if (m.matches()) { | ||
| tagType = tagType + ":" + m.group(1); | ||
| value = m.group(2); | ||
| } | ||
| } | ||
|
|
||
| switch (tagType) { | ||
| case "A": | ||
| builder.setAttribute(tagName, value.charAt(0)); | ||
| case "i": | ||
| builder.setAttribute(tagName, Integer.valueOf(value)); | ||
| case "f": | ||
| builder.setAttribute(tagName, Float.valueOf(value)); | ||
| case "Z": | ||
| builder.setAttribute(tagName, value); | ||
| case "H": | ||
| builder.setAttribute(tagName, value.getBytes()); | ||
| case "B:c,": | ||
| case "B:C,": | ||
| builder.setAttribute(tagName, splitToByteArray(value)); | ||
| case "B:i,": | ||
| case "B:I,": | ||
| builder.setAttribute(tagName, splitToIntegerArray(value)); | ||
| case "B:s,": | ||
| case "B:S,": | ||
| builder.setAttribute(tagName, splitToShortArray(value)); | ||
| case "B:f,": | ||
| builder.setAttribute(tagName, splitToFloatArray(value)); | ||
| default: | ||
| warnOrThrow(alignmentRecord, "invalid attribute type " + tagType, null, stringency, logger); | ||
| } | ||
| } | ||
| } | ||
| } | ||
|
|
||
| return builder; | ||
| } | ||
|
|
||
| /** | ||
| * Split the specified value to a byte array. | ||
| * | ||
| * @param value value | ||
| * @return the specified value split to a byte array | ||
| */ | ||
| static byte[] splitToByteArray(final String value) { | ||
| String[] tokens = value.split(","); | ||
| byte[] bytes = new byte[tokens.length]; | ||
| for (int i = 0; i < tokens.length; i++) { | ||
| bytes[i] = Byte.valueOf(tokens[i]); | ||
| } | ||
| return bytes; | ||
| } | ||
|
|
||
| /** | ||
| * Split the specified value to an integer array. | ||
| * | ||
| * @param value value | ||
| * @return the specified value split to an integer array | ||
| */ | ||
| static int[] splitToIntegerArray(final String value) { | ||
| String[] tokens = value.split(","); | ||
| int[] ints = new int[tokens.length]; | ||
| for (int i = 0; i < tokens.length; i++) { | ||
| ints[i] = Integer.valueOf(tokens[i]); | ||
| } | ||
| return ints; | ||
| } | ||
|
|
||
| /** | ||
| * Split the specified value to a short array. | ||
| * | ||
| * @param value value | ||
| * @return the specified value split to a short array | ||
| */ | ||
| static short[] splitToShortArray(final String value) { | ||
| String[] tokens = value.split(","); | ||
| short[] shorts = new short[tokens.length]; | ||
| for (int i = 0; i < tokens.length; i++) { | ||
| shorts[i] = Short.valueOf(tokens[i]); | ||
| } | ||
| return shorts; | ||
| } | ||
|
|
||
| /** | ||
| * Split the specified value to a float array. | ||
| * | ||
| * @param value value | ||
| * @return the specified value split to a float array | ||
| */ | ||
| static float[] splitToFloatArray(final String value) { | ||
| String[] tokens = value.split(","); | ||
| float[] floats = new float[tokens.length]; | ||
| for (int i = 0; i < tokens.length; i++) { | ||
| floats[i] = Float.valueOf(tokens[i]); | ||
| } | ||
| return floats; | ||
| } | ||
| } |
Oops, something went wrong.