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Merge branch 'master' of github.com:broadinstitute/gsa-unstable

This commit is contained in:
Ryan Poplin 2012-12-07 15:35:17 -05:00
parent 9573648f85 3b0e3767bf
commit 3355216366
2 changed files with 80 additions and 9 deletions
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69
public/java/test/org/broadinstitute/sting/gatk/traversals/TraverseActiveRegionsTest.java
View File

@ -109,12 +109,16 @@ public class TraverseActiveRegionsTest extends BaseTest {
dictionary = reference.getSequenceDictionary();
genomeLocParser = new GenomeLocParser(dictionary);
// TODO: test shard boundaries
intervals = new ArrayList<GenomeLoc>();
intervals.add(genomeLocParser.createGenomeLoc("1", 10, 20));
intervals.add(genomeLocParser.createGenomeLoc("1", 1, 999));
intervals.add(genomeLocParser.createGenomeLoc("1", 1000, 1999));
intervals.add(genomeLocParser.createGenomeLoc("1", 2000, 2999));
intervals.add(genomeLocParser.createGenomeLoc("1", 10000, 20000));
intervals.add(genomeLocParser.createGenomeLoc("1", 249250600, 249250621));
intervals.add(genomeLocParser.createGenomeLoc("2", 1, 100));
intervals.add(genomeLocParser.createGenomeLoc("20", 10000, 10100));
intervals = IntervalUtils.sortAndMergeIntervals(genomeLocParser, intervals, IntervalMergingRule.OVERLAPPING_ONLY).toList();
@ -126,6 +130,7 @@ public class TraverseActiveRegionsTest extends BaseTest {
reads.add(buildSAMRecord("boundary_unequal", "1", 1990, 2008));
reads.add(buildSAMRecord("extended_and_np", "1", 990, 1990));
reads.add(buildSAMRecord("outside_intervals", "1", 5000, 6000));
reads.add(buildSAMRecord("end_of_chr1", "1", 249250600, 249250700));
reads.add(buildSAMRecord("simple20", "20", 10025, 10075));
// required by LocusIteratorByState, and I prefer to list them in test case order above
@ -139,8 +144,6 @@ public class TraverseActiveRegionsTest extends BaseTest {
List<GenomeLoc> activeIntervals = getIsActiveIntervals(walker, intervals);
// Contract: Every genome position in the analysis interval(s) is processed by the walker's isActive() call
verifyEqualIntervals(intervals, activeIntervals);
// TODO: more tests and edge cases
}
private List<GenomeLoc> getIsActiveIntervals(DummyActiveRegionWalker walker, List<GenomeLoc> intervals) {
@ -171,8 +174,6 @@ public class TraverseActiveRegionsTest extends BaseTest {
Collection<ActiveRegion> activeRegions = getActiveRegions(walker, intervals).values();
verifyActiveRegionCoverage(intervals, activeRegions);
// TODO: more tests and edge cases
}
private void verifyActiveRegionCoverage(List<GenomeLoc> intervals, Collection<ActiveRegion> activeRegions) {
@ -231,6 +232,7 @@ public class TraverseActiveRegionsTest extends BaseTest {
// boundary_unequal: Primary in 1:1000-1999, Non-Primary 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
// end_of_chr1: Primary in 1:249250600-249250621
// simple20: Primary in 20:10000-10100
Map<GenomeLoc, ActiveRegion> activeRegions = getActiveRegions(walker, intervals);
@ -245,6 +247,7 @@ public class TraverseActiveRegionsTest extends BaseTest {
verifyReadNotPlaced(region, "boundary_unequal");
verifyReadNotPlaced(region, "extended_and_np");
verifyReadNotPlaced(region, "outside_intervals");
verifyReadNotPlaced(region, "end_of_chr1");
verifyReadNotPlaced(region, "simple20");
region = activeRegions.get(genomeLocParser.createGenomeLoc("1", 1000, 1999));
@ -256,6 +259,7 @@ public class TraverseActiveRegionsTest extends BaseTest {
getRead(region, "boundary_unequal");
