Merge remote-tracking branch 'unstable/master'

broadgsa · Nov 9, 2017 · fcf2061 · fcf2061
2 parents 50aa013 + 5ec70e2
commit fcf2061
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Showing 11 changed files with 55 additions and 51 deletions.
diff --git a/...tk-engine/src/test/java/org/broadinstitute/gatk/engine/EngineFeaturesIntegrationTest.java b/...tk-engine/src/test/java/org/broadinstitute/gatk/engine/EngineFeaturesIntegrationTest.java
@@ -324,12 +324,12 @@ public WalkerTestSpec testDefaultBaseQualities(final Integer value, final String
 
     @Test()
     public void testDefaultBaseQualities20() {
-        executeTest("testDefaultBaseQualities20", testDefaultBaseQualities(20, "90a450f74554bbd2cc3a9e0f9de68e26"));
+        executeTest("testDefaultBaseQualities20", testDefaultBaseQualities(20, "da5a4293e125f00ecbdfd450b80d8357"));
     }
 
     @Test()
     public void testDefaultBaseQualities30() {
-        executeTest("testDefaultBaseQualities30", testDefaultBaseQualities(30, "ec11db4173ce3b8e43997f00dab5ae26"));
+        executeTest("testDefaultBaseQualities30", testDefaultBaseQualities(30, "c82e72ee08d545266927a7f2e8ab24c3"));
     }
 
     @Test(expectedExceptions = Exception.class)
@@ -732,10 +732,10 @@ private File testBAMFeatures(final String args, final String md5) {
     public void testSAMWriterFeatures() {
         testBAMFeatures("-compress 0", "49228d4f5b14c4cfed4a09372eb71139");
         testBAMFeatures("-compress 9", "bc61a1b2b53a2ec7c63b533fa2f8701b");
-        testBAMFeatures("-simplifyBAM", "a1127bab46674b165496b79bb9fa7964");
+        testBAMFeatures("-simplifyBAM", "f66b671b32d1bbbf65a88585a64b556a");
 
         //Validate MD5
-        final String expectedMD5 = "c58b9114fc15b53655f2c03c819c29fd";
+        final String expectedMD5 = "a0c0f1fafc248ac82a84b8ca71292caf";
         final File md5Target = testBAMFeatures("--generate_md5", expectedMD5);
         final File md5File = new File(md5Target.getAbsoluteFile() + ".md5");
         md5File.deleteOnExit();

diff --git a/...tk-engine/src/test/java/org/broadinstitute/gatk/engine/arguments/CramIntegrationTest.java b/...tk-engine/src/test/java/org/broadinstitute/gatk/engine/arguments/CramIntegrationTest.java
@@ -41,16 +41,16 @@ public Object[][] getCRAMData() {
         return new Object[][] {
                 {"PrintReads", "exampleBAM.bam", "", "cram", ""}, // Bypass MD5 check since the CRAM header stores the file name
                 {"PrintReads", "exampleCRAM.cram", "", "cram", ""},
-                {"PrintReads", "exampleCRAM.cram", "", "bam", "e7834d5992a69143d7c463275213bbf8"},
-                {"PrintReads", "exampleCRAM.cram", " -L chr1:200", "bam", "d362fbf30a2c77a2653f1c8eb2dd8fc1"},
+                {"PrintReads", "exampleCRAM.cram", "", "bam", "50c55e1040aa0ffd4036aa581fcfe8af"},
+                {"PrintReads", "exampleCRAM.cram", " -L chr1:200", "bam", "f74f78bd16aed8a395f0e79e3898ab19"},
                 {"CountLoci", "exampleCRAM.cram", "", "txt", "ade93df31a6150321c1067e749cae9be"},
                 {"CountLoci", "exampleCRAM.cram", " -L chr1:200", "txt", "b026324c6904b2a9cb4b88d6d61c81d1"},
                 {"CountReads", "exampleCRAM.cram", "", "txt", "4fbafd6948b6529caa2b78e476359875"},
                 {"CountReads", "exampleCRAM.cram", " -L chr1:200", "txt", "b026324c6904b2a9cb4b88d6d61c81d1"},
-                {"PrintReads", "exampleCRAM.cram", " -L chr1:200 -L chr1:89597", "bam", "a11bd125b69f651aaa2ae68c8ccab22f"},
+                {"PrintReads", "exampleCRAM.cram", " -L chr1:200 -L chr1:89597", "bam", "1a6331f0e7afdccd07425df251d28811"},
                 {"CountLoci", "exampleCRAM.cram", " -L chr1:200 -L chr1:89597", "txt", "26ab0db90d72e28ad0ba1e22ee510510"},
                 {"CountReads", "exampleCRAM.cram", " -L chr1:200 -L chr1:89597", "txt", "6d7fce9fee471194aa8b5b6e47267f03"},
-                {"PrintReads", "exampleCRAM-nobai-withcrai.cram", " -L chr1:200 -L chr1:89597", "bam", "9e3e8b5a58dfcb50f5b270547c01d56a"},
+                {"PrintReads", "exampleCRAM-nobai-withcrai.cram", " -L chr1:200 -L chr1:89597", "bam", "41f8ebb256120befc6ea7d228915b349"},
                 {"CountLoci", "exampleCRAM-nobai-withcrai.cram", " -L chr1:200 -L chr1:89597", "txt", "26ab0db90d72e28ad0ba1e22ee510510"},
                 {"CountReads", "exampleCRAM-nobai-withcrai.cram", " -L chr1:200 -L chr1:89597", "txt", "6d7fce9fee471194aa8b5b6e47267f03"},
         };

