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

public/java/test/org/broadinstitute/sting/gatk/traversals/TraverseActiveRegionsTest.java

@@ -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) {

public/java/test/org/broadinstitute/sting/gatk/walkers/PrintReadsLargeScaleTest.java

@@ -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);
+    }
+}