private void updateProgress() {
   if (mBasicProgress) {
     synchronized (mJobs) {
       mTotalJobsFinished++;
       final String message =
           mThreadPoolName + ": " + mTotalJobsFinished + "/" + mTotalJobs + " Jobs Finished";
       Diagnostic.progress(message);
       Diagnostic.developerLog(message);
     }
   }
 }
 /**
  * Alternative to other one with similar name
  *
  * @param directory directory containing SDF
  * @param indexFile index file
  * @param loadNames should we load names
  * @param loadFullNames should we load full names
  * @param region region to restrict to
  * @throws IOException IO exception occurs
  */
 CompressedMemorySequencesReader2(
     File directory,
     IndexFile indexFile,
     boolean loadNames,
     boolean loadFullNames,
     LongRange region)
     throws IOException {
   mIndexFile = indexFile;
   mRegion = SequencesReaderFactory.resolveRange(indexFile, region);
   mStart = mRegion.getStart();
   mEnd = mRegion.getEnd();
   mNumberSequences = mEnd - mStart;
   mData =
       DataInMemory.loadDelayQuality(
           directory,
           indexFile,
           DataFileIndex.loadSequenceDataFileIndex(indexFile.dataIndexVersion(), directory),
           mStart,
           mEnd);
   if (mNumberSequences > Integer.MAX_VALUE) {
     throw new IllegalArgumentException(
         "Too many sequences in region: " + region + ", maximum is: " + Integer.MAX_VALUE);
   }
   mDirectory = directory;
   if (loadNames && mIndexFile.hasNames()) {
     loadNames();
     loadNameSuffixes(loadFullNames, mIndexFile.hasSequenceNameSuffixes());
   }
   final StringBuilder sb = new StringBuilder("CMSR2 statistics");
   sb.append(LS);
   this.infoString(sb);
   Diagnostic.userLog(sb.toString());
 }
示例#3
0
 @Override
 public void close() throws IOException {
   mReader.close();
   Diagnostic.developerLog(
       "There were "
           + mDoubleFetched
           + " tabixed records double-fetched due to overlapping blocks");
 }
示例#4
0
 /**
  * Reads a set of read group priors.
  *
  * @param remap optional read group id remapping (used to merge read group ids)
  * @param files the files containing the priors.
  * @return a map from read group name to a ReadGroupStats object.
  * @exception IOException if an error occurs.
  */
 static Map<String, ReadGroupStats> loadReadGroupStats(Map<String, String> remap, File... files)
     throws IOException {
   final HashMap<String, ReadGroupStats> rgStats = new HashMap<>();
   Diagnostic.userLog("Loading read group statistics");
   for (final File statsFile : files) {
     try (BufferedReader br = new BufferedReader(new FileReader(statsFile))) {
       String line;
       while ((line = br.readLine()) != null) {
         if (line.length() > 0) {
           if (line.startsWith("#")) {
             if (line.startsWith("#Version") && !line.contains(ReadGroupStatsCalculator.VERSION)) {
               throw new NoTalkbackSlimException(
                   "Unsupported rgstats version: " + line + " - rerun svprep");
             }
           } else {
             try {
               final ReadGroupStats stats = new ReadGroupStats(remap, line);
               if (rgStats.containsKey(stats.id())) {
                 rgStats.get(stats.id()).add(stats);
               } else {
                 rgStats.put(stats.id(), stats);
               }
             } catch (final IllegalArgumentException e) {
               throw new IOException(e.getMessage());
             }
           }
         }
       }
       if (rgStats.size() == 0) {
         throw new IOException("No read group statistics contained in file " + statsFile);
       }
     }
   }
   for (final ReadGroupStats stats : rgStats.values()) {
     stats.calculate();
     Diagnostic.userLog(stats.toString());
     if (stats.detectOverflow()) {
       throw new NoTalkbackSlimException(
           "Overflow detected in read group statistics calculation for read group: " + stats.id());
     } else if (!stats.isValid()) {
       throw new NoTalkbackSlimException(
           "Invalid read group statistics for read group: " + stats.id());
     }
   }
   return rgStats;
 }
  public void testArrayPrereadNames() {
    Diagnostic.setLogStream();
    final String seqString = "acgtcacgtcacgtcacgtcacgtcacgtcacgtc";