diff --git a/...ngine/src/test/java/org/broadinstitute/gatk/engine/arguments/IntervalIntegrationTest.java b/...ngine/src/test/java/org/broadinstitute/gatk/engine/arguments/IntervalIntegrationTest.java
@@ -62,7 +62,7 @@ public void testUnmappedReadInclusion() {
         // our base file
         File baseOutputFile = createTempFile("testUnmappedReadInclusion",".bam");
         spec.setOutputFileLocation(baseOutputFile);
-        spec.addAuxFile("c66bb2c3c5382e2acff09b2b359562bb",createTempFileFromBase(baseOutputFile.getAbsolutePath()));
+        spec.addAuxFile("4eeb9b07d3c9ddd4ea9eada7805903a2",createTempFileFromBase(baseOutputFile.getAbsolutePath()));
         spec.addAuxFile("fadcdf88597b9609c5f2a17f4c6eb455", createTempFileFromBase(baseOutputFile.getAbsolutePath().substring(0,baseOutputFile.getAbsolutePath().indexOf(".bam"))+".bai"));
 
         executeTest("testUnmappedReadInclusion",spec);
@@ -109,8 +109,8 @@ public void testMixedMappedAndUnmapped() {
         // our base file
         File baseOutputFile = createTempFile("testMixedMappedAndUnmapped",".bam");
         spec.setOutputFileLocation(baseOutputFile);
-        spec.addAuxFile("c64cff3ed376bc8f2977078dbdac4518",createTempFileFromBase(baseOutputFile.getAbsolutePath()));
-        spec.addAuxFile("fa90ff91ac0cc689c71a3460a3530b8b", createTempFileFromBase(baseOutputFile.getAbsolutePath().substring(0,baseOutputFile.getAbsolutePath().indexOf(".bam"))+".bai"));
+        spec.addAuxFile("70ac0317c0c13d885e6c2de4f837cdd3",createTempFileFromBase(baseOutputFile.getAbsolutePath()));
+        spec.addAuxFile("df469db01610ddb731868dfb28917142", createTempFileFromBase(baseOutputFile.getAbsolutePath().substring(0,baseOutputFile.getAbsolutePath().indexOf(".bam"))+".bai"));
 
         executeTest("testMixedMappedAndUnmapped",spec);
     }

diff --git a/public/gatk-root/pom.xml b/public/gatk-root/pom.xml
@@ -89,7 +89,7 @@
             <dependency>
                 <groupId>com.intel.gkl</groupId>
                 <artifactId>gkl</artifactId>
-                <version>0.5.2</version>
+                <version>0.6.0</version>
             </dependency>
             <dependency>
                 <groupId>log4j</groupId>

diff --git a/...lic/src/main/java/org/broadinstitute/gatk/tools/walkers/variantutils/VariantsToTable.java b/...lic/src/main/java/org/broadinstitute/gatk/tools/walkers/variantutils/VariantsToTable.java
@@ -98,7 +98,7 @@
  *
  * <h3>Caveats</h3>
  * <ul>
- *     <li>Some annotations cannot be applied to all variant sites, so VCFs typically contain records where some annotation values are missing. By default this tool the tool will emit the special value NA for the missing annotations if you request export of an annotation for which not all records have values. You can override this behavior by setting --errorIfMissingData in the command line. As a result, the tool will throw an error if a record is missing a value.</li>
+ *     <li>Some annotations cannot be applied to all variant sites, so VCFs typically contain records where some annotation values are missing. By default this tool will emit the special value NA for the missing annotations if you request export of an annotation for which not all records have values. You can override this behavior by setting --errorIfMissingData in the command line. As a result, the tool will throw an error if a record is missing a value.</li>
  *     <li>When you request export of sample-level annotations (FORMAT field annotations such as GT), the annotations will be identified per-sample. If multiple samples are present in the VCF, the columns will be ordered alphabetically by sample name (SM tag).</li>
  * </ul>
  *
@@ -181,7 +181,7 @@ public class VariantsToTable extends RodWalker<Integer, Integer> {
 
