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Merge branch 'master' into ped

This commit is contained in:
Mark DePristo 2011-09-29 17:18:51 -04:00
parent 9458f01409 98ecaf8aa0
commit 1765fbeb6b
4 changed files with 32 additions and 39 deletions
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4
public/java/src/org/broadinstitute/sting/gatk/walkers/indels/PairHMMIndelErrorModel.java
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@ -415,10 +415,6 @@ public class PairHMMIndelErrorModel {
if (read == null) if (read == null)
continue; continue;
if ( isReduced ) {
read = ReadUtils.reducedReadWithReducedQuals(read);
}
if(ReadUtils.is454Read(read)) { if(ReadUtils.is454Read(read)) {
continue; continue;
} }

6
public/java/src/org/broadinstitute/sting/utils/pileup/PileupElement.java
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@ -87,11 +87,11 @@ public class PileupElement {
public int getReducedCount() { public int getReducedCount() {
if ( ! isReducedRead() ) throw new IllegalArgumentException("Cannot get reduced count for non-reduced read " + getRead().getReadName()); if ( ! isReducedRead() ) throw new IllegalArgumentException("Cannot get reduced count for non-reduced read " + getRead().getReadName());
return (int)getQual(); return ReadUtils.getReducedCount(getRead(), offset);
} }
public byte getReducedQual() { public byte getReducedQual() {
return (byte)(int)ReadUtils.getReducedReadQualityTagValue(getRead()); if ( ! isReducedRead() ) throw new IllegalArgumentException("Cannot get reduced qual for non-reduced read " + getRead().getReadName());
return ReadUtils.getReducedQual(getRead(), offset);
} }
} }

33
public/java/src/org/broadinstitute/sting/utils/sam/ReadUtils.java
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@ -54,26 +54,35 @@ public class ReadUtils {
public static final String REDUCED_READ_QUALITY_TAG = "RQ"; public static final String REDUCED_READ_QUALITY_TAG = "RQ";
public static final String REDUCED_READ_CONSENSUS_COUNTS_TAG = "CC"; public static final String REDUCED_READ_CONSENSUS_COUNTS_TAG = "CC";
public final static Integer getReducedReadQualityTagValue(final SAMRecord read) { public final static byte[] getReducedReadQualityTagValue(final SAMRecord read) {
return read.getIntegerAttribute(ReadUtils.REDUCED_READ_QUALITY_TAG); return read.getByteArrayAttribute(ReadUtils.REDUCED_READ_QUALITY_TAG);
} }
public final static boolean isReducedRead(final SAMRecord read) { public final static boolean isReducedRead(final SAMRecord read) {
return getReducedReadQualityTagValue(read) != null; return getReducedReadQualityTagValue(read) != null;
} }
public final static byte getReducedQual(final SAMRecord read, final int i) {
return read.getBaseQualities()[i];
}
public final static byte getReducedCount(final SAMRecord read, final int i) {
return getReducedReadQualityTagValue(read)[i];
}
public final static SAMRecord reducedReadWithReducedQuals(final SAMRecord read) { public final static SAMRecord reducedReadWithReducedQuals(final SAMRecord read) {
if ( ! isReducedRead(read) ) throw new IllegalArgumentException("read must be a reduced read"); if ( ! isReducedRead(read) ) throw new IllegalArgumentException("read must be a reduced read");
try { return read;
SAMRecord newRead = (SAMRecord)read.clone(); // try {
byte reducedQual = (byte)(int)getReducedReadQualityTagValue(read); // SAMRecord newRead = (SAMRecord)read.clone();
byte[] newQuals = new byte[read.getBaseQualities().length]; // byte reducedQual = (byte)(int)getReducedReadQualityTagValue(read);
Arrays.fill(newQuals, reducedQual); // byte[] newQuals = new byte[read.getBaseQualities().length];
newRead.setBaseQualities(newQuals); // Arrays.fill(newQuals, reducedQual);
return newRead; // newRead.setBaseQualities(newQuals);
} catch ( CloneNotSupportedException e ) { // return newRead;
throw new ReviewedStingException("SAMRecord no longer supports clone", e); // } catch ( CloneNotSupportedException e ) {
} // throw new ReviewedStingException("SAMRecord no longer supports clone", e);
// }
} }
// ---------------------------------------------------------------------------------------------------- // ----------------------------------------------------------------------------------------------------

