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Add reads which overstep a boundary by a single base

This commit is contained in:
Joel Thibault 2012-12-18 18:32:48 -05:00
parent 9828b2990f
commit 2b1db519d7
1 changed files with 14 additions and 6 deletions
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20
public/java/test/org/broadinstitute/sting/gatk/traversals/TraverseActiveRegionsTest.java
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@ -129,6 +129,8 @@ public class TraverseActiveRegionsTest extends BaseTest {
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("boundary_1_pre", "1", 1950, 2000));
reads.add(buildSAMRecord("boundary_1_post", "1", 1999, 2050));
reads.add(buildSAMRecord("extended_and_np", "1", 990, 1990));
reads.add(buildSAMRecord("outside_intervals", "1", 5000, 6000));
reads.add(buildSAMRecord("simple20", "20", 10025, 10075));
@ -240,6 +242,8 @@ 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
// boundary_1_pre: Primary in 1:1000-1999, Non-Primary in 1:2000-2999
// boundary_1_post: Non-Primary in 1:1000-1999, 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
// simple20: Primary in 20:10000-10100
@ -251,10 +255,10 @@ public class TraverseActiveRegionsTest extends BaseTest {
verifyReadMapping(region, "simple", "overlap_equal", "overlap_unequal");
region = activeRegions.get(genomeLocParser.createGenomeLoc("1", 1000, 1999));
verifyReadMapping(region, "boundary_unequal", "extended_and_np");
verifyReadMapping(region, "boundary_unequal", "extended_and_np", "boundary_1_pre");
region = activeRegions.get(genomeLocParser.createGenomeLoc("1", 2000, 2999));
verifyReadMapping(region, "boundary_equal");
verifyReadMapping(region, "boundary_equal", "boundary_1_post");
region = activeRegions.get(genomeLocParser.createGenomeLoc("20", 10000, 10100));
verifyReadMapping(region, "simple20");
@ -275,6 +279,8 @@ 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
// boundary_1_pre: Primary in 1:1000-1999, Non-Primary in 1:2000-2999
// boundary_1_post: Non-Primary in 1:1000-1999, 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
// simple20: Primary in 20:10000-10100
@ -286,10 +292,10 @@ public class TraverseActiveRegionsTest extends BaseTest {
verifyReadMapping(region, "simple", "overlap_equal", "overlap_unequal", "extended_and_np");
region = activeRegions.get(genomeLocParser.createGenomeLoc("1", 1000, 1999));
verifyReadMapping(region, "boundary_equal", "boundary_unequal", "extended_and_np");
verifyReadMapping(region, "boundary_equal", "boundary_unequal", "extended_and_np", "boundary_1_pre", "boundary_1_post");
region = activeRegions.get(genomeLocParser.createGenomeLoc("1", 2000, 2999));
verifyReadMapping(region, "boundary_equal", "boundary_unequal");
verifyReadMapping(region, "boundary_equal", "boundary_unequal", "boundary_1_pre", "boundary_1_post");
region = activeRegions.get(genomeLocParser.createGenomeLoc("20", 10000, 10100));
verifyReadMapping(region, "simple20");
@ -311,6 +317,8 @@ 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
// boundary_1_pre: Primary in 1:1000-1999, Non-Primary in 1:2000-2999
// boundary_1_post: Non-Primary in 1:1000-1999, 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
// simple20: Primary in 20:10000-10100
@ -322,10 +330,10 @@ public class TraverseActiveRegionsTest extends BaseTest {
verifyReadMapping(region, "simple", "overlap_equal", "overlap_unequal", "extended_and_np");
region = activeRegions.get(genomeLocParser.createGenomeLoc("1", 1000, 1999));
verifyReadMapping(region, "boundary_equal", "boundary_unequal", "extended_and_np");
verifyReadMapping(region, "boundary_equal", "boundary_unequal", "extended_and_np", "boundary_1_pre", "boundary_1_post");
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", "boundary_1_pre", "boundary_1_post");
region = activeRegions.get(genomeLocParser.createGenomeLoc("20", 10000, 10100));
verifyReadMapping(region, "simple20");