getRead(region, "extended_and_np");
verifyReadNotPlaced(region, "outside_intervals");
verifyReadNotPlaced(region, "end_of_chr1");
verifyReadNotPlaced(region, "simple20");
region = activeRegions.get(genomeLocParser.createGenomeLoc("1", 2000, 2999));
@ -267,6 +271,19 @@ public class TraverseActiveRegionsTest extends BaseTest {
verifyReadNotPlaced(region, "boundary_unequal");
verifyReadNotPlaced(region, "extended_and_np");
verifyReadNotPlaced(region, "outside_intervals");
verifyReadNotPlaced(region, "end_of_chr1");
verifyReadNotPlaced(region, "simple20");
region = activeRegions.get(genomeLocParser.createGenomeLoc("1", 249250600, 249250621));
verifyReadNotPlaced(region, "simple");
verifyReadNotPlaced(region, "overlap_equal");
verifyReadNotPlaced(region, "overlap_unequal");
verifyReadNotPlaced(region, "boundary_equal");
verifyReadNotPlaced(region, "boundary_unequal");
verifyReadNotPlaced(region, "extended_and_np");
verifyReadNotPlaced(region, "outside_intervals");
getRead(region, "end_of_chr1");
verifyReadNotPlaced(region, "simple20");
region = activeRegions.get(genomeLocParser.createGenomeLoc("20", 10000, 10100));
@ -278,9 +295,8 @@ public class TraverseActiveRegionsTest extends BaseTest {
verifyReadNotPlaced(region, "boundary_unequal");
verifyReadNotPlaced(region, "extended_and_np");
verifyReadNotPlaced(region, "outside_intervals");
verifyReadNotPlaced(region, "end_of_chr1");
getRead(region, "simple20");
// TODO: more tests and edge cases
}
@Test
@ -300,6 +316,7 @@ public class TraverseActiveRegionsTest extends BaseTest {
// boundary_unequal: Primary in 1:1000-1999, Non-Primary 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
// end_of_chr1: Primary in 1:249250600-249250621
// simple20: Primary in 20:10000-10100
Map<GenomeLoc, ActiveRegion> activeRegions = getActiveRegions(walker, intervals);
@ -314,6 +331,7 @@ public class TraverseActiveRegionsTest extends BaseTest {
verifyReadNotPlaced(region, "boundary_unequal");
getRead(region, "extended_and_np");
verifyReadNotPlaced(region, "outside_intervals");
verifyReadNotPlaced(region, "end_of_chr1");
verifyReadNotPlaced(region, "simple20");
region = activeRegions.get(genomeLocParser.createGenomeLoc("1", 1000, 1999));
@ -325,6 +343,7 @@ public class TraverseActiveRegionsTest extends BaseTest {
getRead(region, "boundary_unequal");
getRead(region, "extended_and_np");
verifyReadNotPlaced(region, "outside_intervals");
verifyReadNotPlaced(region, "end_of_chr1");
verifyReadNotPlaced(region, "simple20");
region = activeRegions.get(genomeLocParser.createGenomeLoc("1", 2000, 2999));
@ -336,6 +355,19 @@ public class TraverseActiveRegionsTest extends BaseTest {
getRead(region, "boundary_unequal");
verifyReadNotPlaced(region, "extended_and_np");
verifyReadNotPlaced(region, "outside_intervals");
verifyReadNotPlaced(region, "end_of_chr1");
verifyReadNotPlaced(region, "simple20");
region = activeRegions.get(genomeLocParser.createGenomeLoc("1", 249250600, 249250621));
verifyReadNotPlaced(region, "simple");
verifyReadNotPlaced(region, "overlap_equal");
verifyReadNotPlaced(region, "overlap_unequal");
verifyReadNotPlaced(region, "boundary_equal");
verifyReadNotPlaced(region, "boundary_unequal");
verifyReadNotPlaced(region, "extended_and_np");
verifyReadNotPlaced(region, "outside_intervals");
getRead(region, "end_of_chr1");
verifyReadNotPlaced(region, "simple20");
region = activeRegions.get(genomeLocParser.createGenomeLoc("20", 10000, 10100));
@ -347,9 +379,8 @@ public class TraverseActiveRegionsTest extends BaseTest {
