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Reads are required to be sorted 

- Remove the extended_only case because it's outside intervals
This commit is contained in:
Joel Thibault 2012-11-28 11:09:12 -05:00
parent 198923b597
commit c76c808268
1 changed files with 15 additions and 27 deletions
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42
public/java/test/org/broadinstitute/sting/gatk/traversals/TraverseActiveRegionsTest.java
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@ -25,6 +25,7 @@ import org.broadinstitute.sting.utils.activeregion.ActiveRegion;
import org.broadinstitute.sting.utils.activeregion.ActivityProfileResult;
import org.broadinstitute.sting.utils.fasta.CachingIndexedFastaSequenceFile;
import org.broadinstitute.sting.utils.sam.ArtificialSAMUtils;
import org.broadinstitute.sting.utils.sam.ReadUtils;
import org.testng.Assert;
import org.testng.annotations.BeforeClass;
import org.testng.annotations.Test;
@ -100,7 +101,7 @@ public class TraverseActiveRegionsTest extends BaseTest {
private GenomeLocParser genomeLocParser;
private List<GenomeLoc> intervals;
private List<SAMRecord> reads;
private List<GATKSAMRecord> reads;
@BeforeClass
private void init() throws FileNotFoundException {
@ -117,16 +118,18 @@ public class TraverseActiveRegionsTest extends BaseTest {
intervals.add(genomeLocParser.createGenomeLoc("20", 10000, 10100));
intervals = IntervalUtils.sortAndMergeIntervals(genomeLocParser, intervals, IntervalMergingRule.OVERLAPPING_ONLY).toList();
reads = new ArrayList<SAMRecord>();
reads = new ArrayList<GATKSAMRecord>();
reads.add(buildSAMRecord("simple", "1", 100, 200));
reads.add(buildSAMRecord("overlap_equal", "1", 10, 20));
reads.add(buildSAMRecord("overlap_unequal", "1", 10, 21));
reads.add(buildSAMRecord("boundary_equal", "1", 1990, 2009));
reads.add(buildSAMRecord("boundary_unequal", "1", 1990, 2008));
reads.add(buildSAMRecord("extended_only", "1", 3000, 3100));
reads.add(buildSAMRecord("extended_and_np", "1", 990, 1990));
reads.add(buildSAMRecord("outside_intervals", "1", 5000, 6000));
reads.add(buildSAMRecord("simple20", "20", 10025, 10075));
// required by LocusIteratorByState, and I prefer to list them in test case order above
ReadUtils.sortReadsByCoordinate(reads);
}
@Test
@ -226,7 +229,6 @@ public class TraverseActiveRegionsTest extends BaseTest {
// overlap_unequal: Primary in 1:1-999
// boundary_equal: Non-Primary in 1:1000-1999, Primary in 1:2000-2999
// boundary_unequal: Primary in 1:1000-1999, Non-Primary in 1:2000-2999
// extended_only: Extended in 1:2000-2999
// extended_and_np: Non-Primary in 1:1-999, Primary in 1:1000-1999, Extended in 1:2000-2999
// outside_intervals: none
// simple20: Primary in 20:10000-10100
@ -241,7 +243,6 @@ public class TraverseActiveRegionsTest extends BaseTest {
getRead(region, "overlap_unequal");
verifyReadNotPlaced(region, "boundary_equal");
verifyReadNotPlaced(region, "boundary_unequal");
verifyReadNotPlaced(region, "extended_only");
verifyReadNotPlaced(region, "extended_and_np");
verifyReadNotPlaced(region, "outside_intervals");
verifyReadNotPlaced(region, "simple20");
@ -253,8 +254,7 @@ public class TraverseActiveRegionsTest extends BaseTest {
verifyReadNotPlaced(region, "overlap_unequal");
verifyReadNotPlaced(region, "boundary_equal");
getRead(region, "boundary_unequal");
verifyReadNotPlaced(region, "extended_only");
// TODO: fail getRead(region, "extended_and_np");
getRead(region, "extended_and_np");
verifyReadNotPlaced(region, "outside_intervals");
verifyReadNotPlaced(region, "simple20");
@ -265,7 +265,6 @@ public class TraverseActiveRegionsTest extends BaseTest {
verifyReadNotPlaced(region, "overlap_unequal");
getRead(region, "boundary_equal");
verifyReadNotPlaced(region, "boundary_unequal");
verifyReadNotPlaced(region, "extended_only");
verifyReadNotPlaced(region, "extended_and_np");
verifyReadNotPlaced(region, "outside_intervals");
verifyReadNotPlaced(region, "simple20");
@ -277,7 +276,6 @@ public class TraverseActiveRegionsTest extends BaseTest {
verifyReadNotPlaced(region, "overlap_unequal");
verifyReadNotPlaced(region, "boundary_equal");
verifyReadNotPlaced(region, "boundary_unequal");
verifyReadNotPlaced(region, "extended_only");
verifyReadNotPlaced(region, "extended_and_np");
verifyReadNotPlaced(region, "outside_intervals");
getRead(region, "simple20");
@ -300,7 +298,6 @@ public class TraverseActiveRegionsTest extends BaseTest {
// overlap_unequal: Primary in 1:1-999
// boundary_equal: Non-Primary in 1:1000-1999, Primary in 1:2000-2999
// boundary_unequal: Primary in 1:1000-1999, Non-Primary in 1:2000-2999
// extended_only: Extended in 1:2000-2999
