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After verifying that the changes to these tests were all in the RankSum annotations, I'm commiting fixes to the test md5s. 

git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@5918 348d0f76-0448-11de-a6fe-93d51630548a
This commit is contained in:
chartl 2011-06-02 13:01:18 +00:00
parent c7fe062cb7
commit 092952db44
3 changed files with 18 additions and 18 deletions
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2
java/src/org/broadinstitute/sting/utils/MannWhitneyU.java
View File

@ -298,7 +298,7 @@ public class MannWhitneyU {
public static Pair<Double,Double> calculatePRecursively(int n, int m, long u, boolean twoSided, ExactMode mode) {
if ( m > 8 && n > 5 ) { throw new StingException(String.format("Please use the appropriate (normal or sum of uniform) approximation. Values n: %d, m: %d",n,m)); }
double p = mode == ExactMode.POINT ? cpr(n,m,u) : cumulativeCPR(n,m,u);
p *= twoSided ? 2.0 : 1.0;
//p *= twoSided ? 2.0 : 1.0;
double z;
try {

4
java/test/org/broadinstitute/sting/gatk/walkers/annotator/VariantAnnotatorIntegrationTest.java
View File

@ -39,7 +39,7 @@ public class VariantAnnotatorIntegrationTest extends WalkerTest {
public void testHasAnnotsAsking2() {
WalkerTestSpec spec = new WalkerTestSpec(
baseTestString() + " -G \"Standard\" -B:variant,VCF3 " + validationDataLocation + "vcfexample3.vcf -I " + validationDataLocation + "NA12878.1kg.p2.chr1_10mb_11_mb.SLX.bam -L 1:10,000,000-10,050,000", 1,
Arrays.asList("f559fa1754f82a00454894ecd518a3b0"));
Arrays.asList("248233148af03e39f104bfb161899136"));
executeTest("test file has annotations, asking for annotations, #2", spec);
}
@ -71,7 +71,7 @@ public class VariantAnnotatorIntegrationTest extends WalkerTest {
public void testNoAnnotsAsking2() {
WalkerTestSpec spec = new WalkerTestSpec(
baseTestString() + " -G \"Standard\" -B:variant,VCF3 " + validationDataLocation + "vcfexample3empty.vcf -I " + validationDataLocation + "NA12878.1kg.p2.chr1_10mb_11_mb.SLX.bam -L 1:10,000,000-10,050,000", 1,
Arrays.asList("709a1f482cce68992c637da3cff824a8"));
Arrays.asList("25068fff13c928ca1b70e5d67af32775"));
executeTest("test file doesn't have annotations, asking for annotations, #2", spec);
}

30
java/test/org/broadinstitute/sting/gatk/walkers/genotyper/UnifiedGenotyperIntegrationTest.java
View File

