@BeforeTest
void setupBuilder() throws IOException {
tempSamFileChrM_O = File.createTempFile("CollectGcBias", ".bam", TEST_DIR);
tempSamFileAllChr = File.createTempFile("CollectGcBias", ".bam", TEST_DIR);
tempSamFileChrM_O.deleteOnExit();
tempSamFileAllChr.deleteOnExit();
final File tempSamFileUnsorted = File.createTempFile("CollectGcBias", ".bam", TEST_DIR);
tempSamFileUnsorted.deleteOnExit();
final SAMFileHeader header = new SAMFileHeader();
try {
header.setSequenceDictionary(SAMSequenceDictionaryExtractor.extractDictionary(dict));
header.setSortOrder(SAMFileHeader.SortOrder.unsorted);
} catch (final SAMException e) {
e.printStackTrace();
}
// build different levels to put into the same bam file for testing multi level collection
setupTest1(
1,
readGroupId1,
readGroupRecord1,
sample1,
library1,
header,
setBuilder1); // Sample 1, Library 1, RG 1
setupTest1(
2,
readGroupId2,
readGroupRecord2,
sample1,
library2,
header,
setBuilder2); // Sample 1, Library 2, RG 2
setupTest1(
3,
readGroupId3,
readGroupRecord3,
sample2,
library3,
header,
setBuilder3); // Sample 2, Library 3, RG 3
// build one last readgroup for comparing that window count stays the same whether you use all
// contigs or not
setupTest2(1, readGroupId1, readGroupRecord1, sample1, library1, header, setBuilder4);
final List<SAMRecordSetBuilder> test1Builders = new ArrayList<SAMRecordSetBuilder>();
test1Builders.add(setBuilder1);
test1Builders.add(setBuilder2);
test1Builders.add(setBuilder3);
final List<SAMRecordSetBuilder> test2Builders = new ArrayList<SAMRecordSetBuilder>();
test2Builders.add(setBuilder4);
tempSamFileChrM_O = build(test1Builders, tempSamFileUnsorted, header);
tempSamFileAllChr = build(test2Builders, tempSamFileUnsorted, header);
}
public void onTraversalDone(EventPair sum) {
if (sum.left != null && sum.left.isReportableEvent()) sum.intervals.add(sum.left.getLoc());
if (sum.right != null && sum.right.isReportableEvent()) sum.intervals.add(sum.right.getLoc());
if (FilenameUtils.getExtension(out.getName()).equals("interval_list")) {
final SAMFileHeader masterSequenceDictionaryHeader = new SAMFileHeader();
masterSequenceDictionaryHeader.setSequenceDictionary(
getToolkit().getMasterSequenceDictionary());
final IntervalList intervalList = new IntervalList(masterSequenceDictionaryHeader);
for (GenomeLoc loc : sum.intervals) {
intervalList.add(new Interval(loc.getContig(), loc.getStart(), loc.getStop()));
}
intervalList.write(out);
} else {
try (BufferedWriter bufferedWriter = IOUtil.openFileForBufferedWriting(out)) {
for (GenomeLoc loc : sum.intervals) {
bufferedWriter.write(loc.toString());
bufferedWriter.newLine();
}
} catch (final IOException e) {
throw new GATKException("Error writing out intervals to file: " + out.getAbsolutePath(), e);
}
}
}