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Adding a synthetic read for filtered data 

* Generalized the concept of a synthetic read to cread both running consensus and a synthetic reads of filtered data.
* Synthetic reads can now have deletions (but not insertions)
* New reduced read tag for filtered data synthetic reads *(RF)*
* Sliding window header now keeps information of consensus and filtered data
* Synthetic reads are created simultaneously, new functionality is controlled internally by addToSyntheticReads
This commit is contained in:
Mauricio Carneiro 2011-11-09 20:09:12 -05:00
parent 3afbd0e526
commit d00b2c6599
2 changed files with 5 additions and 3 deletions
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6
public/java/src/org/broadinstitute/sting/utils/sam/GATKSAMRecord.java
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@ -46,7 +46,9 @@ import java.util.Map;
*
*/
public class GATKSAMRecord extends BAMRecord {
public static final String REDUCED_READ_QUALITY_TAG = "RR";
public static final String REDUCED_READ_CONSENSUS_TAG = "RR";
public static final String REDUCED_READ_FILTERED_TAG = "RF";
// the SAMRecord data we're caching
private String mReadString = null;
private GATKSAMReadGroupRecord mReadGroup = null;
@ -173,7 +175,7 @@ public class GATKSAMRecord extends BAMRecord {
public byte[] getReducedReadCounts() {
if ( ! retrievedReduceReadCounts ) {
reducedReadCounts = getByteArrayAttribute(REDUCED_READ_QUALITY_TAG);
reducedReadCounts = getByteArrayAttribute(REDUCED_READ_CONSENSUS_TAG);
retrievedReduceReadCounts = true;
}

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.setReadBases(BASES.getBytes());
reducedRead.setBaseQualityString(QUALS);
reducedRead.setAttribute(GATKSAMRecord.REDUCED_READ_QUALITY_TAG, REDUCED_READ_COUNTS);
reducedRead.setAttribute(GATKSAMRecord.REDUCED_READ_CONSENSUS_TAG, REDUCED_READ_COUNTS);
}
private void testReadBasesAndQuals(GATKSAMRecord read, int expectedStart, int expectedStop) {