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Updates for broken integration tests. Counting annotations (AC, AF) now work correctly for AC = 0 sites 

git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@4640 348d0f76-0448-11de-a6fe-93d51630548a
This commit is contained in:
depristo 2010-11-09 19:43:43 +00:00
parent 33b3f2adaa
commit 5ef4b234d8
3 changed files with 9 additions and 8 deletions
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11
java/test/org/broadinstitute/sting/gatk/contexts/variantcontext/VariantContextIntegrationTest.java
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@ -1,4 +1,5 @@
package org.broadinstitute.sting.gatk.contexts.variantcontext;
import org.broadinstitute.sting.WalkerTest;
@ -18,11 +19,11 @@ public class VariantContextIntegrationTest extends WalkerTest {
static HashMap<String, String> expectations = new HashMap<String, String>();
static {
expectations.put("-L 1:1-10000 --printPerLocus", "63fd69e4ab430b79fb213dd27b58ae1c");
expectations.put("-L 1:1-10000 --printPerLocus --takeFirstOnly", "276ed96efaaffc2fc1c3b3deb4e04d1d");
expectations.put("-L 1:1-10000 --printPerLocus --onlyContextsStartinAtCurrentPosition", "a37f7bc34c1824688d3e475945c19d5a");
expectations.put("-L 1:1-10000 --printPerLocus --takeFirstOnly --onlyContextsStartinAtCurrentPosition", "1715a6e0daf873f2e2cd10cb56085174");
expectations.put("-L 1:1-10000 --printPerLocus --onlyContextsOfType SNP", "bf33ab1ed65da7f56c02ca7956d9c31e");
expectations.put("-L 1:1-10000 --printPerLocus", "fcc9b7ea66c4407f60317112c7d17aa0");
expectations.put("-L 1:1-10000 --printPerLocus --takeFirstOnly", "897de66b05e10c80de01492c03842083");
expectations.put("-L 1:1-10000 --printPerLocus --onlyContextsStartinAtCurrentPosition", "566ea10d38e8b7685ec95e4774a6fa05");
expectations.put("-L 1:1-10000 --printPerLocus --takeFirstOnly --onlyContextsStartinAtCurrentPosition", "81fd480369c7e98a479a79b792d42305");
expectations.put("-L 1:1-10000 --printPerLocus --onlyContextsOfType SNP", "2097e32988d603d3b353b50218c86d3b");
expectations.put("-L 1:1-10000 --printPerLocus --onlyContextsOfType INDEL", "629ffd6b3b9ea1bce29cb715576f5c8a");
expectations.put("-L 1:1-10000 --printPerLocus --onlyContextsOfType INDEL --onlyContextsStartinAtCurrentPosition", "d4b812b2fec231f8f5b61d6f26cf86a5");
expectations.put("-L 1:1-10000 --printPerLocus --onlyContextsOfType MIXED", "546e8e546f2cdfba31f91ed083137c42");

4
java/test/org/broadinstitute/sting/gatk/walkers/genotyper/UnifiedGenotyperIntegrationTest.java
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@ -105,8 +105,8 @@ public class
@Test
public void testParameter() {
HashMap<String, String> e = new HashMap<String, String>();
e.put( "-genotype", "0bcea27abc956352d18ae2de23dcaa9c" );
e.put( "-all_bases", "aab0acf3e7f494a57cb2ad673ae8d32e" );
e.put( "-genotype", "243630a53c3881e23d89ce6bec448109" );
e.put( "-all_bases", "feae0bc485e01bf102d190c7234f3c59" );
e.put( "--min_base_quality_score 26", "48837ae22a75002d448806f6b46dd3b3" );
e.put( "--min_mapping_quality_score 26", "d388e847b655abf56a7fd945bdff5dee" );
e.put( "--max_mismatches_in_40bp_window 5", "416ba33cf1cfc0b4b4a2ad3256c8b56b" );

2
java/test/org/broadinstitute/sting/gatk/walkers/variantutils/CombineVariantsIntegrationTest.java
View File

@ -87,7 +87,7 @@ public class CombineVariantsIntegrationTest extends WalkerTest {
" -priority NA19240_BGI,NA19240_ILLUMINA,NA19240_WUGSC,denovoInfo" +
" -genotypeMergeOptions UNIQUIFY -L 1"),
1,
Arrays.asList("81f53a9f2a6d410c1236266e2516bf6f"));
Arrays.asList("13cb75cf37ec370763a34910ba48e42f"));
executeTest("threeWayWithRefs", spec);
}