verifyReadNotPlaced(region, "boundary_unequal");
verifyReadNotPlaced(region, "extended_and_np");
verifyReadNotPlaced(region, "outside_intervals");
verifyReadNotPlaced(region, "end_of_chr1");
getRead(region, "simple20");
// TODO: more tests and edge cases
}
@Test
@ -370,6 +401,7 @@ public class TraverseActiveRegionsTest extends BaseTest {
// boundary_unequal: Primary in 1:1000-1999, Non-Primary 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
// end_of_chr1: Primary in 1:249250600-249250621
// simple20: Primary in 20:10000-10100
Map<GenomeLoc, ActiveRegion> activeRegions = getActiveRegions(walker, intervals);
@ -384,6 +416,7 @@ public class TraverseActiveRegionsTest extends BaseTest {
verifyReadNotPlaced(region, "boundary_unequal");
getRead(region, "extended_and_np");
verifyReadNotPlaced(region, "outside_intervals");
verifyReadNotPlaced(region, "end_of_chr1");
verifyReadNotPlaced(region, "simple20");
region = activeRegions.get(genomeLocParser.createGenomeLoc("1", 1000, 1999));
@ -395,6 +428,7 @@ public class TraverseActiveRegionsTest extends BaseTest {
getRead(region, "boundary_unequal");
getRead(region, "extended_and_np");
verifyReadNotPlaced(region, "outside_intervals");
verifyReadNotPlaced(region, "end_of_chr1");
verifyReadNotPlaced(region, "simple20");
region = activeRegions.get(genomeLocParser.createGenomeLoc("1", 2000, 2999));
@ -406,6 +440,19 @@ public class TraverseActiveRegionsTest extends BaseTest {
getRead(region, "boundary_unequal");
getRead(region, "extended_and_np");
verifyReadNotPlaced(region, "outside_intervals");
verifyReadNotPlaced(region, "end_of_chr1");
verifyReadNotPlaced(region, "simple20");
region = activeRegions.get(genomeLocParser.createGenomeLoc("1", 249250600, 249250621));
verifyReadNotPlaced(region, "simple");
verifyReadNotPlaced(region, "overlap_equal");
verifyReadNotPlaced(region, "overlap_unequal");
verifyReadNotPlaced(region, "boundary_equal");
verifyReadNotPlaced(region, "boundary_unequal");
verifyReadNotPlaced(region, "extended_and_np");
verifyReadNotPlaced(region, "outside_intervals");
getRead(region, "end_of_chr1");
verifyReadNotPlaced(region, "simple20");
region = activeRegions.get(genomeLocParser.createGenomeLoc("20", 10000, 10100));
@ -417,9 +464,13 @@ public class TraverseActiveRegionsTest extends BaseTest {
verifyReadNotPlaced(region, "boundary_unequal");
verifyReadNotPlaced(region, "extended_and_np");
verifyReadNotPlaced(region, "outside_intervals");
verifyReadNotPlaced(region, "end_of_chr1");
getRead(region, "simple20");
}
// TODO: more tests and edge cases
@Test
public void testUnmappedReads() {
// TODO
}
private void verifyReadNotPlaced(ActiveRegion region, String readName) {

20
public/java/test/org/broadinstitute/sting/gatk/walkers/PrintReadsLargeScaleTest.java 100755
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@ -0,0 +1,20 @@
package org.broadinstitute.sting.gatk.walkers;
import org.broadinstitute.sting.WalkerTest;
import org.testng.annotations.Test;
import java.util.ArrayList;
public class PrintReadsLargeScaleTest extends WalkerTest {
@Test( timeOut = 1000 * 60 * 60 * 20 ) // 60 seconds * 60 seconds / minute * 20 minutes
public void testRealignerTargetCreator() {
WalkerTestSpec spec = new WalkerTestSpec(
"-R " + b37KGReference +
" -T PrintReads" +
" -I " + evaluationDataLocation + "CEUTrio.HiSeq.WEx.b37.NA12892.clean.dedup.recal.1.bam" +
" -o /dev/null",
0,
new ArrayList<String>(0));
executeTest("testPrintReadsWholeExomeChr1", spec);
}
}