From 8026199e4cfc2cb7dba2b8f9129b7060a7a86ef9 Mon Sep 17 00:00:00 2001
From: Mark DePristo <depristo@broadinstitute.org>
Date: Wed, 23 Jan 2013 09:47:22 -0500
Subject: [PATCH] Updating md5s for CountReadsInActiveRegions and
 HaplotypeCaller to reflect new activity profile mechanics

-- In this process I discovered a few missed sites in the old code.  The new approach actually produces better HC results than the previous version.
---
 .../HaplotypeCallerIntegrationTest.java       | 22 +++++++++----------
 1 file changed, 11 insertions(+), 11 deletions(-)

diff --git a/protected/java/test/org/broadinstitute/sting/gatk/walkers/haplotypecaller/HaplotypeCallerIntegrationTest.java b/protected/java/test/org/broadinstitute/sting/gatk/walkers/haplotypecaller/HaplotypeCallerIntegrationTest.java
index 939b9873c..41f9ab680 100644
--- a/protected/java/test/org/broadinstitute/sting/gatk/walkers/haplotypecaller/HaplotypeCallerIntegrationTest.java
+++ b/protected/java/test/org/broadinstitute/sting/gatk/walkers/haplotypecaller/HaplotypeCallerIntegrationTest.java
@@ -68,12 +68,12 @@ public class HaplotypeCallerIntegrationTest extends WalkerTest {
 
     @Test
     public void testHaplotypeCallerMultiSample() {
-        HCTest(CEUTRIO_BAM, "", "b8f7b741445ce6b6ea491c794ce75c17");
+        HCTest(CEUTRIO_BAM, "", "c142bc73447c72286ca48f4a4966d9b6");
     }
 
     @Test
     public void testHaplotypeCallerSingleSample() {
-        HCTest(NA12878_BAM, "", "a2c63f6e6e51a01019bdbd23125bdb15");
+        HCTest(NA12878_BAM, "", "d172eb9447015ea50220c6947be145ea");
     }
 
     @Test(enabled = false)
@@ -84,7 +84,7 @@ public class HaplotypeCallerIntegrationTest extends WalkerTest {
     @Test
     public void testHaplotypeCallerMultiSampleGGA() {
         HCTest(CEUTRIO_BAM, "--max_alternate_alleles 3 -gt_mode GENOTYPE_GIVEN_ALLELES -out_mode EMIT_ALL_SITES -alleles " + validationDataLocation + "combined.phase1.chr20.raw.indels.sites.vcf",
-                "c679ae7f04bdfda896b5c046d35e043c");
+                "2c56ffc3b7fbbf154ae9ca355780a78f");
     }
 
     private void HCTestComplexGGA(String bam, String args, String md5) {
@@ -96,13 +96,13 @@ public class HaplotypeCallerIntegrationTest extends WalkerTest {
     @Test
     public void testHaplotypeCallerMultiSampleGGAComplex() {
         HCTestComplexGGA(NA12878_CHR20_BAM, "-L 20:119673-119823 -L 20:121408-121538",
-                "8730a9ebaeecae913dca2fb5a0d4e946");
+                "66bd513d25b691a5b0c5084924b4a308");
     }
 
     @Test
     public void testHaplotypeCallerMultiSampleGGAMultiAllelic() {
         HCTestComplexGGA(NA12878_CHR20_BAM, "-L 20:133041-133161 -L 20:300207-300337",
-                "d590c8d6d5e58d685401b65a23846893");
+                "d0fcbfa2ccce0ca4a2e81f31dc43d79d");
     }
 
     private void HCTestComplexVariants(String bam, String args, String md5) {
@@ -113,7 +113,7 @@ public class HaplotypeCallerIntegrationTest extends WalkerTest {
 
