private Collection<Throwable> execute_bam(String source) throws IOException {
SamReader in = null;
SAMRecordIterator iter = null;
try {
SamReaderFactory srf =
SamReaderFactory.makeDefault().validationStringency(ValidationStringency.SILENT);
if (source == null) {
in = srf.open(SamInputResource.of(stdin()));
} else {
in = srf.open(SamInputResource.of(source));
}
iter = in.iterator();
bindings.put("header", in.getFileHeader());
bindings.put("iter", iter);
bindings.put("format", "sam");
this.script.eval(bindings);
return RETURN_OK;
} catch (Exception e) {
LOG.error(e);
return wrapException(e);
} finally {
CloserUtil.close(in);
CloserUtil.close(iter);
bindings.remove("header");
bindings.remove("iter");
bindings.remove("format");
}
}
public SamReader getSamReader(ResourceLocator locator, boolean requireIndex) throws IOException {
if (requireIndex) {
final SamReaderFactory factory =
SamReaderFactory.makeDefault().validationStringency(ValidationStringency.SILENT);
SeekableStream indexStream = getIndexStream(locator.getBamIndexPath());
this.indexed = true;
SeekableStream ss =
new IGVSeekableBufferedStream(
IGVSeekableStreamFactory.getInstance().getStreamFor(url), 128000);
SamInputResource resource = SamInputResource.of(ss).index(indexStream);
return factory.open(resource);
} else {
InputStream is = HttpUtils.getInstance().openConnectionStream(url);
return new SAMFileReader(new BufferedInputStream(is));
}
}
@Test
public void testAddCommentsToBam() throws Exception {
final File outputFile =
File.createTempFile("addCommentsToBamTest.", BamFileIoUtils.BAM_FILE_EXTENSION);
runIt(BAM_FILE, outputFile, commentList);
final SAMFileHeader newHeader = SamReaderFactory.makeDefault().getFileHeader(outputFile);
// The original comments are massaged when they're added to the header. Perform the same
// massaging here,
// and then compare the lists
final List<String> massagedComments = new LinkedList<>();
for (final String comment : commentList) {
massagedComments.add(SAMTextHeaderCodec.COMMENT_PREFIX + comment);
}
Assert.assertEquals(newHeader.getComments(), massagedComments);
}
@Exec
public void exec() throws IOException, CommandArgumentException {
if (filename == null) {
throw new CommandArgumentException("You must specify an input BAM filename!");
}
SamReaderFactory readerFactory = SamReaderFactory.makeDefault();
if (lenient) {
readerFactory.validationStringency(ValidationStringency.LENIENT);
} else if (silent) {
readerFactory.validationStringency(ValidationStringency.SILENT);
}
SamReader reader = null;
String name;
FileChannel channel = null;
if (filename.equals("-")) {
reader = readerFactory.open(SamInputResource.of(System.in));
name = "<stdin>";
} else {
File f = new File(filename);
FileInputStream fis = new FileInputStream(f);
channel = fis.getChannel();
reader = readerFactory.open(SamInputResource.of(fis));
name = f.getName();
}
Iterator<SAMRecord> it =
ProgressUtils.getIterator(
name,
reader.iterator(),
(channel == null) ? null : new FileChannelStats(channel),
new ProgressMessage<SAMRecord>() {
long i = 0;
@Override
public String msg(SAMRecord current) {
i++;
return i + " " + current.getReadName();
}
},
new CloseableFinalizer<SAMRecord>());
long i = 0;
while (it.hasNext()) {
i++;
it.next();
}
reader.close();
System.err.println("Successfully read: " + i + " records.");
}
@Override
protected Object doWork() {
IOUtil.assertFileIsReadable(INPUT);
IOUtil.assertFileIsWritable(OUTPUT);
if (INPUT.getAbsolutePath().endsWith(".sam")) {
