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Add a test for a read that extends off the end of chr1

This commit is contained in:
Joel Thibault 2012-12-07 13:46:41 -05:00
parent cc4e3ec589
commit 3b0e3767bf
1 changed files with 54 additions and 0 deletions
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54
public/java/test/org/broadinstitute/sting/gatk/traversals/TraverseActiveRegionsTest.java
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@ -117,6 +117,8 @@ public class TraverseActiveRegionsTest extends BaseTest {
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();
@ -128,6 +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
@ -229,6 +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);
@ -243,6 +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));
@ -254,6 +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));
@ -265,6 +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));
@ -276,6 +295,7 @@ 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");
}
@ -296,6 +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);
@ -310,6 +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));
@ -321,6 +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));
@ -332,6 +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));
@ -343,6 +379,7 @@ 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");
}
@ -364,6 +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);
@ -378,6 +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));
@ -389,6 +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));
@ -400,6 +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));
@ -411,6 +464,7 @@ 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");
}