    new MyMemorySequencesReader(
        new byte[][] {DnaUtils.encodeArray(seqString.getBytes())},
        new String[] {"seq1"},
        new long[] {35},
        35,
        35,
        SequenceType.DNA);
  }
 /**
  * Load the names if they haven't already been loaded.
  *
  * @throws IOException if an I/O related error occurs
  */
 private void loadNames() throws IOException {
   mNames = new PrereadNames(mDirectory, mRegion, false);
   if (mIndexFile.getVersion() >= IndexFile.SEPARATE_CHECKSUM_VERSION
       && mRegion.getStart() == 0
       && mRegion.getEnd() == mIndexFile.getNumberSequences()) {
     if (mNames.calcChecksum() != mIndexFile.getNameChecksum()) {
       throw new CorruptSdfException(
           "Sequence names failed checksum - SDF may be corrupt: \"" + mDirectory + "\"");
     } else {
       Diagnostic.developerLog("Sequence names passed checksum");
     }
   }
 }
 /**
  * Constructor for a thread pool. Basic progress output enabled by default.
  *
  * @param numberThreads maximum number of threads that will be used.
  * @param subname textual label to use in threads.
  * @param logLifecycleEvents logs thread life cycle events
  */
 public SimpleThreadPool(
     final int numberThreads, final String subname, boolean logLifecycleEvents) {
   mThreadPoolName = subname;
   assert numberThreads > 0;
   mMaxThreads = numberThreads;
   mQueueThread =
       new QueueThread(
           "SimpleThreadPool-" + mThreadPoolName + "-Queue", subname, logLifecycleEvents);
   mQueueThread.setDaemon(true);
   mQueueThread.start();
   Diagnostic.developerLog(
       mThreadPoolName + ": Starting SimpleThreadPool with maximum " + numberThreads + " threads");
 }
 public void testBad() {
   Diagnostic.setLogStream();
   final SAMRecord rec = new SAMRecord(new SAMFileHeader());
   rec.setReadString("TATTAGGATTGAGACTGGTAAAATGGNCCACCAAG");
   rec.setBaseQualityString("/725361840-525251.68,0,.52!222254/2");
   final VariantParams params = VariantParams.builder().create();
   try {
     new AlignmentEnvironmentCG(
         new VariantAlignmentRecord(rec),
         params,
         MachineErrorParams.builder().machine(MachineType.COMPLETE_GENOMICS).create(),
         null);
     fail();
   } catch (final NoTalkbackSlimException e) {
     assertTrue(e.getMessage(), e.getMessage().startsWith("Invalid CG alignment."));
   }
 }
 private void loadNameSuffixes(boolean attemptLoad, boolean suffixExists) throws IOException {
   mNameSuffixes =
       attemptLoad && suffixExists
           ? new PrereadNames(mDirectory, mRegion, true)
           : new EmptyStringPrereadNames(mEnd - mStart);
   if (attemptLoad && suffixExists) {
     if (mRegion.getStart() == 0 && mRegion.getEnd() == mIndexFile.getNumberSequences()) {
       if (mNameSuffixes.calcChecksum() != mIndexFile.getNameSuffixChecksum()) {
         throw new CorruptSdfException(
             "Sequence name suffixes failed checksum - SDF may be corrupt: \""
                 + mDirectory
                 + "\"");
       } else {
         Diagnostic.developerLog("Sequence name suffixes passed checksum");
       }
     }
   }
 }
示例#10
0
 /**
  * Reads a set of read group name remappings from source name to destination name. This is used to
  * merge multiple read groups into one. Format is tab-separated lines consisting of input read
  * group name, output read group name.
  *
  * @param relabelFile the file containing the group name mappings.
  * @return a map from input read group name to output read group name.
  * @exception IOException if an error occurs.
  */
 static Map<String, String> loadRelabelFile(File relabelFile) throws IOException {
   final HashMap<String, String> remap = new HashMap<>();
   Diagnostic.userLog("Loading read group relabelling file");
   try (BufferedReader br = new BufferedReader(new FileReader(relabelFile))) {
     String line;
     while ((line = br.readLine()) != null) {
       if (!line.startsWith("#") && line.length() > 0) {
         final String[] parts = line.split("\t");
         if (parts.length != 2) {
           throw new IOException("Expected input_name<tab>output_name on line: " + line);
         }
         remap.put(parts[0], parts[1]);
       }
     }
     if (remap.size() == 0) {
       throw new IOException("No read group relabellings contained in file " + relabelFile);
     }
   }
   return remap;
 }
示例#11
0
    private void populateNext(boolean force) throws IOException {
      final int previousStart = mNextAlignmentStart;
      final int previousTemplateId = mNextTemplateId;
      mNextRecord = null;
      if (force) {
        advanceSubIterator();
      }
      while (mCurrentOffset <= mOffsets.size()) {
        if (!mBuffered
            && !mReader
                .hasNext()) { // Only happens when stream is exhausted, so effectively just closes
                              // things out.
          advanceSubIterator();
        } else {
          if (mBuffered) {
            mBuffered = false;
          } else {
            mReader.next();
          }
          final String refName = mReader.getReferenceName();
          final Integer refId =
              mSequenceLookup.get(
                  refName); // Note that we cannot rely on mReader.getReferenceId in this scenario,
                            // as that is built up incrementally
          if (refId == null) {
            throw new IOException(
                "Tabixed input contained a sequence name not found in the corresponding index: "
                    + refName);
          }