     @Test
     public void testHaplotypeCallerMultiSampleComplex() {
-        HCTestComplexVariants(privateTestDir + "AFR.complex.variants.bam", "", "6c0c441b71848c2eea38ab5e2afe1120");
+        HCTestComplexVariants(privateTestDir + "AFR.complex.variants.bam", "", "7e8a6ed62f866fc47c92af0e255ca180");
     }
 
     private void HCTestSymbolicVariants(String bam, String args, String md5) {
@@ -135,7 +135,7 @@ public class HaplotypeCallerIntegrationTest extends WalkerTest {
 
     @Test
     public void testHaplotypeCallerSingleSampleIndelQualityScores() {
-        HCTestIndelQualityScores(NA12878_RECALIBRATED_BAM, "", "29f1125df5ab27cc937a144ae08ac735");
+        HCTestIndelQualityScores(NA12878_RECALIBRATED_BAM, "", "602aabbbe710ac90b16e474c869e8a86");
     }
 
     // That problem bam came from a user on the forum and it spotted a problem where the ReadClipper
@@ -146,14 +146,14 @@ public class HaplotypeCallerIntegrationTest extends WalkerTest {
     @Test
     public void HCTestProblematicReadsModifiedInActiveRegions() {
         final String base = String.format("-T HaplotypeCaller -R %s -I %s", REF, privateTestDir + "haplotype-problem-4.bam") + " --no_cmdline_in_header -o %s -minPruning 3 -L 4:49139026-49139965";
-        final WalkerTestSpec spec = new WalkerTestSpec(base, Arrays.asList("31db0a2d9eb07f86e0a89f0d97169072"));
+        final WalkerTestSpec spec = new WalkerTestSpec(base, Arrays.asList("c23b589be3072027ff2da93067dbf549"));
         executeTest("HCTestProblematicReadsModifiedInActiveRegions: ", spec);
     }
 
     @Test
     public void HCTestStructuralIndels() {
         final String base = String.format("-T HaplotypeCaller -R %s -I %s", REF, privateTestDir + "AFR.structural.indels.bam") + " --no_cmdline_in_header -o %s -minPruning 6 -L 20:8187565-8187800 -L 20:18670537-18670730";
-        final WalkerTestSpec spec = new WalkerTestSpec(base, Arrays.asList("add0f4f51969b7caeea99005a7ba1aa4"));
+        final WalkerTestSpec spec = new WalkerTestSpec(base, Arrays.asList("a612fe84dd7f80c4ad2d20d27fc6744e"));
         executeTest("HCTestStructuralIndels: ", spec);
     }
 
@@ -175,7 +175,7 @@ public class HaplotypeCallerIntegrationTest extends WalkerTest {
     public void HCTestReducedBam() {
         WalkerTest.WalkerTestSpec spec = new WalkerTest.WalkerTestSpec(
                 "-T HaplotypeCaller -R " + b37KGReference + " --no_cmdline_in_header -I " + privateTestDir + "bamExample.ReducedRead.ADAnnotation.bam -o %s -L 1:67,225,396-67,288,518", 1,
-                Arrays.asList("8a400b0c46f41447fcc35a907e34f384"));
+                Arrays.asList("0cb9132967fa9811e04f528be9f686dc"));
         executeTest("HC calling on a ReducedRead BAM", spec);
     }
 
@@ -183,7 +183,7 @@ public class HaplotypeCallerIntegrationTest extends WalkerTest {
     public void testReducedBamWithReadsNotFullySpanningDeletion() {
         WalkerTest.WalkerTestSpec spec = new WalkerTest.WalkerTestSpec(
                 "-T HaplotypeCaller -R " + b37KGReference + " --no_cmdline_in_header -I " + privateTestDir + "reduced.readNotFullySpanningDeletion.bam -o %s -L 1:167871297", 1,
-                Arrays.asList("4e8121dd9dc90478f237bd6ae4d19920"));
+                Arrays.asList("36a90309dde1a325c274388e302ffaa5"));
         executeTest("test calling on a ReducedRead BAM where the reads do not fully span a deletion", spec);
     }
 }