throw new UserException("SAM files are not supported");
}
final SAMFileHeader samFileHeader =
SamReaderFactory.makeDefault().referenceSequence(REFERENCE_SEQUENCE).getFileHeader(INPUT);
for (final String comment : COMMENT) {
if (comment.contains("\n")) {
throw new UserException("Comments can not contain a new line");
}
samFileHeader.addComment(comment);
}
BamFileIoUtils.reheaderBamFile(samFileHeader, INPUT, OUTPUT, CREATE_MD5_FILE, CREATE_INDEX);
return null;
}
@Override
protected int doWork() {
IOUtil.assertFileIsReadable(INPUT);
IOUtil.assertFileIsWritable(OUTPUT);
IOUtil.assertFileIsReadable(REFERENCE_SEQUENCE);
// Setup all the inputs
final ProgressLogger progress = new ProgressLogger(log, 10000000, "Processed", "loci");
final ReferenceSequenceFileWalker refWalker =
new ReferenceSequenceFileWalker(REFERENCE_SEQUENCE);
final SamReader in =
SamReaderFactory.makeDefault().referenceSequence(REFERENCE_SEQUENCE).open(INPUT);
final SamLocusIterator iterator = getLocusIterator(in);
final List<SamRecordFilter> filters = new ArrayList<SamRecordFilter>();
final CountingFilter dupeFilter = new CountingDuplicateFilter();
final CountingFilter mapqFilter = new CountingMapQFilter(MINIMUM_MAPPING_QUALITY);
final CountingPairedFilter pairFilter = new CountingPairedFilter();
filters.add(mapqFilter);
filters.add(dupeFilter);
if (!COUNT_UNPAIRED) {
filters.add(pairFilter);
}
filters.add(
new SecondaryAlignmentFilter()); // Not a counting filter because we never want to count
// reads twice
iterator.setSamFilters(filters);
iterator.setEmitUncoveredLoci(true);
iterator.setMappingQualityScoreCutoff(0); // Handled separately because we want to count bases
iterator.setQualityScoreCutoff(0); // Handled separately because we want to count bases
iterator.setIncludeNonPfReads(false);
final int max = COVERAGE_CAP;
final long[] HistogramArray = new long[max + 1];
final long[] baseQHistogramArray = new long[Byte.MAX_VALUE];
final boolean usingStopAfter = STOP_AFTER > 0;
final long stopAfter = STOP_AFTER - 1;
long counter = 0;
long basesExcludedByBaseq = 0;
long basesExcludedByOverlap = 0;
long basesExcludedByCapping = 0;
// Loop through all the loci
while (iterator.hasNext()) {
final SamLocusIterator.LocusInfo info = iterator.next();
// Check that the reference is not N
final ReferenceSequence ref = refWalker.get(info.getSequenceIndex());
final byte base = ref.getBases()[info.getPosition() - 1];
if (base == 'N') continue;
// Figure out the coverage while not counting overlapping reads twice, and excluding various
// things
final HashSet<String> readNames = new HashSet<String>(info.getRecordAndPositions().size());
int pileupSize = 0;
for (final SamLocusIterator.RecordAndOffset recs : info.getRecordAndPositions()) {
if (recs.getBaseQuality() < MINIMUM_BASE_QUALITY) {
++basesExcludedByBaseq;
continue;
}
if (!readNames.add(recs.getRecord().getReadName())) {
++basesExcludedByOverlap;
continue;
}
pileupSize++;
if (pileupSize <= max) {
baseQHistogramArray[recs.getRecord().getBaseQualities()[recs.getOffset()]]++;
}
}
final int depth = Math.min(readNames.size(), max);
if (depth < readNames.size()) basesExcludedByCapping += readNames.size() - max;
HistogramArray[depth]++;
// Record progress and perhaps stop
progress.record(info.getSequenceName(), info.getPosition());
if (usingStopAfter && ++counter > stopAfter) break;
}
// Construct and write the outputs
final Histogram<Integer> histo = new Histogram<Integer>("coverage", "count");
