zzh
/
gatk-3.8
1
0
Fork 0
Code Issues Pull Requests Packages Projects Releases Wiki Activity

Equal overlap should match right/later region

This commit is contained in:
Joel Thibault 2012-11-26 14:29:22 -05:00
parent d83ad906ef
commit 9bfe39411e
1 changed files with 7 additions and 7 deletions
Show Stats Download Patch File Download Diff File Expand all files Collapse all files

14
public/java/test/org/broadinstitute/sting/gatk/traversals/TraverseActiveRegionsTest.java
View File

@ -109,7 +109,7 @@ public class TraverseActiveRegionsTest extends BaseTest {
reads.add(buildSAMRecord("overlap_equal", "1", 10, 20)); reads.add(buildSAMRecord("overlap_equal", "1", 10, 20));
reads.add(buildSAMRecord("overlap_unequal", "1", 10, 21)); reads.add(buildSAMRecord("overlap_unequal", "1", 10, 21));
reads.add(buildSAMRecord("boundary_equal", "1", 1990, 2009)); reads.add(buildSAMRecord("boundary_equal", "1", 1990, 2009));
reads.add(buildSAMRecord("boundary_unequal", "1", 1995, 2050)); reads.add(buildSAMRecord("boundary_unequal", "1", 1990, 2008));
reads.add(buildSAMRecord("extended_only", "1", 3000, 3100)); reads.add(buildSAMRecord("extended_only", "1", 3000, 3100));
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));
@ -214,8 +214,8 @@ public class TraverseActiveRegionsTest extends BaseTest {
// simple: Primary in 1:1-999 // simple: Primary in 1:1-999
// overlap_equal: Primary in 1:1-999 // overlap_equal: Primary in 1:1-999
// overlap_unequal: Primary in 1:1-999 // overlap_unequal: Primary in 1:1-999
// boundary_equal: Primary in 1:1000-1999, Non-Primary in 1:2000-2999 // boundary_equal: Non-Primary in 1:1000-1999, Primary in 1:2000-2999
// boundary_unequal: Non-Primary in 1:1000-1999, Primary in 1:2000-2999 // boundary_unequal: Primary in 1:1000-1999, Non-Primary in 1:2000-2999
// extended_only: Extended in 1:2000-2999 // extended_only: Extended 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
@ -241,8 +241,8 @@ public class TraverseActiveRegionsTest extends BaseTest {
verifyReadNotPlaced(region, "simple"); verifyReadNotPlaced(region, "simple");
verifyReadNotPlaced(region, "overlap_equal"); verifyReadNotPlaced(region, "overlap_equal");
verifyReadNotPlaced(region, "overlap_unequal"); verifyReadNotPlaced(region, "overlap_unequal");
// TODO: fail verifyReadPrimary(region, "boundary_equal"); // TODO: fail verifyReadNonPrimary(region, "boundary_equal");
// TODO: fail verifyReadNonPrimary(region, "boundary_unequal"); verifyReadPrimary(region, "boundary_unequal");
verifyReadNotPlaced(region, "extended_only"); verifyReadNotPlaced(region, "extended_only");
// TODO: fail verifyReadPrimary(region, "extended_and_np"); // TODO: fail verifyReadPrimary(region, "extended_and_np");
verifyReadNotPlaced(region, "outside_intervals"); verifyReadNotPlaced(region, "outside_intervals");
@ -253,8 +253,8 @@ public class TraverseActiveRegionsTest extends BaseTest {
verifyReadNotPlaced(region, "simple"); verifyReadNotPlaced(region, "simple");
verifyReadNotPlaced(region, "overlap_equal"); verifyReadNotPlaced(region, "overlap_equal");
verifyReadNotPlaced(region, "overlap_unequal"); verifyReadNotPlaced(region, "overlap_unequal");
// TODO: fail verifyReadNonPrimary(region, "boundary_equal"); verifyReadPrimary(region, "boundary_equal");
verifyReadPrimary(region, "boundary_unequal"); // TODO: fail verifyReadNonPrimary(region, "boundary_unequal");
// TODO: fail verifyReadExtended(region, "extended_only"); // TODO: fail verifyReadExtended(region, "extended_only");
// TODO: fail verifyReadExtended(region, "extended_and_np"); // TODO: fail verifyReadExtended(region, "extended_and_np");
verifyReadNotPlaced(region, "outside_intervals"); verifyReadNotPlaced(region, "outside_intervals");