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Reads off the end of a contig fail SAM validation when using actual BAMs

This commit is contained in:
Joel Thibault 2012-12-18 17:37:36 -05:00
parent 72e2394b26
commit 9828b2990f
1 changed files with 0 additions and 14 deletions
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14
public/java/test/org/broadinstitute/sting/gatk/traversals/TraverseActiveRegionsTest.java
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@ -119,7 +119,6 @@ public class TraverseActiveRegionsTest extends BaseTest {
intervals.add(genomeLocParser.createGenomeLoc("1", 1000, 1999)); intervals.add(genomeLocParser.createGenomeLoc("1", 1000, 1999));
intervals.add(genomeLocParser.createGenomeLoc("1", 2000, 2999)); intervals.add(genomeLocParser.createGenomeLoc("1", 2000, 2999));
intervals.add(genomeLocParser.createGenomeLoc("1", 10000, 20000)); 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("2", 1, 100));
intervals.add(genomeLocParser.createGenomeLoc("20", 10000, 10100)); intervals.add(genomeLocParser.createGenomeLoc("20", 10000, 10100));
intervals = IntervalUtils.sortAndMergeIntervals(genomeLocParser, intervals, IntervalMergingRule.OVERLAPPING_ONLY).toList(); intervals = IntervalUtils.sortAndMergeIntervals(genomeLocParser, intervals, IntervalMergingRule.OVERLAPPING_ONLY).toList();
@ -132,7 +131,6 @@ public class TraverseActiveRegionsTest extends BaseTest {
reads.add(buildSAMRecord("boundary_unequal", "1", 1990, 2008)); reads.add(buildSAMRecord("boundary_unequal", "1", 1990, 2008));
reads.add(buildSAMRecord("extended_and_np", "1", 990, 1990)); reads.add(buildSAMRecord("extended_and_np", "1", 990, 1990));
reads.add(buildSAMRecord("outside_intervals", "1", 5000, 6000)); reads.add(buildSAMRecord("outside_intervals", "1", 5000, 6000));
reads.add(buildSAMRecord("end_of_chr1", "1", 249250600, 249250700));
reads.add(buildSAMRecord("simple20", "20", 10025, 10075)); reads.add(buildSAMRecord("simple20", "20", 10025, 10075));
createBAM(reads); createBAM(reads);
@ -244,7 +242,6 @@ public class TraverseActiveRegionsTest extends BaseTest {
// boundary_unequal: Primary in 1:1000-1999, Non-Primary in 1:2000-2999 // 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 // extended_and_np: Non-Primary in 1:1-999, Primary in 1:1000-1999, Extended in 1:2000-2999
// outside_intervals: none // outside_intervals: none
// end_of_chr1: Primary in 1:249250600-249250621
// simple20: Primary in 20:10000-10100 // simple20: Primary in 20:10000-10100
Map<GenomeLoc, ActiveRegion> activeRegions = getActiveRegions(walker, intervals); Map<GenomeLoc, ActiveRegion> activeRegions = getActiveRegions(walker, intervals);
@ -259,9 +256,6 @@ public class TraverseActiveRegionsTest extends BaseTest {
region = activeRegions.get(genomeLocParser.createGenomeLoc("1", 2000, 2999)); region = activeRegions.get(genomeLocParser.createGenomeLoc("1", 2000, 2999));
verifyReadMapping(region, "boundary_equal"); verifyReadMapping(region, "boundary_equal");
region = activeRegions.get(genomeLocParser.createGenomeLoc("1", 249250600, 249250621));
verifyReadMapping(region, "end_of_chr1");
region = activeRegions.get(genomeLocParser.createGenomeLoc("20", 10000, 10100)); region = activeRegions.get(genomeLocParser.createGenomeLoc("20", 10000, 10100));
verifyReadMapping(region, "simple20"); verifyReadMapping(region, "simple20");
} }
@ -283,7 +277,6 @@ public class TraverseActiveRegionsTest extends BaseTest {
// boundary_unequal: Primary in 1:1000-1999, Non-Primary in 1:2000-2999 // 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 // extended_and_np: Non-Primary in 1:1-999, Primary in 1:1000-1999, Extended in 1:2000-2999
// outside_intervals: none // outside_intervals: none
// end_of_chr1: Primary in 1:249250600-249250621
// simple20: Primary in 20:10000-10100 // simple20: Primary in 20:10000-10100
Map<GenomeLoc, ActiveRegion> activeRegions = getActiveRegions(walker, intervals); Map<GenomeLoc, ActiveRegion> activeRegions = getActiveRegions(walker, intervals);
@ -298,9 +291,6 @@ public class TraverseActiveRegionsTest extends BaseTest {
region = activeRegions.get(genomeLocParser.createGenomeLoc("1", 2000, 2999)); region = activeRegions.get(genomeLocParser.createGenomeLoc("1", 2000, 2999));
verifyReadMapping(region, "boundary_equal", "boundary_unequal"); verifyReadMapping(region, "boundary_equal", "boundary_unequal");
region = activeRegions.get(genomeLocParser.createGenomeLoc("1", 249250600, 249250621));
verifyReadMapping(region, "end_of_chr1");
region = activeRegions.get(genomeLocParser.createGenomeLoc("20", 10000, 10100)); region = activeRegions.get(genomeLocParser.createGenomeLoc("20", 10000, 10100));
verifyReadMapping(region, "simple20"); verifyReadMapping(region, "simple20");
} }
@ -323,7 +313,6 @@ public class TraverseActiveRegionsTest extends BaseTest {
// boundary_unequal: Primary in 1:1000-1999, Non-Primary in 1:2000-2999 // 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 // extended_and_np: Non-Primary in 1:1-999, Primary in 1:1000-1999, Extended in 1:2000-2999
// outside_intervals: none // outside_intervals: none
// end_of_chr1: Primary in 1:249250600-249250621
// simple20: Primary in 20:10000-10100 // simple20: Primary in 20:10000-10100
Map<GenomeLoc, ActiveRegion> activeRegions = getActiveRegions(walker, intervals); Map<GenomeLoc, ActiveRegion> activeRegions = getActiveRegions(walker, intervals);
@ -338,9 +327,6 @@ public class TraverseActiveRegionsTest extends BaseTest {
region = activeRegions.get(genomeLocParser.createGenomeLoc("1", 2000, 2999)); region = activeRegions.get(genomeLocParser.createGenomeLoc("1", 2000, 2999));
verifyReadMapping(region, "boundary_equal", "boundary_unequal", "extended_and_np"); verifyReadMapping(region, "boundary_equal", "boundary_unequal", "extended_and_np");
region = activeRegions.get(genomeLocParser.createGenomeLoc("1", 249250600, 249250621));
verifyReadMapping(region, "end_of_chr1");
region = activeRegions.get(genomeLocParser.createGenomeLoc("20", 10000, 10100)); region = activeRegions.get(genomeLocParser.createGenomeLoc("20", 10000, 10100));
verifyReadMapping(region, "simple20"); verifyReadMapping(region, "simple20");
} }