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Refactored reduced read utilities 

-- UnitTests for key functions on reduced reads
-- PileupElement calls static functions in ReadUtils
-- Simple routine that takes a reduced read and fills in its quals with its reduced qual
This commit is contained in:
Mark DePristo 2011-09-26 12:58:31 -04:00
parent b76dbc72f0
commit 4f09453470
3 changed files with 82 additions and 9 deletions
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9
public/java/src/org/broadinstitute/sting/utils/pileup/PileupElement.java
View File

@ -81,20 +81,17 @@ public class PileupElement {
//
// --------------------------------------------------------------------------
private Integer getReducedReadQualityTagValue() {
return getRead().getIntegerAttribute(ReadUtils.REDUCED_READ_QUALITY_TAG);
}
public boolean isReducedRead() {
return getReducedReadQualityTagValue() != null;
return ReadUtils.isReducedRead(getRead());
}
public int getReducedCount() {
if ( ! isReducedRead() ) throw new IllegalArgumentException("Cannot get reduced count for non-reduced read " + getRead().getReadName());
return (int)getQual();
}
public byte getReducedQual() {
return (byte)(int)getReducedReadQualityTagValue();
return (byte)(int)ReadUtils.getReducedReadQualityTagValue(getRead());
}
}

37
public/java/src/org/broadinstitute/sting/utils/sam/ReadUtils.java
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@ -43,10 +43,43 @@ import java.util.*;
* @version 0.1
*/
public class ReadUtils {
public static final String REDUCED_READ_QUALITY_TAG = "RQ";
private ReadUtils() { }
// ----------------------------------------------------------------------------------------------------
//
// Reduced read utilities
//
// ----------------------------------------------------------------------------------------------------
public static final String REDUCED_READ_QUALITY_TAG = "RQ";
public final static Integer getReducedReadQualityTagValue(final SAMRecord read) {
return read.getIntegerAttribute(ReadUtils.REDUCED_READ_QUALITY_TAG);
}
public final static boolean isReducedRead(final SAMRecord read) {
return getReducedReadQualityTagValue(read) != null;
}
public final static SAMRecord reducedReadWithReducedQuals(final SAMRecord read) {
if ( ! isReducedRead(read) ) throw new IllegalArgumentException("read must be a reduced read");
try {
SAMRecord newRead = (SAMRecord)read.clone();
byte reducedQual = (byte)(int)getReducedReadQualityTagValue(read);
byte[] newQuals = new byte[read.getBaseQualities().length];
Arrays.fill(newQuals, reducedQual);
newRead.setBaseQualities(newQuals);
return newRead;
} catch ( CloneNotSupportedException e ) {
throw new ReviewedStingException("SAMRecord no longer supports clone", e);
}
}
// ----------------------------------------------------------------------------------------------------
//
// General utilities
//
// ----------------------------------------------------------------------------------------------------
public static SAMFileHeader copySAMFileHeader(SAMFileHeader toCopy) {
SAMFileHeader copy = new SAMFileHeader();

45
public/java/test/org/broadinstitute/sting/utils/ReadUtilsUnitTest.java
View File

@ -3,6 +3,7 @@ package org.broadinstitute.sting.utils;
import net.sf.samtools.SAMFileHeader;
import net.sf.samtools.SAMRecord;
import org.broadinstitute.sting.BaseTest;
import org.broadinstitute.sting.utils.pileup.PileupElement;
import org.broadinstitute.sting.utils.sam.ArtificialSAMUtils;
import org.broadinstitute.sting.utils.sam.ReadUtils;
import org.testng.Assert;
@ -12,9 +13,10 @@ import org.testng.annotations.Test;
public class ReadUtilsUnitTest extends BaseTest {
SAMRecord read;
SAMRecord read, reducedRead;
final static String BASES = "ACTG";
final static String QUALS = "!+5?";
final private static int REDUCED_READ_QUAL = 20;
@BeforeTest
public void init() {
@ -23,6 +25,11 @@ public class ReadUtilsUnitTest extends BaseTest {
read.setReadUnmappedFlag(true);
read.setReadBases(new String(BASES).getBytes());
read.setBaseQualityString(new String(QUALS));
reducedRead = ArtificialSAMUtils.createArtificialRead(header, "reducedRead", 0, 1, BASES.length());
reducedRead.setReadBases(BASES.getBytes());
reducedRead.setBaseQualityString(QUALS);
reducedRead.setAttribute(ReadUtils.REDUCED_READ_QUALITY_TAG, REDUCED_READ_QUAL);
}
private void testReadBasesAndQuals(SAMRecord read, int expectedStart, int expectedStop) {
@ -38,4 +45,40 @@ public class ReadUtilsUnitTest extends BaseTest {
@Test public void testClip2Front() { testReadBasesAndQuals(read, 2, 4); }
@Test public void testClip1Back() { testReadBasesAndQuals(read, 0, 3); }
@Test public void testClip2Back() { testReadBasesAndQuals(read, 0, 2); }
@Test
public void testReducedReads() {
Assert.assertFalse(ReadUtils.isReducedRead(read), "isReducedRead is false for 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.assertEquals((int) ReadUtils.getReducedReadQualityTagValue(reducedRead), REDUCED_READ_QUAL, "Reduced read tag is set to expected value");
}
@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
public void testReducedReadPileupElement() {
PileupElement readp = new PileupElement(read,0);
PileupElement reducedreadp = new PileupElement(reducedRead,0);
Assert.assertFalse(readp.isReducedRead());
Assert.assertTrue(reducedreadp.isReducedRead());
Assert.assertEquals(reducedreadp.getReducedCount(), 0);
Assert.assertEquals(reducedreadp.getReducedQual(), REDUCED_READ_QUAL);
}
}