26
public/java/test/org/broadinstitute/sting/utils/ReadUtilsUnitTest.java
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@ -16,7 +16,7 @@ public class ReadUtilsUnitTest extends BaseTest {
SAMRecord read, reducedRead; SAMRecord read, reducedRead;
final static String BASES = "ACTG"; final static String BASES = "ACTG";
final static String QUALS = "!+5?"; final static String QUALS = "!+5?";
final private static int REDUCED_READ_QUAL = 20; final private static byte[] REDUCED_READ_COUNTS = new byte[]{10, 20, 30, 40};
@BeforeTest @BeforeTest
public void init() { public void init() {
@ -29,7 +29,7 @@ public class ReadUtilsUnitTest extends BaseTest {
reducedRead = ArtificialSAMUtils.createArtificialRead(header, "reducedRead", 0, 1, BASES.length()); reducedRead = ArtificialSAMUtils.createArtificialRead(header, "reducedRead", 0, 1, BASES.length());
reducedRead.setReadBases(BASES.getBytes()); reducedRead.setReadBases(BASES.getBytes());
reducedRead.setBaseQualityString(QUALS); reducedRead.setBaseQualityString(QUALS);
reducedRead.setAttribute(ReadUtils.REDUCED_READ_QUALITY_TAG, REDUCED_READ_QUAL); reducedRead.setAttribute(ReadUtils.REDUCED_READ_QUALITY_TAG, REDUCED_READ_COUNTS);
} }
private void testReadBasesAndQuals(SAMRecord read, int expectedStart, int expectedStop) { private void testReadBasesAndQuals(SAMRecord read, int expectedStart, int expectedStop) {
@ -52,21 +52,10 @@ public class ReadUtilsUnitTest extends BaseTest {
Assert.assertEquals(ReadUtils.getReducedReadQualityTagValue(read), null, "No reduced read tag in normal read"); Assert.assertEquals(ReadUtils.getReducedReadQualityTagValue(read), null, "No reduced read tag in normal read");
Assert.assertTrue(ReadUtils.isReducedRead(reducedRead), "isReducedRead is true for reduced read"); Assert.assertTrue(ReadUtils.isReducedRead(reducedRead), "isReducedRead is true for reduced read");
Assert.assertEquals((int) ReadUtils.getReducedReadQualityTagValue(reducedRead), REDUCED_READ_QUAL, "Reduced read tag is set to expected value"); for ( int i = 0; i < reducedRead.getReadLength(); i++) {
Assert.assertEquals(ReadUtils.getReducedQual(reducedRead, i), read.getBaseQualities()[i], "Reduced read quality not set to the expected value at " + i);
Assert.assertEquals(ReadUtils.getReducedCount(reducedRead, i), REDUCED_READ_COUNTS[i], "Reduced read count not set to the expected value at " + i);
} }
@Test
public void testreducedReadWithReducedQualsWithReducedRead() {
SAMRecord replacedRead = ReadUtils.reducedReadWithReducedQuals(reducedRead);
Assert.assertEquals(replacedRead.getReadBases(), reducedRead.getReadBases());
Assert.assertEquals(replacedRead.getBaseQualities().length, reducedRead.getBaseQualities().length);
for ( int i = 0; i < replacedRead.getBaseQualities().length; i++)
Assert.assertEquals(replacedRead.getBaseQualities()[i], REDUCED_READ_QUAL);
}
@Test(expectedExceptions = IllegalArgumentException.class)
public void testreducedReadWithReducedQualsWithNormalRead() {
ReadUtils.reducedReadWithReducedQuals(read);
} }
@Test @Test
@ -77,8 +66,7 @@ public class ReadUtilsUnitTest extends BaseTest {
Assert.assertFalse(readp.isReducedRead()); Assert.assertFalse(readp.isReducedRead());
Assert.assertTrue(reducedreadp.isReducedRead()); Assert.assertTrue(reducedreadp.isReducedRead());
Assert.assertEquals(reducedreadp.getReducedCount(), 0); Assert.assertEquals(reducedreadp.getReducedCount(), REDUCED_READ_COUNTS[0]);
Assert.assertEquals(reducedreadp.getReducedQual(), REDUCED_READ_QUAL); Assert.assertEquals(reducedreadp.getReducedQual(), readp.getQual());
} }
} }