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Merge branch 'master' of ssh://gsa2.broadinstitute.org/humgen/gsa-scr1/gsa-engineering/git/unstable

This commit is contained in:
Ryan Poplin 2012-08-09 16:31:06 -04:00
parent f4c72a26d5 abb168e1ba
commit 9887bc4410
5 changed files with 29 additions and 4 deletions
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11
protected/java/src/org/broadinstitute/sting/gatk/walkers/compression/reducereads/ReduceReads.java
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@ -251,7 +251,7 @@ public class ReduceReads extends ReadWalker<LinkedList<GATKSAMRecord>, ReduceRea
LinkedList<GATKSAMRecord> mappedReads;
totalReads++;
if (!debugRead.isEmpty() && read.getReadName().contains(debugRead))
System.out.println("Found debug read!");
System.out.println("Found debug read!");
if (debugLevel == 1)
System.out.printf("\nOriginal: %s %s %d %d\n", read, read.getCigar(), read.getAlignmentStart(), read.getAlignmentEnd());
@ -260,7 +260,14 @@ public class ReduceReads extends ReadWalker<LinkedList<GATKSAMRecord>, ReduceRea
// attribute hash so we can determine later if we need to write down the alignment shift to the reduced BAM file
read.setTemporaryAttribute(GATKSAMRecord.REDUCED_READ_ORIGINAL_ALIGNMENT_START_SHIFT, read.getAlignmentStart());
read.setTemporaryAttribute(GATKSAMRecord.REDUCED_READ_ORIGINAL_ALIGNMENT_END_SHIFT, read.getAlignmentEnd());
// Check if the read goes beyond the boundaries of the chromosome, and hard clip those boundaries.
int chromosomeLength = ref.getGenomeLocParser().getContigInfo(read.getReferenceName()).getSequenceLength();
if (read.getSoftStart() < 0)
read = ReadClipper.hardClipByReadCoordinates(read, 0, -read.getSoftStart() - 1);
if (read.getSoftEnd() > chromosomeLength)
read = ReadClipper.hardClipByReadCoordinates(read, chromosomeLength - read.getSoftStart() + 1, read.getReadLength() - 1);
if (!DONT_SIMPLIFY_READS)
read.simplify(); // Clear all unnecessary attributes
if (!DONT_CLIP_ADAPTOR_SEQUENCES)

5
protected/java/src/org/broadinstitute/sting/gatk/walkers/compression/reducereads/SlidingWindow.java
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@ -536,6 +536,10 @@ public class SlidingWindow {
* @return a list of reads selected by the downsampler to cover the window to at least the desired coverage
*/
protected List<GATKSAMRecord> downsampleVariantRegion(final List<GATKSAMRecord> allReads) {
int nReads = allReads.size();
if (nReads == 0)
return allReads;
double fraction = 100 / allReads.size();
if (fraction >= 1)
return allReads;
@ -545,6 +549,7 @@ public class SlidingWindow {
return downsampler.consumeDownsampledItems();
}
/**
* Properly closes a Sliding Window, finalizing all consensus and variant
* regions that still exist regardless of being able to fulfill the

2
protected/java/src/org/broadinstitute/sting/gatk/walkers/compression/reducereads/SyntheticRead.java
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@ -102,7 +102,7 @@ public class SyntheticRead {
* @param base the base to add
* @param count number of reads with this base
*/
@Requires("count < Byte.MAX_VALUE")
@Requires("count <= Byte.MAX_VALUE")
public void add(BaseIndex base, byte count, byte qual, byte insQual, byte delQual, double mappingQuality) {
counts.add(count);
bases.add(base);

13
protected/java/test/org/broadinstitute/sting/gatk/walkers/compression/reducereads/ReduceReadsIntegrationTest.java
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@ -11,6 +11,8 @@ public class ReduceReadsIntegrationTest extends WalkerTest {
final String DELETION_BAM = validationDataLocation + "filtered_deletion_for_reduce_reads.bam";
final String STASH_BAM = validationDataLocation + "ReduceReadsStashBug.bam";
final String STASH_L = " -L 14:73718184-73718284 -L 14:73718294-73718330 -L 14:73718360-73718556";
final String DIVIDEBYZERO_BAM = validationDataLocation + "ReduceReadsDivideByZeroBug.bam";
final String DIVIDEBYZERO_L = " -L " + validationDataLocation + "ReduceReadsDivideByZeroBug.intervals";
final String L = " -L 20:10,100,000-10,120,000 ";
private void RRTest(String testName, String args, String md5) {
@ -64,5 +66,16 @@ public class ReduceReadsIntegrationTest extends WalkerTest {
String base = String.format("-T ReduceReads %s -npt -R %s -I %s", STASH_L, REF, STASH_BAM) + " -o %s ";
executeTest("testAddingReadAfterTailingTheStash", new WalkerTestSpec(base, Arrays.asList("886b43e1f26ff18425814dc7563931c6")));
}
/**
* Divide by zero bug reported by GdA and users in the forum. Happens when the downsampler goes over a region where all reads get
* filtered out.
*/
@Test(enabled = true)
public void testDivideByZero() {
String base = String.format("-T ReduceReads %s -npt -R %s -I %s", DIVIDEBYZERO_L, REF, DIVIDEBYZERO_BAM) + " -o %s ";
executeTest("testDivideByZero", new WalkerTestSpec(base, Arrays.asList("137505c3efd1e9f8d9209dbdf8419ff9")));
}
}

2
public/java/src/org/broadinstitute/sting/gatk/walkers/diagnostics/targets/FindCoveredIntervals.java
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@ -78,7 +78,7 @@ public class FindCoveredIntervals extends ActiveRegionWalker<GenomeLoc, Long> {
public Long reduce(final GenomeLoc value, Long reduce) {
if (value != null) {
out.println(value.toString());
return reduce++;
return ++reduce;
} else
return reduce;
}