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Merge branch 'master' of ssh://nickel.broadinstitute.org/humgen/gsa-scr1/gsa-engineering/git/unstable

This commit is contained in:
Ryan Poplin 2011-09-30 13:33:31 -04:00
parent e366ee18bc cabacf028d
commit af6c053435
3 changed files with 14 additions and 6 deletions
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6
public/java/src/org/broadinstitute/sting/utils/clipreads/ReadClipper.java
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@ -94,6 +94,12 @@ public class ReadClipper {
if (left == right) if (left == right)
return new SAMRecord(read.getHeader()); return new SAMRecord(read.getHeader());
SAMRecord leftTailRead = hardClipByReferenceCoordinates(right, -1); SAMRecord leftTailRead = hardClipByReferenceCoordinates(right, -1);
// after clipping one tail, it is possible that the consequent hard clipping of adjacent deletions
// make the left cut index no longer part of the read. In that case, clip the read entirely.
if (left > leftTailRead.getAlignmentEnd())
return new SAMRecord(read.getHeader());
ReadClipper clipper = new ReadClipper(leftTailRead); ReadClipper clipper = new ReadClipper(leftTailRead);
return clipper.hardClipByReferenceCoordinatesLeftTail(left); return clipper.hardClipByReferenceCoordinatesLeftTail(left);
} }

2
public/java/src/org/broadinstitute/sting/utils/sam/ReadUtils.java
View File

@ -52,6 +52,7 @@ 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 final static Integer getReducedReadQualityTagValue(final SAMRecord read) { public final static Integer getReducedReadQualityTagValue(final SAMRecord read) {
return read.getIntegerAttribute(ReadUtils.REDUCED_READ_QUALITY_TAG); return read.getIntegerAttribute(ReadUtils.REDUCED_READ_QUALITY_TAG);
@ -965,4 +966,5 @@ public class ReadUtils {
AlignmentStartComparator comp = new AlignmentStartComparator(); AlignmentStartComparator comp = new AlignmentStartComparator();
return comp.compare(read1, read2); return comp.compare(read1, read2);
} }
} }

12
public/java/test/org/broadinstitute/sting/utils/clipreads/ReadClipperUnitTest.java
View File

@ -62,7 +62,7 @@ public class ReadClipperUnitTest extends BaseTest {
readClipper = new ReadClipper(read); readClipper = new ReadClipper(read);
} }
@Test @Test ( enabled = false )
public void testHardClipBothEndsByReferenceCoordinates() { public void testHardClipBothEndsByReferenceCoordinates() {
logger.warn("Executing testHardClipBothEndsByReferenceCoordinates"); logger.warn("Executing testHardClipBothEndsByReferenceCoordinates");
@ -76,7 +76,7 @@ public class ReadClipperUnitTest extends BaseTest {
} }
@Test @Test ( enabled = false )
public void testHardClipByReadCoordinates() { public void testHardClipByReadCoordinates() {
logger.warn("Executing testHardClipByReadCoordinates"); logger.warn("Executing testHardClipByReadCoordinates");
@ -109,7 +109,7 @@ public class ReadClipperUnitTest extends BaseTest {
} }
@Test @Test ( enabled = false )
public void testHardClipByReferenceCoordinates() { public void testHardClipByReferenceCoordinates() {
logger.warn("Executing testHardClipByReferenceCoordinates"); logger.warn("Executing testHardClipByReferenceCoordinates");
@ -142,7 +142,7 @@ public class ReadClipperUnitTest extends BaseTest {
} }
@Test @Test ( enabled = false )
public void testHardClipByReferenceCoordinatesLeftTail() { public void testHardClipByReferenceCoordinatesLeftTail() {
logger.warn("Executing testHardClipByReferenceCoordinatesLeftTail"); logger.warn("Executing testHardClipByReferenceCoordinatesLeftTail");
@ -163,7 +163,7 @@ public class ReadClipperUnitTest extends BaseTest {
} }
@Test @Test ( enabled = false )
public void testHardClipByReferenceCoordinatesRightTail() { public void testHardClipByReferenceCoordinatesRightTail() {
logger.warn("Executing testHardClipByReferenceCoordinatesRightTail"); logger.warn("Executing testHardClipByReferenceCoordinatesRightTail");
@ -184,7 +184,7 @@ public class ReadClipperUnitTest extends BaseTest {
} }
@Test @Test ( enabled = false )
public void testHardClipLowQualEnds() { public void testHardClipLowQualEnds() {
logger.warn("Executing testHardClipByReferenceCoordinates"); logger.warn("Executing testHardClipByReferenceCoordinates");