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Updates to ReduceReads 

* Added optional parameter to not hard clip on the interval border
   * Made not clipping the default behavior (hence integration tests changed)
   * Updated integration tests.
This commit is contained in:
Mauricio Carneiro 2012-07-09 13:46:31 -04:00
parent dd0c47ab7e
commit 6c17c50fa2
2 changed files with 21 additions and 8 deletions
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17
protected/java/src/org/broadinstitute/sting/gatk/walkers/compression/reducereads/ReduceReadsWalker.java
View File

@ -154,6 +154,13 @@ public class ReduceReadsWalker extends ReadWalker<LinkedList<GATKSAMRecord>, Red
@Argument(fullName = "dont_compress_read_names", shortName = "nocmp_names", doc = "", required = false)
protected boolean DONT_COMPRESS_READ_NAMES = false;
/**
* Optionally hard clip all incoming reads to the desired intervals. The hard clips will happen exactly at the interval
* border.
*/
@Argument(fullName = "hard_clip_to_interval", shortName = "clip_int", doc = "", required = false)
protected boolean HARD_CLIP_TO_INTERVAL = false;
/**
* Minimum proportion of mismatches in a site to trigger a variant region. Anything below this will be
* considered consensus.
@ -260,8 +267,14 @@ public class ReduceReadsWalker extends ReadWalker<LinkedList<GATKSAMRecord>, Red
read = ReadClipper.hardClipAdaptorSequence(read); // Strip away adaptor sequences, if any.
if (!DONT_CLIP_LOW_QUAL_TAILS)
read = ReadClipper.hardClipLowQualEnds(read, minTailQuality); // Clip low quality tails
if (!isWholeGenome())
mappedReads = hardClipReadToInterval(read); // Hard clip the remainder of the read to the desired interval
if (!isWholeGenome()) {
if (HARD_CLIP_TO_INTERVAL)
mappedReads = hardClipReadToInterval(read); // Hard clip the remainder of the read to the desired interval
else {
mappedReads = new LinkedList<GATKSAMRecord>();
mappedReads.add(read);
}
}
else {
mappedReads = new LinkedList<GATKSAMRecord>();
if (!read.isEmpty())

12
protected/java/test/org/broadinstitute/sting/gatk/walkers/compression/reducereads/ReduceReadsIntegrationTest.java
View File

@ -21,28 +21,28 @@ public class ReduceReadsIntegrationTest extends WalkerTest {
@Test(enabled = true)
public void testDefaultCompression() {
RRTest("testDefaultCompression ", L, "4c92d59d4a5292af1f968dc922c2c63e");
RRTest("testDefaultCompression ", L, "887d05e3bdbe831a2584305088806a39");
}
@Test(enabled = true)
public void testMultipleIntervals() {
String intervals = "-L 20:10,100,000-10,100,500 -L 20:10,200,000-10,200,500 -L 20:10,300,000-10,300,500 -L 20:10,400,000-10,500,000 -L 20:10,500,050-10,500,060 -L 20:10,600,000-10,600,015 -L 20:10,700,000-10,700,110";
RRTest("testMultipleIntervals ", intervals, "97d5c3fda5551741676793ba325ec7ed");
RRTest("testMultipleIntervals ", intervals, "04208b8e2c2e65bcb9d0eb038702b006");
}
@Test(enabled = true)
public void testHighCompression() {
RRTest("testHighCompression ", " -cs 10 -minvar 0.3 -mindel 0.3 " + L, "e6bc1cd0e9de961cf0fb1789bf6ab108");
RRTest("testHighCompression ", " -cs 10 -minvar 0.3 -mindel 0.3 " + L, "3a607bc3ebaf84e9dc44e005c5f8a047");
}
@Test(enabled = true)
public void testLowCompression() {
RRTest("testLowCompression ", " -cs 30 -minvar 0.01 -mindel 0.01 -minmap 5 -minqual 5 " + L, "f33ec7cd0b98eebd73d1025ca656cd7e");
RRTest("testLowCompression ", " -cs 30 -minvar 0.01 -mindel 0.01 -minmap 5 -minqual 5 " + L, "afd39459c841b68a442abdd5ef5f8f27");
}
@Test(enabled = true)
public void testIndelCompression() {
RRTest("testIndelCompression ", " -cs 50 -L 20:10,100,500-10,100,600 ", "e6e2bc889e4f342a7fedc5d38b391d20");
RRTest("testIndelCompression ", " -cs 50 -L 20:10,100,500-10,100,600 ", "f7b9fa44c10bc4b2247813d2b8dc1973");
}
@Test(enabled = true)
@ -62,7 +62,7 @@ public class ReduceReadsIntegrationTest extends WalkerTest {
@Test(enabled = true)
public void testAddingReadAfterTailingTheStash() {
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("022931f032a4122cfe41e58e74d0aede")));
executeTest("testAddingReadAfterTailingTheStash", new WalkerTestSpec(base, Arrays.asList("886b43e1f26ff18425814dc7563931c6")));
}
}