private static Map<String, File> createOutputMap(final List<SAMReadGroupRecord> readGroups, final File outputDir, final String extension) { final Map<String, File> outputMap = new HashMap<>(); for (final SAMReadGroupRecord readGroup : readGroups) { final String id = readGroup.getId(); final String fileName = id + extension; final Path outputPath = Paths.get(outputDir.toString(), fileName); outputMap.put(id, outputPath.toFile()); } return outputMap; }
private static Map<String, File> createOutputMap(final List<SAMReadGroupRecord> readGroups, final File outputDir, final String extension) { final Map<String, File> outputMap = new HashMap<>(); for (final SAMReadGroupRecord readGroup : readGroups) { final String id = readGroup.getId(); final String fileName = id + extension; final Path outputPath = Paths.get(outputDir.toString(), fileName); outputMap.put(id, outputPath.toFile()); } return outputMap; }
public Sam2CramRecordFactory(final byte[] refBases, final SAMFileHeader samFileHeader, final Version version) { this.refBases = refBases; this.version = version; this.header = samFileHeader; final List<SAMReadGroupRecord> readGroups = samFileHeader.getReadGroups(); for (int i = 0; i < readGroups.size(); i++) { final SAMReadGroupRecord readGroupRecord = readGroups.get(i); readGroupMap.put(readGroupRecord.getId(), i); } }
static void assertAllReadGroupsMapped(final Map<String, File> outputMap, final List<SAMReadGroupRecord> readGroups) { for (final SAMReadGroupRecord readGroup : readGroups) { final String id = readGroup.getId(); final File output = outputMap.get(id); if (output == null) { throw new PicardException("Read group id " + id + " not found in OUTPUT_MAP " + outputMap); } } }
public Sam2CramRecordFactory(final byte[] refBases, final SAMFileHeader samFileHeader, final Version version) { this.refBases = refBases; this.version = version; this.header = samFileHeader; final List<SAMReadGroupRecord> readGroups = samFileHeader.getReadGroups(); for (int i = 0; i < readGroups.size(); i++) { final SAMReadGroupRecord readGroupRecord = readGroups.get(i); readGroupMap.put(readGroupRecord.getId(), i); } }
static void assertAllReadGroupsMapped(final Map<String, File> outputMap, final List<SAMReadGroupRecord> readGroups) { for (final SAMReadGroupRecord readGroup : readGroups) { final String id = readGroup.getId(); final File output = outputMap.get(id); if (output == null) { throw new PicardException("Read group id " + id + " not found in OUTPUT_MAP " + outputMap); } } }
void addAlignment(final SAMRecord rec) { final SAMFileWriter writer; if (outputByReadGroup) { writer = writerMap.get(rec.getReadGroup().getId()); } else { writer = singleWriter; } writer.addAlignment(rec); }
void addAlignment(final SAMRecord rec) { final SAMFileWriter writer; if (outputByReadGroup) { writer = writerMap.get(rec.getReadGroup().getId()); } else { writer = singleWriter; } writer.addAlignment(rec); }
void add(final SAMRecord rec) { final SortingCollection<SAMRecord> sorter; if (outputByReadGroup) { sorter = sorterMap.get(rec.getReadGroup().getId()); } else { sorter = singleSorter; } sorter.add(rec); }
void add(final SAMRecord rec) { final SortingCollection<SAMRecord> sorter; if (outputByReadGroup) { sorter = sorterMap.get(rec.getReadGroup().getId()); } else { sorter = singleSorter; } sorter.add(rec); }
private Map<String, SAMFileHeader> createHeaderMap( final SAMFileHeader inHeader, final SortOrder sortOrder, final boolean removeAlignmentInformation) { final Map<String, SAMFileHeader> headerMap = new HashMap<>(); for (final SAMReadGroupRecord readGroup : inHeader.getReadGroups()) { final SAMFileHeader header = createOutHeader(inHeader, sortOrder, removeAlignmentInformation); header.addReadGroup(readGroup); headerMap.put(readGroup.getId(), header); } return headerMap; }
private Map<String, SAMFileHeader> createHeaderMap( final SAMFileHeader inHeader, final SortOrder sortOrder, final boolean removeAlignmentInformation) { final Map<String, SAMFileHeader> headerMap = new HashMap<>(); for (final SAMReadGroupRecord readGroup : inHeader.getReadGroups()) { final SAMFileHeader header = createOutHeader(inHeader, sortOrder, removeAlignmentInformation); header.addReadGroup(readGroup); headerMap.put(readGroup.getId(), header); } return headerMap; }
@Override public void initialize() { for ( final SAMReadGroupRecord rg : getToolkit().getSAMFileHeader().getReadGroups() ) { readGroupInfo.put(rg.getId(), new PerReadGroupInfo()); } }
@Test public void testReadGroupIdGetters() throws Exception { final SAMReadGroupRecord rg = new SAMReadGroupRecord("rg1"); Assert.assertEquals(rg.getId(), "rg1"); Assert.assertEquals(rg.getReadGroupId(), "rg1"); }
@Test public void testNullHeaderGetReadGroup() { final SAMRecord sam = createTestRecordHelper(); Assert.assertTrue(null != sam.getHeader()); Assert.assertTrue(null != sam.getReadGroup() && sam.getReadGroup().getId().equals("1")); sam.setHeader(null); Assert.assertNull(sam.getReadGroup()); }
private GATKSAMRecord makeRead() { final SAMReadGroupRecord rg = header.getReadGroups().get(0); final String readName = String.format("%s.%d.%s", "read", readI, rg.getId()); final GATKSAMRecord read = ArtificialSAMUtils.createArtificialRead(header, readName, 0, 1, readLength); read.setReadGroup(new GATKSAMReadGroupRecord(rg)); if ( payloadInBytes > 0 ) // add a payload byte array to push memory use per read even higher read.setAttribute("PL", new byte[payloadInBytes]); return read; } }
private void validateReadGroup(final SAMRecord record, final SAMFileHeader header) { final SAMReadGroupRecord rg = record.getReadGroup(); if (rg == null) { addError(new SAMValidationError(Type.RECORD_MISSING_READ_GROUP, "A record is missing a read group", record.getReadName())); } else if (header.getReadGroup(rg.getId()) == null) { addError(new SAMValidationError(Type.READ_GROUP_NOT_FOUND, "A record has a read group not found in the header: ", record.getReadName() + ", " + rg.getReadGroupId())); } }
private void validateReadGroup(final SAMRecord record, final SAMFileHeader header) { final SAMReadGroupRecord rg = record.getReadGroup(); if (rg == null) { addError(new SAMValidationError(Type.RECORD_MISSING_READ_GROUP, "A record is missing a read group", record.getReadName())); } else if (header.getReadGroup(rg.getId()) == null) { addError(new SAMValidationError(Type.READ_GROUP_NOT_FOUND, "A record has a read group not found in the header: ", record.getReadName() + ", " + rg.getReadGroupId())); } }
private void validateReadGroup(final SAMRecord record, final SAMFileHeader header) { final SAMReadGroupRecord rg = record.getReadGroup(); if (rg == null) { addError(new SAMValidationError(Type.RECORD_MISSING_READ_GROUP, "A record is missing a read group", record.getReadName())); } else if (header.getReadGroup(rg.getId()) == null) { addError(new SAMValidationError(Type.READ_GROUP_NOT_FOUND, "A record has a read group not found in the header: ", record.getReadName() + ", " + rg.getReadGroupId())); } }