          if (refId
              > mCurrentTemplate) { // current offset has exceeded region and block overlapped next
                                    // template
            mBuffered = true;
            advanceSubIterator();
          } else {

            if (refId
                < mCurrentTemplate) { // Current block may occasionally return records from the
                                      // previous template if the block overlaps
              // Diagnostic.developerLog("Ignoring record from earlier template at " +
              // mReader.getReferenceName() + ":" + (mReader.getStartPosition() + 1) + " (" + refId
              // + "<" + mCurrentTemplate + ")");
              continue;
            }

            final int alignmentStart = mReader.getStartPosition();
            final int alignmentEnd = alignmentStart + mReader.getLengthOnReference();

            if (alignmentEnd <= mCurrentRegion.getStart()) { // before region
              // Diagnostic.developerLog("Ignoring record from earlier than start at " +
              // mReader.getReferenceName() + ":" + (mReader.getStartPosition() + 1));
              continue;
            }

            if (alignmentStart
                <= mPreviousAlignmentStart) { // this record would have been already returned by an
                                              // earlier region
              // Diagnostic.developerLog("Ignoring record from earlier block at " +
              // mReader.getReferenceName() + ":" + (alignmentStart + 1));
              mDoubleFetched++;
              if (mDoubleFetched % 100000 == 0) {
                Diagnostic.developerLog(
                    "Many double-fetched records noticed at "
                        + mReader.getReferenceName()
                        + ":"
                        + (alignmentStart + 1)
                        + " in region "
                        + mCurrentRegion
                        + " (skipping through to "
                        + mPreviousAlignmentStart
                        + ")");
              }
              continue;
            }

            if (alignmentStart
                >= mCurrentRegion
                    .getEnd()) { // past current region, advance the iterator and record the
                                 // furtherest we got
              if (previousStart != Integer.MIN_VALUE && previousTemplateId == mCurrentTemplate) {
                mPreviousAlignmentStart = previousStart;
              } else {
                mPreviousAlignmentStart = Integer.MIN_VALUE;
              }
              mBuffered = true;
              advanceSubIterator();
              continue;
            }