@ -34,7 +34,7 @@ public class UnifiedGenotyperIntegrationTest extends WalkerTest {
@Test
public void testMultiSamplePilot2AndRecallingWithAlleles() {
String md5 = "24876505e3526a58fc709ecf44372cfb";
String md5 = "00bf111cb80f1acb29679647f9433e2f";
WalkerTest.WalkerTestSpec spec1 = new WalkerTest.WalkerTestSpec(
baseCommand + " -I " + validationDataLocation + "pilot2_daughters.chr20.10k-11k.bam -o %s -L 20:10,000,000-10,050,000", 1,
@ -66,7 +66,7 @@ public class UnifiedGenotyperIntegrationTest extends WalkerTest {
public void testSingleSamplePilot2() {
WalkerTest.WalkerTestSpec spec = new WalkerTest.WalkerTestSpec(
baseCommand + " -I " + validationDataLocation + "NA12878.1kg.p2.chr1_10mb_11_mb.SLX.bam -o %s -L 1:10,000,000-10,100,000", 1,
Arrays.asList("3474828a82c070242346b78dc8b760c9"));
Arrays.asList("61db698ea6d11deba2fc900bd544b082"));
executeTest("test SingleSample Pilot2", spec);
}
@ -76,7 +76,7 @@ public class UnifiedGenotyperIntegrationTest extends WalkerTest {
//
// --------------------------------------------------------------------------------------------------------------
private final static String COMPRESSED_OUTPUT_MD5 = "a5e0673fdda01a1bcdfe122299c734f9";
private final static String COMPRESSED_OUTPUT_MD5 = "af5e98318f56e203b25361fee4d41548";
@Test
public void testCompressedOutput() {
@ -138,8 +138,8 @@ public class UnifiedGenotyperIntegrationTest extends WalkerTest {
public void testCallingParameters() {
HashMap<String, String> e = new HashMap<String, String>();
e.put( "--min_base_quality_score 26", "93ad1ed265be26e0c1fe05975d01edd1" );
e.put( "--min_mapping_quality_score 26", "01882d04939a5a6085fc5cadec019d3e" );
e.put( "--p_nonref_model GRID_SEARCH", "7b0b7f536c66afe006174ff9a094dd95" );
e.put( "--min_mapping_quality_score 26", "8f470d3622c0eb9fcc78b9ef3c9b0a0d" );
e.put( "--p_nonref_model GRID_SEARCH", "cb8f353e0b1c252ef09dcbebe50d95af" );
for ( Map.Entry<String, String> entry : e.entrySet() ) {
WalkerTest.WalkerTestSpec spec = new WalkerTest.WalkerTestSpec(
@ -152,9 +152,9 @@ public class UnifiedGenotyperIntegrationTest extends WalkerTest {
@Test
public void testOutputParameter() {
HashMap<String, String> e = new HashMap<String, String>();
e.put( "-sites_only", "919d4b034ef0e07c8d50ea05b8fa0725" );
e.put( "--output_mode EMIT_ALL_CONFIDENT_SITES", "b793fca3450c0afcde2418d79bbf2724" );
e.put( "--output_mode EMIT_ALL_SITES", "6e47e30c029e4bba63a492d7deb022f2" );
e.put( "-sites_only", "71f61655f725cda56bc46d99d1cc24eb" );
e.put( "--output_mode EMIT_ALL_CONFIDENT_SITES", "8193a4c06ddbd82d0a328491118b16a8" );
e.put( "--output_mode EMIT_ALL_SITES", "89859bd987e8b797d37f5dec54d37e9c" );
for ( Map.Entry<String, String> entry : e.entrySet() ) {
WalkerTest.WalkerTestSpec spec = new WalkerTest.WalkerTestSpec(
@ -168,12 +168,12 @@ public class UnifiedGenotyperIntegrationTest extends WalkerTest {
public void testConfidence() {
WalkerTest.WalkerTestSpec spec1 = new WalkerTest.WalkerTestSpec(
baseCommand + " -I " + validationDataLocation + "NA12878.1kg.p2.chr1_10mb_11_mb.SLX.bam -o %s -L 1:10,000,000-10,010,000 -stand_call_conf 10 ", 1,
Arrays.asList("01882d04939a5a6085fc5cadec019d3e"));
Arrays.asList("8f470d3622c0eb9fcc78b9ef3c9b0a0d"));
executeTest("test confidence 1", spec1);
WalkerTest.WalkerTestSpec spec2 = new WalkerTest.WalkerTestSpec(
baseCommand + " -I " + validationDataLocation + "NA12878.1kg.p2.chr1_10mb_11_mb.SLX.bam -o %s -L 1:10,000,000-10,010,000 -stand_emit_conf 10 ", 1,
Arrays.asList("00807e8a5bc9172c34a5b4bd2e8afba7"));
Arrays.asList("50d03e71ed2b4eb20db82e22541ac2f2"));
executeTest("test confidence 2", spec2);
}
@ -185,8 +185,8 @@ public class UnifiedGenotyperIntegrationTest extends WalkerTest {
@Test
public void testHeterozyosity() {
HashMap<Double, String> e = new HashMap<Double, String>();
e.put( 0.01, "966ceb5a7a6d87ad417046c2f60e69fd" );
e.put( 1.0 / 1850, "85057e3f2df0433392409c586af1be33" );
e.put( 0.01, "649590cbfc67bddf82416a0b82027696" );
e.put( 1.0 / 1850, "22153b7d06d13ea1a1ffdc45d7668974" );
for ( Map.Entry<Double, String> entry : e.entrySet() ) {
WalkerTest.WalkerTestSpec spec = new WalkerTest.WalkerTestSpec(
@ -210,7 +210,7 @@ public class UnifiedGenotyperIntegrationTest extends WalkerTest {
" -o %s" +
" -L 1:10,000,000-10,100,000",
1,
Arrays.asList("f9d92a81294569b9c918848932c1a0ca"));
Arrays.asList("d453f2e44fb7f0ec027c2a5f791da6aa"));
executeTest(String.format("test multiple technologies"), spec);
}
@ -229,7 +229,7 @@ public class UnifiedGenotyperIntegrationTest extends WalkerTest {
" -L 1:10,000,000-10,100,000" +
" -baq CALCULATE_AS_NECESSARY",
1,
Arrays.asList("930dc1d9bc2006b86e8c90a50d349151"));
Arrays.asList("60cc4c793caaf891075d862a2376d73c"));
executeTest(String.format("test calling with BAQ"), spec);
}
@ -243,7 +243,7 @@ public class UnifiedGenotyperIntegrationTest extends WalkerTest {
" -L 1:10,000,000-10,100,000" +
" -baq OFF",
1,
Arrays.asList("f9d92a81294569b9c918848932c1a0ca"));
Arrays.asList("d453f2e44fb7f0ec027c2a5f791da6aa"));
executeTest(String.format("test calling with BAQ OFF"), spec);
}