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Fixing merge conflict

This commit is contained in:
Eric Banks 2011-11-02 12:50:32 -04:00
parent 54331b44e9 53c9f49050
commit 4501dce58d
5 changed files with 750 additions and 762 deletions
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4
public/java/src/org/broadinstitute/sting/utils/MathUtils.java
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@ -408,12 +408,12 @@ public class MathUtils {
return Math.sqrt(rms); return Math.sqrt(rms);
} }
public static double rms(Collection<Double> l) { public static double rms(Collection<Integer> l) {
if (l.size() == 0) if (l.size() == 0)
return 0.0; return 0.0;
double rms = 0.0; double rms = 0.0;
for (Double i : l) for (int i : l)
rms += i*i; rms += i*i;
rms /= l.size(); rms /= l.size();
return Math.sqrt(rms); return Math.sqrt(rms);

1501
public/java/src/org/broadinstitute/sting/utils/sam/AlignmentUtils.java
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File diff suppressed because it is too large Load Diff

3
public/java/src/org/broadinstitute/sting/utils/sam/GATKSAMRecord.java
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@ -43,6 +43,7 @@ import java.util.Map;
* *
*/ */
public class GATKSAMRecord extends BAMRecord { public class GATKSAMRecord extends BAMRecord {
public static final String REDUCED_READ_QUALITY_TAG = "RR";
// the SAMRecord data we're caching // the SAMRecord data we're caching
private String mReadString = null; private String mReadString = null;
private GATKSAMReadGroupRecord mReadGroup = null; private GATKSAMReadGroupRecord mReadGroup = null;
@ -151,7 +152,7 @@ public class GATKSAMRecord extends BAMRecord {
public byte[] getReducedReadCounts() { public byte[] getReducedReadCounts() {
if ( ! retrievedReduceReadCounts ) { if ( ! retrievedReduceReadCounts ) {
reducedReadCounts = getByteArrayAttribute(ReadUtils.REDUCED_READ_QUALITY_TAG); reducedReadCounts = getByteArrayAttribute(REDUCED_READ_QUALITY_TAG);
retrievedReduceReadCounts = true; retrievedReduceReadCounts = true;
} }

2
public/java/src/org/broadinstitute/sting/utils/sam/ReadUtils.java
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@ -51,8 +51,6 @@ public class ReadUtils {
// //
// ---------------------------------------------------------------------------------------------------- // ----------------------------------------------------------------------------------------------------
public static final String REDUCED_READ_QUALITY_TAG = "RQ";
// ---------------------------------------------------------------------------------------------------- // ----------------------------------------------------------------------------------------------------
// //
// General utilities // General utilities

2
public/java/test/org/broadinstitute/sting/utils/ReadUtilsUnitTest.java
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@ -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_COUNTS); reducedRead.setAttribute(GATKSAMRecord.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) {