            mNextRecord = mReader.getRecord();
            mNextTemplateId = mCurrentTemplate;
            mNextAlignmentStart = alignmentStart;
            break;
          }
        }
      }
    }
 @Override
 public void run() {
   try {
     Diagnostic.developerLog(mSubName + ": Started");
     while (mProcessJobs) {
       boolean localBusy = false;
       synchronized (mJobs) {
         for (final WorkerThread t : mThreads) {
           if (!t.hasJob()) {
             if (!mJobs.isEmpty()) {
               t.enqueueJob(mJobs.remove());
               localBusy = true;
               if (mLogLifecycleEvents) {
                 Diagnostic.developerLog(
                     mSubName
                         + ": New Job Started by thread: "
                         + t.getName()
                         + " - "
                         + mJobs.size()
                         + " Jobs Left Queued");
               }
             }
           } else {
             localBusy = true;
           }
         }
         while (!mJobs.isEmpty() && mThreads.size() < mMaxThreads) {
           final WorkerThread t = new WorkerThread(mSubName + "-" + mThreads.size(), mJobs);
           mThreads.add(t);
           if (mLogLifecycleEvents) {
             Diagnostic.developerLog(
                 mSubName
                     + ": Worker Thread Created - "
                     + t.getName()
                     + " - "
                     + mThreads.size()
                     + "/"
                     + mMaxThreads
                     + " Threads");
           }
           t.enqueueJob(mJobs.remove());
           t.start();
           localBusy = true;
           if (mLogLifecycleEvents) {
             Diagnostic.developerLog(
                 mSubName
                     + ": New Job Started by thread: "
                     + t.getName()
                     + " - "
                     + mJobs.size()
                     + " Jobs Left Queued");
           }
         }
         mBusy = localBusy;
         mJobs.notifyAll();
         try {
           if (mProcessJobs) {
             mJobs.wait(NOT_DONE_SLEEP_TIME);
           }
         } catch (final InterruptedException e) {
           // dont care
         }
       }
     }
   } catch (final Throwable t) {
     mThrown = t;
     mProcessJobs = false;
     ProgramState.setAbort();
   } finally {
     for (final WorkerThread t : mThreads) {
       t.die();
     }
     mBusy = false;
     synchronized (mJobs) {
       mJobs.clear();
     }
     Diagnostic.developerLog(mSubName + ": Finished");
     synchronized (this) {
       mQueueDone = true;
       notifyAll();
     }
   }
 }
 /**
  * Enable the basic progress output with the total number of jobs that this thread pool will
  * process.
  *
  * @param totalJobs the total number of jobs this thread pool will be processing.
  */
 public void enableBasicProgress(long totalJobs) {
   mTotalJobs = totalJobs;
   mBasicProgress = true;
   Diagnostic.progress(mThreadPoolName + ": Starting " + mTotalJobs + " Jobs");
 }
示例#14
0
 @Override
 public void setUp() throws IOException {
   Diagnostic.setLogStream();
   mDir = FileHelper.createTempDirectory();
 }
  public void testFilterUnmated() throws IOException {
    final ByteArrayOutputStream log = new ByteArrayOutputStream();
    try (PrintStream prLog = new PrintStream(log)) {
      Diagnostic.setLogStream(prLog);
      final int numReads = 100;
      final MapQScoringReadBlocker blocker = new MapQScoringReadBlocker(numReads, 2);
      blocker.increment(1, 3);
      blocker.increment(20, 4);
      blocker.increment(20, 4);
      blocker.increment(20, 4); // read 20 is blocked for score=4
      blocker.increment(3, 1);
      blocker.increment(3, 1);
      blocker.increment(3, 1); // read 3 is blocked for score=1
      blocker.increment(3, 0);
      blocker.increment(3, 0); // read 3 is just not blocked for score=0
      final File dir = FileUtils.createTempDir("test", "unmatedSamFilter");
      OutputStream out = null;
      try {
        final File in1 = File.createTempFile("sam", "_1.gz", dir);
        writeTempFile(in1);
        final File outFile = File.createTempFile("out", ".gz", dir);
        out = new GZIPOutputStream(new FileOutputStream(outFile));

        final StatusListener listener = new StatusListener(numReads);
        final ReadBlocker freqBlocker = new ReadBlocker(numReads, 2);
        freqBlocker.increment(66);
        freqBlocker.increment(66);

        final MockSequencesReader msr =
            new MockSequencesReader(SequenceType.DNA) {
              @Override
              public PrereadType getPrereadType() {
                return PrereadType.UNKNOWN;
              }

              @Override
              public boolean hasQualityData() {
                return true;
              }

              @Override
              public int read(long sequenceIndex, byte[] dataOut) {
                dataOut[0] = 1;
                if (sequenceIndex == 3) {
                  dataOut[1] = 3;
                  dataOut[2] = 3;
                } else {
                  dataOut[1] = 3;
                  dataOut[2] = 2;
                }
                dataOut[3] = 4;
                return 4;
              }

              @Override
              public int readQuality(final long sequenceIndex, final byte[] dest) {
                dest[0] = dest[1] = dest[2] = dest[3] = '<' - 33;
                return 4;
              }
            };

        final SingleEndSamResultsFilter filter =
            new SingleEndSamResultsFilter(blocker, freqBlocker, listener, 0, msr, null, false);
        assertEquals("Alignment", filter.getName());
        filter.filterConcat(makeHeader(), out, null, null, mTemplateReader, false, in1);
        out.close();
        final String contents = FileHelper.gzFileToString(outFile);
        // System.out.println("contents=" + contents);
        assertTrue(
            TestUtils.sameLines(SAM_UNMATED_EXPECTED, TestUtils.stripSAMHeader(contents), false));

