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Addressing comments

This commit is contained in:
meganshand 2015-11-04 11:00:01 -05:00
parent b5165b8d30
commit e4627ed5c3
2 changed files with 9 additions and 1 deletions
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2
protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/tools/walkers/variantutils/SelectVariantsIntegrationTest.java
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@ -612,6 +612,8 @@ public class SelectVariantsIntegrationTest extends WalkerTest {
/** /**
* Test excluding variants with IDs * Test excluding variants with IDs
* Also tests --forceValidOutput flag, which changes the GQ from floats to ints to match
* header spec.
*/ */
@Test @Test
public void testExcludeSelectionID() { public void testExcludeSelectionID() {

8
public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/tools/walkers/variantutils/SelectVariants.java
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@ -574,7 +574,13 @@ public class SelectVariants extends RodWalker<Integer, Integer> implements TreeR
@Argument(fullName="ALLOW_NONOVERLAPPING_COMMAND_LINE_SAMPLES", required=false, doc="Allow samples other than those in the VCF to be specified on the command line. These samples will be ignored.") @Argument(fullName="ALLOW_NONOVERLAPPING_COMMAND_LINE_SAMPLES", required=false, doc="Allow samples other than those in the VCF to be specified on the command line. These samples will be ignored.")
private boolean allowNonOverlappingCommandLineSamples = false; private boolean allowNonOverlappingCommandLineSamples = false;
@Argument(fullName="forceValidOutput", required=false, doc="Forces output VCF to be compliant to up to date version") /**
* If this argument is provided, the output will be compliant with the version in the header, however it will also
* cause the tool to run slower than without the argument. Without the argument the header will be compliant with
* the up-to-date version, but the output in the body may not be compliant. If an up-to-date input file is used,
* then the output will also be up-to-date regardless of this argument.
*/
@Argument(fullName="forceValidOutput", required=false, doc="Forces output VCF to be compliant to up-to-date version")
private boolean forceValidOutput = false; private boolean forceValidOutput = false;
public enum NumberAlleleRestriction { public enum NumberAlleleRestriction {