for (int i = 0; i < HistogramArray.length; ++i) {
histo.increment(i, HistogramArray[i]);
}
// Construct and write the outputs
final Histogram<Integer> baseQHisto = new Histogram<Integer>("value", "baseq_count");
for (int i = 0; i < baseQHistogramArray.length; ++i) {
baseQHisto.increment(i, baseQHistogramArray[i]);
}
final WgsMetrics metrics = generateWgsMetrics();
metrics.GENOME_TERRITORY = (long) histo.getSumOfValues();
metrics.MEAN_COVERAGE = histo.getMean();
metrics.SD_COVERAGE = histo.getStandardDeviation();
metrics.MEDIAN_COVERAGE = histo.getMedian();
metrics.MAD_COVERAGE = histo.getMedianAbsoluteDeviation();
final long basesExcludedByDupes = getBasesExcludedBy(dupeFilter);
final long basesExcludedByMapq = getBasesExcludedBy(mapqFilter);
final long basesExcludedByPairing = getBasesExcludedBy(pairFilter);
final double total = histo.getSum();
final double totalWithExcludes =
total
+ basesExcludedByDupes
+ basesExcludedByMapq
+ basesExcludedByPairing
+ basesExcludedByBaseq
+ basesExcludedByOverlap
+ basesExcludedByCapping;
metrics.PCT_EXC_DUPE = basesExcludedByDupes / totalWithExcludes;
metrics.PCT_EXC_MAPQ = basesExcludedByMapq / totalWithExcludes;
metrics.PCT_EXC_UNPAIRED = basesExcludedByPairing / totalWithExcludes;
metrics.PCT_EXC_BASEQ = basesExcludedByBaseq / totalWithExcludes;
metrics.PCT_EXC_OVERLAP = basesExcludedByOverlap / totalWithExcludes;
metrics.PCT_EXC_CAPPED = basesExcludedByCapping / totalWithExcludes;
metrics.PCT_EXC_TOTAL = (totalWithExcludes - total) / totalWithExcludes;
metrics.PCT_1X =
MathUtil.sum(HistogramArray, 1, HistogramArray.length) / (double) metrics.GENOME_TERRITORY;
metrics.PCT_5X =
MathUtil.sum(HistogramArray, 5, HistogramArray.length) / (double) metrics.GENOME_TERRITORY;
metrics.PCT_10X =
MathUtil.sum(HistogramArray, 10, HistogramArray.length) / (double) metrics.GENOME_TERRITORY;
metrics.PCT_15X =
MathUtil.sum(HistogramArray, 15, HistogramArray.length) / (double) metrics.GENOME_TERRITORY;
metrics.PCT_20X =
MathUtil.sum(HistogramArray, 20, HistogramArray.length) / (double) metrics.GENOME_TERRITORY;
metrics.PCT_25X =
MathUtil.sum(HistogramArray, 25, HistogramArray.length) / (double) metrics.GENOME_TERRITORY;
metrics.PCT_30X =
MathUtil.sum(HistogramArray, 30, HistogramArray.length) / (double) metrics.GENOME_TERRITORY;
metrics.PCT_40X =
MathUtil.sum(HistogramArray, 40, HistogramArray.length) / (double) metrics.GENOME_TERRITORY;
metrics.PCT_50X =
MathUtil.sum(HistogramArray, 50, HistogramArray.length) / (double) metrics.GENOME_TERRITORY;
metrics.PCT_60X =
MathUtil.sum(HistogramArray, 60, HistogramArray.length) / (double) metrics.GENOME_TERRITORY;
metrics.PCT_70X =
MathUtil.sum(HistogramArray, 70, HistogramArray.length) / (double) metrics.GENOME_TERRITORY;
metrics.PCT_80X =
MathUtil.sum(HistogramArray, 80, HistogramArray.length) / (double) metrics.GENOME_TERRITORY;
metrics.PCT_90X =
MathUtil.sum(HistogramArray, 90, HistogramArray.length) / (double) metrics.GENOME_TERRITORY;
metrics.PCT_100X =
MathUtil.sum(HistogramArray, 100, HistogramArray.length)
/ (double) metrics.GENOME_TERRITORY;
final MetricsFile<WgsMetrics, Integer> out = getMetricsFile();
out.addMetric(metrics);
out.addHistogram(histo);
if (INCLUDE_BQ_HISTOGRAM) {
out.addHistogram(baseQHisto);
}
out.write(OUTPUT);
return 0;
}
/**
* Main method for the program. Checks that all input files are present and readable and that the
* output file can be written to. Then iterates through all the records accumulating metrics.
