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Removing arbitrary selects 

git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3169 348d0f76-0448-11de-a6fe-93d51630548a
This commit is contained in:
ebanks 2010-04-14 17:46:39 +00:00
parent f1189bac5a
commit 04909fa6ad
2 changed files with 7 additions and 7 deletions
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4
java/src/org/broadinstitute/sting/oneoffprojects/walkers/varianteval2/VariantEval2Walker.java
View File

@ -89,10 +89,10 @@ public class VariantEval2Walker extends RodWalker<Integer, Integer> {
// --------------------------------------------------------------------------------------------------------------
@Argument(shortName="select", doc="One or more stratifications to use when evaluating the data", required=false)
protected String[] SELECT_EXPS = {"QUAL > 500.0", "HARD_TO_VALIDATE==1", "GATK_STANDARD==1"};
protected String[] SELECT_EXPS = {};
@Argument(shortName="selectName", doc="Names to use for the list of stratifications (must be a 1-to-1 mapping)", required=false)
protected String[] SELECT_NAMES = {"q500plus", "low_mapq", "gatk_std_filters"};
protected String[] SELECT_NAMES = {};
@Argument(shortName="known", doc="Name of ROD bindings containing variant sites that should be treated as known when splitting eval rods into known and novel subsets", required=false)
protected String[] KNOWN_NAMES = {"dbsnp"};

10
java/test/org/broadinstitute/sting/oneoffprojects/walkers/varianteval2/VariantEval2IntegrationTest.java
View File

@ -18,8 +18,8 @@ public class VariantEval2IntegrationTest extends WalkerTest {
@Test
public void testVE2Simple() {
HashMap<String, String> expectations = new HashMap<String, String>();
expectations.put("-L 1:1-10,000,000", "44fca2e43dade85ca16fa9e323e4cc9b");
expectations.put("-L 1:1-10,000,000 -family NA19238+NA19239=NA19240 -MVQ 0", "6910a9a49625a8df2ad797d751be9ed6");
expectations.put("-L 1:1-10,000,000", "8b93fda4a4b61c8b284063de62c84644");
expectations.put("-L 1:1-10,000,000 -family NA19238+NA19239=NA19240 -MVQ 0", "d232220a2b0d13e3a2b077310cad4540");
for ( Map.Entry<String, String> entry : expectations.entrySet() ) {
String extraArgs = entry.getKey();
@ -39,10 +39,10 @@ public class VariantEval2IntegrationTest extends WalkerTest {
" -B dbsnp_130,dbSNP," + GATKDataLocation + "dbsnp_130_b36.rod" +
" -B comp_hapmap,VCF," + validationDataLocation + "CEU_hapmap_nogt_23.vcf";
String eqMD5s = "a525597a34cd3fa84c75263dbd026acb"; // next two examples should be the same!
String eqMD5s = "9e5a207f445febc8b432254a6cf9a182"; // next two examples should be the same!
expectations.put("", eqMD5s);
expectations.put(" -known comp_hapmap -known dbsnp", eqMD5s);
expectations.put(" -known comp_hapmap", "35feda6c361408755e7f1dae245462d7");
expectations.put(" -known comp_hapmap", "f6aedc4911c5c9ebfd4de1383bb1aafa");
for ( Map.Entry<String, String> entry : expectations.entrySet() ) {
String extraArgs2 = entry.getKey();
@ -60,7 +60,7 @@ public class VariantEval2IntegrationTest extends WalkerTest {
String extraArgs = "-L 1:1-10,000,000 -family NA19238+NA19239=NA19240 -MVQ 30";
WalkerTestSpec spec = new WalkerTestSpec( root + " " + extraArgs + " -o %s -outputVCF %s",
2,
Arrays.asList("0d2ac5ea23f8cd3237836080c722711b", "a3ce1d70d8ae3874807e9d61994d42af"));
Arrays.asList("e11a104981a3d959458bc11d3c540355", "a3ce1d70d8ae3874807e9d61994d42af"));
executeTest("testVE2WriteVCF", spec);
}
}