        // now check that the listener has been updated correctly.
        for (int read = 0; read < numReads; read++) {
          final int expect;
          switch (read) {
            case 1:
            case 3:
              expect = ReadStatusTracker.UNMATED_FIRST;
              break;
            default:
              expect = 0;
              break;
          }
          assertEquals("readId=" + read, expect, listener.getStatus(read));
        }
      } finally {
        if (out != null) {
          out.close();
        }
        assertTrue(FileHelper.deleteAll(dir));
      }
    } finally {
      Diagnostic.setLogStream();
    }
    final String logString = log.toString();
    // System.err.println(logString);
    TestUtils.containsAll(logString, "Alignment SAM filter outputs 2/5 records");
  }
 /**
  * @param calibrator the mapping calibration stats to use when computing coverage
  * @param defaultSequenceLengths map of sequence names to sequence length, used if not already set
  *     in the calibrator
  * @param readGroupToSampleId read group to sample id
  * @param restriction a region restriction, may be null
  */
 public CalibratedPerSequenceExpectedCoverage(
     Calibrator calibrator,
     Map<String, Integer> defaultSequenceLengths,
     Map<String, String> readGroupToSampleId,
     RegionRestriction restriction) {
   mSequenceSampleCoverages = new HashMap<>();
   mSumCoverages = new HashMap<>();
   mSamples = Collections.unmodifiableSet(new HashSet<>(readGroupToSampleId.values()));
   final Map<String, Integer> sequenceLengths =
       calibrator.hasLengths() ? calibrator.getSequenceLengths() : defaultSequenceLengths;
   if (calibrator.getCovariateIndex(CovariateEnum.SEQUENCE)
       == -1) { // No per sequence separation in calibration data, calculate per-genome coverage
                // level
     long length = 0;
     for (final Map.Entry<String, Integer> entry : sequenceLengths.entrySet()) {
       length += entry.getValue();
     }
     final Map<String, HashMap<String, CalibrationStats>> local = new HashMap<>();
     findIndividualGlobalCoverage(calibrator, readGroupToSampleId, local);
     double currentMax = 0;
     double currentSum = 0;
     for (Map.Entry<String, HashMap<String, CalibrationStats>> e : local.entrySet()) {
       final HashMap<String, CalibrationStats> map = e.getValue();
       if (map.containsKey(DUMMY_SEQ)) {
         final double currentCov =
             (length == 0) ? 0 : (double) map.get(DUMMY_SEQ).getTotalLength() / length;
         final String sampleName = e.getKey();
         Diagnostic.userLog(
             "Average coverage for sample "
                 + sampleName
                 + " is "
                 + Utils.realFormat(currentCov, 2));
         for (final Map.Entry<String, Integer> entry : sequenceLengths.entrySet()) {
           final String seqName = entry.getKey();
           Map<String, Double> samples = mSequenceSampleCoverages.get(seqName);
           if (samples == null) {
             samples = new HashMap<>();
             mSequenceSampleCoverages.put(seqName, samples);
           }
           samples.put(sampleName, currentCov);
         }
         currentSum += currentCov;
         if (currentCov > currentMax) {
           currentMax = currentCov;
         }
       }
     }
     Diagnostic.userLog("Average combined coverage is " + Utils.realFormat(currentSum, 2));
     for (final Map.Entry<String, Integer> entry : sequenceLengths.entrySet()) {
       final String seqName = entry.getKey();
       mSumCoverages.put(seqName, currentSum);
     }
   } else { // Per-sequence separation is in calibration data, calculate per-sequence coverage
            // level
     final Map<String, HashMap<String, CalibrationStats>> local = new HashMap<>();
     findIndividualPerSequenceCoverage(
         calibrator, sequenceLengths, readGroupToSampleId, local, restriction);
     for (final Map.Entry<String, Integer> entry : sequenceLengths.entrySet()) {
       final String seqName = entry.getKey();
       if (restriction != null && !seqName.equals(restriction.getSequenceName())) {
         continue;
       }
       final int seqLength = entry.getValue();
       double currentMax = 0;
       double currentSum = 0;
       for (Map.Entry<String, HashMap<String, CalibrationStats>> e : local.entrySet()) {
         final HashMap<String, CalibrationStats> map = e.getValue();
         if (map.containsKey(seqName)) {
           final double currentCov =
               (seqLength == 0) ? 0 : (double) map.get(seqName).getTotalLength() / seqLength;