* Finally writes metrics file
*/
protected int doWork() {
IOUtil.assertFileIsReadable(INPUT);
IOUtil.assertFileIsWritable(OUTPUT);
final SamReader reader =
SamReaderFactory.makeDefault().referenceSequence(REFERENCE_SEQUENCE).open(INPUT);
final Histogram<Integer> mismatchesHist = new Histogram<Integer>("Predicted", "Mismatches");
final Histogram<Integer> totalHist = new Histogram<Integer>("Predicted", "Total_Bases");
final Map<String, Histogram> mismatchesByTypeHist = new HashMap<String, Histogram>();
final Map<String, Histogram> totalByTypeHist = new HashMap<String, Histogram>();
// Set up the histograms
byte[] bases = {'A', 'C', 'G', 'T'};
for (final byte base : bases) {
final Histogram<Integer> h = new Histogram<Integer>("Predicted", (char) base + ">");
mismatchesByTypeHist.put((char) base + ">", h);
final Histogram<Integer> h2 = new Histogram<Integer>("Predicted", ">" + (char) base);
mismatchesByTypeHist.put(">" + (char) base, h2);
}
for (final byte base : bases) {
final Histogram<Integer> h = new Histogram<Integer>("Predicted", (char) base + ">");
totalByTypeHist.put((char) base + ">", h);
final Histogram<Integer> h2 = new Histogram<Integer>("Predicted", ">" + (char) base);
totalByTypeHist.put(">" + (char) base, h2);
}
for (final SAMRecord record : reader) {
// Ignore these as we don't know the truth
if (record.getReadUnmappedFlag() || record.isSecondaryOrSupplementary()) {
continue;
}
final byte[] readBases = record.getReadBases();
final byte[] readQualities = record.getBaseQualities();
final byte[] refBases = SequenceUtil.makeReferenceFromAlignment(record, false);
// We've seen stranger things
if (readQualities.length != readBases.length) {
throw new PicardException(
"Missing Qualities ("
+ readQualities.length
+ ","
+ readBases.length
+ ") : "
+ record.getSAMString());
}
if (refBases.length != readBases.length) {
throw new PicardException(
"The read length did not match the inferred reference length, please check your MD and CIGAR.");
}
int cycleIndex; // zero-based
if (record.getReadNegativeStrandFlag()) {
cycleIndex = readBases.length - 1 + CYCLE_OFFSET;
} else {
cycleIndex = CYCLE_OFFSET;
}
for (int i = 0; i < readBases.length; i++) {
if (-1 == CYCLE || cycleIndex == CYCLE) {
if ('-' != refBases[i] && '0' != refBases[i]) { // not insertion and not soft-clipped
if (!SequenceUtil.basesEqual(readBases[i], refBases[i])) { // mismatch
mismatchesHist.increment((int) readQualities[i]);
if (SequenceUtil.isValidBase(refBases[i])) {
mismatchesByTypeHist
.get((char) refBases[i] + ">")
.increment((int) readQualities[i]);
}
if (SequenceUtil.isValidBase(readBases[i])) {
mismatchesByTypeHist
.get(">" + (char) readBases[i])
.increment((int) readQualities[i]);
}
} else {
mismatchesHist.increment(
(int) readQualities[i], 0); // to make sure the bin will exist
}
totalHist.increment((int) readQualities[i]);
if (SequenceUtil.isValidBase(readBases[i])) {
totalByTypeHist.get(">" + (char) readBases[i]).increment((int) readQualities[i]);
}
if (SequenceUtil.isValidBase(refBases[i])) {
totalByTypeHist.get((char) refBases[i] + ">").increment((int) readQualities[i]);
}
}
}
cycleIndex += record.getReadNegativeStrandFlag() ? -1 : 1;
}
}
CloserUtil.close(reader);
final Histogram<Integer> hist = new Histogram<Integer>("Predicted", "Observed");
double sumOfSquaresError = 0.0;
// compute the aggregate phred values
for (final Integer key : mismatchesHist.keySet()) {
final double numMismatches = mismatchesHist.get(key).getValue();
final double numBases = totalHist.get(key).getValue();
final double phredErr = Math.log10(numMismatches / numBases) * -10.0;
sumOfSquaresError += (0 == numMismatches) ? 0.0 : (key - phredErr) * (key - phredErr);
hist.increment(key, phredErr);
// make sure the bin will exist
for (final byte base : bases) {
