Esempio n. 1
0
  @Test
  public void testBamIntegers() throws IOException {
    final List<String> errorMessages = new ArrayList<String>();
    final SamReader bamReader = SamReaderFactory.makeDefault().open(BAM_INPUT);
    final File bamOutput = File.createTempFile("test", ".bam");
    final File samOutput = File.createTempFile("test", ".sam");
    final SAMFileWriter samWriter =
        new SAMFileWriterFactory().makeWriter(bamReader.getFileHeader(), true, samOutput, null);
    final SAMFileWriter bamWriter =
        new SAMFileWriterFactory().makeWriter(bamReader.getFileHeader(), true, bamOutput, null);
    final SAMRecordIterator iterator = bamReader.iterator();
    while (iterator.hasNext()) {
      try {
        final SAMRecord rec = iterator.next();
        samWriter.addAlignment(rec);
        bamWriter.addAlignment(rec);
      } catch (final Throwable e) {
        System.out.println(e.getMessage());
        errorMessages.add(e.getMessage());
      }
    }

    CloserUtil.close(bamReader);
    samWriter.close();
    bamWriter.close();
    Assert.assertEquals(errorMessages.size(), 0);
    bamOutput.deleteOnExit();
    samOutput.deleteOnExit();
  }
Esempio n. 2
0
 private int countRecords(final SamReader reader) {
   int count = 0;
   try (final SAMRecordIterator iter = reader.iterator()) {
     while (iter.hasNext()) {
       iter.next();
       count++;
     }
   }
   return count;
 }
Esempio n. 3
0
 private int runQueryTest(
     final URL bamURL,
     final String sequence,
     final int startPos,
     final int endPos,
     final boolean contained) {
   verbose("Testing query " + sequence + ":" + startPos + "-" + endPos + " ...");
   final SamReader reader1 =
       SamReaderFactory.makeDefault()
           .disable(SamReaderFactory.Option.EAGERLY_DECODE)
           .open(SamInputResource.of(bamURL).index(BAM_INDEX_FILE));
   final SamReader reader2 =
       SamReaderFactory.makeDefault()
           .disable(SamReaderFactory.Option.EAGERLY_DECODE)
           .open(SamInputResource.of(bamURL).index(BAM_INDEX_FILE));
   final Iterator<SAMRecord> iter1 = reader1.query(sequence, startPos, endPos, contained);
   final Iterator<SAMRecord> iter2 = reader2.iterator();
   // Compare ordered iterators.
   // Confirm that iter1 is a subset of iter2 that properly filters.
   SAMRecord record1 = null;
   SAMRecord record2 = null;
   int count1 = 0;
   int count2 = 0;
   int beforeCount = 0;
   int afterCount = 0;
   while (true) {
     if (record1 == null && iter1.hasNext()) {
       record1 = iter1.next();
       count1++;
     }
     if (record2 == null && iter2.hasNext()) {
       record2 = iter2.next();
       count2++;
     }
     // System.out.println("Iteration:");
     // System.out.println(" Record1 = " + ((record1 == null) ? "null" : record1.format()));
     // System.out.println(" Record2 = " + ((record2 == null) ? "null" : record2.format()));
     if (record1 == null && record2 == null) {
       break;
     }
     if (record1 == null) {
       checkPassesFilter(false, record2, sequence, startPos, endPos, contained);
       record2 = null;
       afterCount++;
       continue;
     }
     assertNotNull(record2);
     final int ordering = compareCoordinates(record1, record2);
     if (ordering > 0) {
       checkPassesFilter(false, record2, sequence, startPos, endPos, contained);
       record2 = null;
       beforeCount++;
       continue;
     }
     assertTrue(ordering == 0);
     checkPassesFilter(true, record1, sequence, startPos, endPos, contained);
     checkPassesFilter(true, record2, sequence, startPos, endPos, contained);
     assertEquals(record1.getReadName(), record2.getReadName());
     assertEquals(record1.getReadString(), record2.getReadString());
     record1 = null;
     record2 = null;
   }
   CloserUtil.close(reader1);
   CloserUtil.close(reader2);
   verbose("Checked " + count1 + " records against " + count2 + " records.");
   verbose("Found " + (count2 - beforeCount - afterCount) + " records matching.");
   verbose("Found " + beforeCount + " records before.");
   verbose("Found " + afterCount + " records after.");
   return count1;
 }