           final String sampleName = e.getKey();
           Diagnostic.userLog(
               "Average coverage across sequence "
                   + seqName
                   + " for sample "
                   + sampleName
                   + " is "
                   + Utils.realFormat(currentCov, 2));
           Map<String, Double> samples = mSequenceSampleCoverages.get(seqName);
           if (samples == null) {
             samples = new HashMap<>();
             mSequenceSampleCoverages.put(seqName, samples);
           }
           samples.put(sampleName, currentCov);
           currentSum += currentCov;
           if (currentCov > currentMax) {
             currentMax = currentCov;
           }
         }
       }
       Diagnostic.userLog(
           "Average combined coverage for sequence "
               + seqName
               + " is "
               + Utils.realFormat(currentSum, 2));
       mSumCoverages.put(seqName, currentSum);
     }
   }
 }
 public void testValidator() throws IOException {
   Diagnostic.setLogStream();
   final MemoryPrintStream err = new MemoryPrintStream();
   final CliDiagnosticListener listener = new CliDiagnosticListener(err.printStream());
   Diagnostic.addListener(listener);
   final File tempDir = FileHelper.createTempDirectory();
   try {
     final CFlags flags =
         new CFlags("PhyloTest", TestUtils.getNullPrintStream(), err.printStream());
     SimilarityCli.initFlags(flags);
     checkErrorMessage(
         flags,
         new String[] {"-o", "blah", "-I", "ba", "-i", "humbug"},
         err,
         "Only set one of --input or --input-list-file");
     checkErrorMessage(
         flags,
         new String[] {"-o", "blah", "-i", "humbug"},
         err,
         "The specified SDF, \"humbug\", does not exist.");
     final File fakePaired = new File(tempDir, "fakePaired");
     assertTrue(fakePaired.mkdir());
     final File left = new File(fakePaired, "left");
     assertTrue(left.mkdir());
     assertTrue(new File(fakePaired, "right").mkdir());
     checkErrorMessage(
         flags,
         new String[] {"-o", "blah", "-i", fakePaired.getPath()},
         err,
         "The specified SDF, \"" + fakePaired.getPath() + "\", is a paired end SDF.");
     checkErrorMessage(
         flags, new String[] {"-o", "blah"}, err, "Must set one of --input or --input-list-file");
     checkErrorMessage(
         flags,
         new String[] {"-o", "blah", "-I", "ba"},
         err,
         "The specified list file, \"ba\", does not exist.");
     checkErrorMessage(
         flags,
         new String[] {"-o", "blah", "-I", fakePaired.getPath()},
         err,
         "The specified list file,",
         "\"" + fakePaired.getPath() + "\",",
         "directory.");
     final File fakeList = new File(tempDir, "fakeList.txt");
     assertTrue(fakeList.createNewFile());
     checkErrorMessage(
         flags,
         new String[] {"-o", fakePaired.getPath(), "-I", fakeList.getPath()},
         err,
         "The directory",
         "\"" + fakePaired.getPath() + "\"",
         "already exists.");
     checkErrorMessage(
         flags,
         new String[] {"-o", "blah", "-I", fakeList.getPath(), "-w", "-1"},
         err,
         "The specified flag \"--word\" has invalid value \"-1\". It should be greater than or equal to \"1\".");
     checkErrorMessage(
         flags,
         new String[] {"-o", "blah", "-I", fakeList.getPath(), "-w", "0"},
         err,
         "The specified flag \"--word\" has invalid value \"0\". It should be greater than or equal to \"1\".");
     checkErrorMessage(
         flags,
         new String[] {"-o", "blah", "-I", fakeList.getPath(), "-w", "33"},
         err,
         "The specified flag \"--word\" has invalid value \"33\". It should be less than or equal to \"32\".");
     checkErrorMessage(
         flags,
         new String[] {"-o", "blah", "-I", fakeList.getPath(), "--max-reads", "0"},
         err,
         "The --max-reads must be greater than 0");
     checkErrorMessage(
         flags,
         new String[] {"-o", "blah", "-I", fakeList.getPath(), "-w", "20", "-s", "20"},
         err);
     checkErrorMessage(
         flags,
         new String[] {"-o", "blah", "-i", left.getPath(), "--max-reads", "1"},
         err,
         "Only set --max-reads when using --input-list-file");
     checkErrorMessage(flags, new String[] {"-o", "blah", "-i", left.getPath()}, err);
   } finally {
     Diagnostic.removeListener(listener);
     err.close();
     assertTrue(FileHelper.deleteAll(tempDir));
   }
 }