// extended_and_np: Non-Primary in 1:1-999, Primary in 1:1000-1999, Extended in 1:2000-2999
// outside_intervals: none
// simple20: Primary in 20:10000-10100
@ -315,8 +312,7 @@ public class TraverseActiveRegionsTest extends BaseTest {
getRead(region, "overlap_unequal");
verifyReadNotPlaced(region, "boundary_equal");
verifyReadNotPlaced(region, "boundary_unequal");
verifyReadNotPlaced(region, "extended_only");
// TODO: fail getRead(region, "extended_and_np");
getRead(region, "extended_and_np");
verifyReadNotPlaced(region, "outside_intervals");
verifyReadNotPlaced(region, "simple20");
@ -327,8 +323,7 @@ public class TraverseActiveRegionsTest extends BaseTest {
verifyReadNotPlaced(region, "overlap_unequal");
getRead(region, "boundary_equal");
getRead(region, "boundary_unequal");
verifyReadNotPlaced(region, "extended_only");
// TODO: fail getRead(region, "extended_and_np");
getRead(region, "extended_and_np");
verifyReadNotPlaced(region, "outside_intervals");
verifyReadNotPlaced(region, "simple20");
@ -339,7 +334,6 @@ public class TraverseActiveRegionsTest extends BaseTest {
verifyReadNotPlaced(region, "overlap_unequal");
getRead(region, "boundary_equal");
getRead(region, "boundary_unequal");
verifyReadNotPlaced(region, "extended_only");
verifyReadNotPlaced(region, "extended_and_np");
verifyReadNotPlaced(region, "outside_intervals");
verifyReadNotPlaced(region, "simple20");
@ -351,7 +345,6 @@ public class TraverseActiveRegionsTest extends BaseTest {
verifyReadNotPlaced(region, "overlap_unequal");
verifyReadNotPlaced(region, "boundary_equal");
verifyReadNotPlaced(region, "boundary_unequal");
verifyReadNotPlaced(region, "extended_only");
verifyReadNotPlaced(region, "extended_and_np");
verifyReadNotPlaced(region, "outside_intervals");
getRead(region, "simple20");
@ -375,7 +368,6 @@ public class TraverseActiveRegionsTest extends BaseTest {
// overlap_unequal: Primary in 1:1-999
// boundary_equal: Non-Primary in 1:1000-1999, Primary in 1:2000-2999
// boundary_unequal: Primary in 1:1000-1999, Non-Primary in 1:2000-2999
// extended_only: Extended in 1:2000-2999
// extended_and_np: Non-Primary in 1:1-999, Primary in 1:1000-1999, Extended in 1:2000-2999
// outside_intervals: none
// simple20: Primary in 20:10000-10100
@ -390,8 +382,7 @@ public class TraverseActiveRegionsTest extends BaseTest {
getRead(region, "overlap_unequal");
verifyReadNotPlaced(region, "boundary_equal");
verifyReadNotPlaced(region, "boundary_unequal");
verifyReadNotPlaced(region, "extended_only");
// TODO: fail getRead(region, "extended_and_np");
getRead(region, "extended_and_np");
verifyReadNotPlaced(region, "outside_intervals");
verifyReadNotPlaced(region, "simple20");
@ -402,8 +393,7 @@ public class TraverseActiveRegionsTest extends BaseTest {
verifyReadNotPlaced(region, "overlap_unequal");
getRead(region, "boundary_equal");
getRead(region, "boundary_unequal");
verifyReadNotPlaced(region, "extended_only");
// TODO: fail getRead(region, "extended_and_np");
getRead(region, "extended_and_np");
verifyReadNotPlaced(region, "outside_intervals");
verifyReadNotPlaced(region, "simple20");
@ -414,8 +404,7 @@ public class TraverseActiveRegionsTest extends BaseTest {
verifyReadNotPlaced(region, "overlap_unequal");
getRead(region, "boundary_equal");
getRead(region, "boundary_unequal");
verifyReadNotPlaced(region, "extended_only");
verifyReadNotPlaced(region, "extended_and_np");
getRead(region, "extended_and_np");
verifyReadNotPlaced(region, "outside_intervals");
verifyReadNotPlaced(region, "simple20");
@ -426,8 +415,7 @@ public class TraverseActiveRegionsTest extends BaseTest {
verifyReadNotPlaced(region, "overlap_unequal");
verifyReadNotPlaced(region, "boundary_equal");
verifyReadNotPlaced(region, "boundary_unequal");
// TODO: fail getRead(region, "extended_only");
// TODO: fail getRead(region, "extended_and_np");
verifyReadNotPlaced(region, "extended_and_np");
verifyReadNotPlaced(region, "outside_intervals");
getRead(region, "simple20");
@ -438,7 +426,7 @@ public class TraverseActiveRegionsTest extends BaseTest {
for (SAMRecord read : region.getReads()) {
if (read.getReadName().equals(readName))
Assert.fail("Read " + readName + " found in active region " + region);
}
}
}
private SAMRecord getRead(ActiveRegion region, String readName) {
@ -520,7 +508,7 @@ public class TraverseActiveRegionsTest extends BaseTest {
engine.setGenomeLocParser(genomeLocParser);
t.initialize(engine);
StingSAMIterator iterator = ArtificialSAMUtils.createReadIterator(reads);
StingSAMIterator iterator = ArtificialSAMUtils.createReadIterator(new ArrayList<SAMRecord>(reads));
Shard shard = new MockLocusShard(genomeLocParser, intervals);
List<LocusShardDataProvider> providers = new ArrayList<LocusShardDataProvider>();