mismatchesByTypeHist.get(">" + (char) base).increment(key, 0.0);
mismatchesByTypeHist.get((char) base + ">").increment(key, 0.0);
totalByTypeHist.get(">" + (char) base).increment(key, 0.0);
totalByTypeHist.get((char) base + ">").increment(key, 0.0);
}
}
final QualityScoreAccuracyMetrics metrics = new QualityScoreAccuracyMetrics();
metrics.SUM_OF_SQUARE_ERROR = sumOfSquaresError;
final MetricsFile<QualityScoreAccuracyMetrics, Integer> out = getMetricsFile();
out.addMetric(metrics);
out.addHistogram(hist);
for (final byte base : bases) {
// >base : histograms for mismatches *to* the given base
Histogram<Integer> m = mismatchesByTypeHist.get(">" + (char) base);
Histogram<Integer> t = totalByTypeHist.get(">" + (char) base);
Histogram<Integer> h = new Histogram<Integer>(m.getBinLabel(), m.getValueLabel());
for (final Integer key : m.keySet()) {
final double numMismatches = m.get(key).getValue();
final double numBases = t.get(key).getValue();
final double phredErr = Math.log10(numMismatches / numBases) * -10.0;
h.increment(key, phredErr);
}
out.addHistogram(h);
// base> : histograms for mismatches *from* the given base
m = mismatchesByTypeHist.get((char) base + ">");
t = totalByTypeHist.get(">" + (char) base);
h = new Histogram<Integer>(m.getBinLabel(), m.getValueLabel());
for (final Integer key : m.keySet()) {
final double numMismatches = m.get(key).getValue();
final double numBases = t.get(key).getValue();
final double phredErr = Math.log10(numMismatches / numBases) * -10.0;
h.increment(key, phredErr);
}
out.addHistogram(h);
}
out.addHistogram(mismatchesHist);
out.addHistogram(totalHist);
out.write(OUTPUT);
return 0;
}
@Override
public int doWork(String[] args) {
String region = null;
com.github.lindenb.jvarkit.util.cli.GetOpt opt =
new com.github.lindenb.jvarkit.util.cli.GetOpt();
int c;
while ((c = opt.getopt(args, getGetOptDefault() + "r:R:")) != -1) {
switch (c) {
case 'r':
region = opt.getOptArg();
break;
case 'R':
this.referenceFile = new File(opt.getOptArg());
break;
default:
{
switch (handleOtherOptions(c, opt, args)) {
case EXIT_FAILURE:
return -1;
case EXIT_SUCCESS:
return 0;
default:
break;
}
}
}
}
File faidx = null;
File bamFile = null;
if (opt.getOptInd() + 1 == args.length) {
bamFile = new File(args[opt.getOptInd()]);
} else if (opt.getOptInd() + 2 == args.length) {
bamFile = new File(args[opt.getOptInd()]);
faidx = new File(args[opt.getOptInd() + 1]);
} else {
System.err.println("Illegal Number of arguments.");
return -1;
}
IndexedFastaSequenceFile ref = null;
PrintWriter out = new PrintWriter(System.out);
SamReader samReader = null;
try {
info("opening " + bamFile);
SamReaderFactory srf =
SamReaderFactory.makeDefault().validationStringency(ValidationStringency.LENIENT);
samReader = srf.open(bamFile);
Interval interval =
IntervalUtils.parseOne(samReader.getFileHeader().getSequenceDictionary(), region);
if (interval == null) {
error("Bad interval " + interval);
return -1;
}
if (faidx != null) {
ref = new IndexedFastaSequenceFile(faidx);
}
TViewHandler handler = new AsciiHandler();
new TView().execute(samReader, ref, interval, handler);
} catch (Exception e) {
e.printStackTrace();
return -1;
} finally {
out.flush();
CloserUtil.close(samReader);
CloserUtil.close(ref);
}
return 0;
}
/** Combines multiple SAM/BAM files into one. */
@Override
protected int doWork() {
boolean matchedSortOrders = true;
// read interval list if it is defined
final List<Interval> intervalList =
(INTERVALS == null ? null : IntervalList.fromFile(INTERVALS).uniqued().getIntervals());
// map reader->iterator used if INTERVALS is defined
final Map<SamReader, CloseableIterator<SAMRecord>> samReaderToIterator =
new HashMap<SamReader, CloseableIterator<SAMRecord>>(INPUT.size());
// Open the files for reading and writing
final List<SamReader> readers = new ArrayList<SamReader>();
