private SAMFileHeader createHeader() { SAMFileHeader header = ArtificialSAMUtils.createArtificialSamHeader(maxContigs, 1, (streamDensity.maxDistanceBetweenStacks + MAX_READ_LENGTH) * streamStacksPerContig.maxStacksPerContig + 100000); List<String> readGroups = new ArrayList<String>(numSamples); List<String> sampleNames = new ArrayList<String>(numSamples); for ( int i = 0; i < numSamples; i++ ) { readGroups.add("ReadGroup" + i); sampleNames.add("Sample" + i); } return ArtificialSAMUtils.createEnumeratedReadGroups(header, readGroups, sampleNames); }
private static final void addSAMHeader() { final SAMFileHeader header = ArtificialSAMUtils.createArtificialSamHeader(1, 1, 10); ArtificialSAMUtils.createEnumeratedReadGroups(header, Arrays.asList("1", "2", "3"), Arrays.asList("kid", "mom", "dad")); builder.addSamplesFromSAMHeader(header); }
@BeforeClass public void beforeClass() { header = composeHeader(); dataSource = composeDataSource(); final List<String> readGroupIDs = new ArrayList<String>(); final List<String> sampleNames = new ArrayList<String>(); for (int i = 1; i <= getReadGroupCount(); i++) { final String readGroupId = composeReadGroupId(i); readGroupIDs.add(readGroupId); sampleNames.add(readGroupId); } ArtificialSAMUtils.createEnumeratedReadGroups( header, readGroupIDs, sampleNames); for (int i = 1; i <= getReadGroupCount(); i++) { final String readGroupId = readGroupIDs.get(i-1); final SAMReadGroupRecord groupRecord = header.getReadGroup(readGroupId); groupRecord.setAttribute("PL", composePlatformName(i)); groupRecord.setAttribute("PU", composePlatformUnitName(i)); } }