final List<SAMFileHeader> headers = new ArrayList<SAMFileHeader>();
{
SAMSequenceDictionary dict = null; // Used to try and reduce redundant SDs in memory
for (final File inFile : INPUT) {
IOUtil.assertFileIsReadable(inFile);
final SamReader in =
SamReaderFactory.makeDefault().referenceSequence(REFERENCE_SEQUENCE).open(inFile);
if (INTERVALS != null) {
if (!in.hasIndex())
throw new PicardException(
"Merging with interval but Bam file is not indexed " + inFile);
final CloseableIterator<SAMRecord> samIterator =
new SamRecordIntervalIteratorFactory()
.makeSamRecordIntervalIterator(in, intervalList, true);
samReaderToIterator.put(in, samIterator);
}
readers.add(in);
headers.add(in.getFileHeader());
// A slightly hackish attempt to keep memory consumption down when merging multiple files
// with
// large sequence dictionaries (10,000s of sequences). If the dictionaries are identical,
// then
// replace the duplicate copies with a single dictionary to reduce the memory footprint.
if (dict == null) {
dict = in.getFileHeader().getSequenceDictionary();
} else if (dict.equals(in.getFileHeader().getSequenceDictionary())) {
in.getFileHeader().setSequenceDictionary(dict);
}
matchedSortOrders = matchedSortOrders && in.getFileHeader().getSortOrder() == SORT_ORDER;
}
}
// If all the input sort orders match the output sort order then just merge them and
// write on the fly, otherwise setup to merge and sort before writing out the final file
IOUtil.assertFileIsWritable(OUTPUT);
final boolean presorted;
final SAMFileHeader.SortOrder headerMergerSortOrder;
final boolean mergingSamRecordIteratorAssumeSorted;
if (matchedSortOrders
|| SORT_ORDER == SAMFileHeader.SortOrder.unsorted
|| ASSUME_SORTED
|| INTERVALS != null) {
log.info(
"Input files are in same order as output so sorting to temp directory is not needed.");
headerMergerSortOrder = SORT_ORDER;
mergingSamRecordIteratorAssumeSorted = ASSUME_SORTED;
presorted = true;
} else {
log.info("Sorting input files using temp directory " + TMP_DIR);
headerMergerSortOrder = SAMFileHeader.SortOrder.unsorted;
mergingSamRecordIteratorAssumeSorted = false;
presorted = false;
}
final SamFileHeaderMerger headerMerger =
new SamFileHeaderMerger(headerMergerSortOrder, headers, MERGE_SEQUENCE_DICTIONARIES);
final MergingSamRecordIterator iterator;
// no interval defined, get an iterator for the whole bam
if (intervalList == null) {
iterator =
new MergingSamRecordIterator(headerMerger, readers, mergingSamRecordIteratorAssumeSorted);
} else {
// show warning related to https://github.com/broadinstitute/picard/pull/314/files
log.info(
"Warning: merged bams from different interval lists may contain the same read in both files");
iterator = new MergingSamRecordIterator(headerMerger, samReaderToIterator, true);
}
final SAMFileHeader header = headerMerger.getMergedHeader();
for (final String comment : COMMENT) {
header.addComment(comment);
}
header.setSortOrder(SORT_ORDER);
final SAMFileWriterFactory samFileWriterFactory = new SAMFileWriterFactory();
if (USE_THREADING) {
samFileWriterFactory.setUseAsyncIo(true);
}
final SAMFileWriter out = samFileWriterFactory.makeSAMOrBAMWriter(header, presorted, OUTPUT);
// Lastly loop through and write out the records
final ProgressLogger progress = new ProgressLogger(log, PROGRESS_INTERVAL);
while (iterator.hasNext()) {
final SAMRecord record = iterator.next();
out.addAlignment(record);
progress.record(record);
}
log.info("Finished reading inputs.");
for (final CloseableIterator<SAMRecord> iter : samReaderToIterator.values())
CloserUtil.close(iter);
CloserUtil.close(readers);
out.close();
return 0;
}
/**
* Test that PG header records are created & chained appropriately (or not created), and that the
* PG record chains are as expected. MarkDuplicates is used both to merge and to mark dupes in
* this case.
*
* @param suppressPg If true, do not create PG header record.
* @param expectedPnVnByReadName For each read, info about the expect chain of PG records.
*/
@Test(dataProvider = "pgRecordChainingTest")
public void pgRecordChainingTest(
final boolean suppressPg, final Map<String, List<ExpectedPnAndVn>> expectedPnVnByReadName) {
final File outputDir = IOUtil.createTempDir(TEST_BASE_NAME + ".", ".tmp");
outputDir.deleteOnExit();
try {
// Run MarkDuplicates, merging the 3 input files, and either enabling or suppressing PG header
// record creation according to suppressPg.
final MarkDuplicates markDuplicates = new MarkDuplicates();
final ArrayList<String> args = new ArrayList<String>();
for (int i = 1; i <= 3; ++i) {
args.add("INPUT=" + new File(TEST_DATA_DIR, "merge" + i + ".sam").getAbsolutePath());
}
final File outputSam = new File(outputDir, TEST_BASE_NAME + ".sam");
args.add("OUTPUT=" + outputSam.getAbsolutePath());
args.add(
"METRICS_FILE="
+ new File(outputDir, TEST_BASE_NAME + ".duplicate_metrics").getAbsolutePath());
if (suppressPg) args.add("PROGRAM_RECORD_ID=null");
// I generally prefer to call doWork rather than invoking the argument parser, but it is
// necessary
// in this case to initialize the command line.
// Note that for the unit test, version won't come through because it is obtained through jar
// manifest, and unit test doesn't run code from a jar.
Assert.assertEquals(markDuplicates.instanceMain(args.toArray(new String[args.size()])), 0);
// Read the MarkDuplicates output file, and get the PG ID for each read. In this particular
// test,
// the PG ID should be the same for both ends of a pair.
final SamReader reader = SamReaderFactory.makeDefault().open(outputSam);
final Map<String, String> pgIdForReadName = new HashMap<String, String>();
for (final SAMRecord rec : reader) {
final String existingPgId = pgIdForReadName.get(rec.getReadName());
final String thisPgId = rec.getStringAttribute(SAMTag.PG.name());
if (existingPgId != null) {
Assert.assertEquals(thisPgId, existingPgId);
} else {
pgIdForReadName.put(rec.getReadName(), thisPgId);
}
}
final SAMFileHeader header = reader.getFileHeader();
CloserUtil.close(reader);
// Confirm that for each read name, the chain of PG records contains exactly the number that
// is expected,
// and that values in the PG chain are as expected.
for (final Map.Entry<String, List<ExpectedPnAndVn>> entry :
expectedPnVnByReadName.entrySet()) {
final String readName = entry.getKey();
final List<ExpectedPnAndVn> expectedList = entry.getValue();
String pgId = pgIdForReadName.get(readName);
for (final ExpectedPnAndVn expected : expectedList) {
final SAMProgramRecord programRecord = header.getProgramRecord(pgId);
if (expected.expectedPn != null)
Assert.assertEquals(programRecord.getProgramName(), expected.expectedPn);
if (expected.expectedVn != null)
Assert.assertEquals(programRecord.getProgramVersion(), expected.expectedVn);
pgId = programRecord.getPreviousProgramGroupId();
}
Assert.assertNull(pgId);
}
} finally {
TestUtil.recursiveDelete(outputDir);
}
}
private BAMProcessorImplDict(File in) {
reader = SamReaderFactory.makeDefault().open(in);
iterator = reader.iterator();
queue = new LinkedList<SAMRecord>();
}