     /**
      * By default, this tool will write out NA values indicating missing data when it encounters a field without a value in a record.
-     * If this flag is added to the command, the tool will instead exit with an error if missing data is encountered..
+     * If this flag is added to the command, the tool will instead exit with an error if missing data is encountered.
      */
     @Advanced
     @Argument(fullName="errorIfMissingData", shortName="EMD", doc="If provided, we will require every record to contain every field", required=false)

diff --git a/...-tools-public/src/test/java/org/broadinstitute/gatk/tools/walkers/BAQIntegrationTest.java b/...-tools-public/src/test/java/org/broadinstitute/gatk/tools/walkers/BAQIntegrationTest.java
@@ -44,13 +44,13 @@ public class BAQIntegrationTest extends WalkerTest {
     // --------------------------------------------------------------------------------------------------------------
     @Test
     public void testPrintReadsNoBAQ() {
-        WalkerTestSpec spec = new WalkerTestSpec( baseCommand +" -baq OFF",  1, Arrays.asList("e33187ca383c7f5c75c5d547ec79e1cb"));
+        WalkerTestSpec spec = new WalkerTestSpec( baseCommand +" -baq OFF",  1, Arrays.asList("526dbbb390dbd36daa70ac35a8eddc36"));
         executeTest(String.format("testPrintReadsNoBAQ"), spec);
     }
 
     @Test
     public void testPrintReadsRecalBAQ() {
-        WalkerTestSpec spec = new WalkerTestSpec( baseCommand +" -baq RECALCULATE",  1, Arrays.asList("a25043edfbfa4f21a13cc21064b460df"));
+        WalkerTestSpec spec = new WalkerTestSpec( baseCommand +" -baq RECALCULATE",  1, Arrays.asList("25cb8f91e31a07cca2e141a119c9e020"));
         executeTest(String.format("testPrintReadsRecalBAQ"), spec);
     }
 }
diff --git a/...java/org/broadinstitute/gatk/tools/walkers/readutils/ClipReadsWalkersIntegrationTest.java b/...java/org/broadinstitute/gatk/tools/walkers/readutils/ClipReadsWalkersIntegrationTest.java
@@ -47,22 +47,22 @@ public void testClipper(String name, String args, String md51, String md52) {
     }
 
     final static String Q10ClipOutput = "b29c5bc1cb9006ed9306d826a11d444f";
-    @Test public void testQClip0() { testClipper("clipQSum0", "-QT 0", "117a4760b54308f81789c39b1c9de578", "bcf0d1e13537f764f006ef6d9b401ea7"); }
-    @Test public void testQClip2() { testClipper("clipQSum2", "-QT 2", Q10ClipOutput, "27847d330b962e60650df23b6efc8c3c"); }
-    @Test public void testQClip10() { testClipper("clipQSum10", "-QT 10", "b29c5bc1cb9006ed9306d826a11d444f", "27847d330b962e60650df23b6efc8c3c"); }
-    @Test public void testQClip20() { testClipper("clipQSum20", "-QT 20", "6c3434dce66ae5c9eeea502f10fb9bee", "f89ec5439e88f5a75433150da0069034"); }
+    @Test public void testQClip0() { testClipper("clipQSum0", "-QT 0", "117a4760b54308f81789c39b1c9de578", "2e617e0f0b4a1bf45dbb666da0a6a16c"); }
+    @Test public void testQClip2() { testClipper("clipQSum2", "-QT 2", Q10ClipOutput, "1b0d2317dfd1fd5a4d14eea3f560ac17"); }
+    @Test public void testQClip10() { testClipper("clipQSum10", "-QT 10", "b29c5bc1cb9006ed9306d826a11d444f", "1b0d2317dfd1fd5a4d14eea3f560ac17"); }
+    @Test public void testQClip20() { testClipper("clipQSum20", "-QT 20", "6c3434dce66ae5c9eeea502f10fb9bee", "3a9a10966cce58baf9e9400a2c5f99ca"); }
 
-    @Test public void testClipRange1() { testClipper("clipRange1", "-CT 1-5", "b5acd753226e25b1e088838c1aab9117", "987007f6e430cad4cb4a8d1cc1f45d91"); }
-    @Test public void testClipRange2() { testClipper("clipRange2", "-CT 1-5,11-15", "be4fcad5b666a5540028b774169cbad7", "ec4cf54ed50a6baf69dbf98782c19aeb"); }
+    @Test public void testClipRange1() { testClipper("clipRange1", "-CT 1-5", "b5acd753226e25b1e088838c1aab9117", "701f03388ffaeb0f92be1e719e2477df"); }
+    @Test public void testClipRange2() { testClipper("clipRange2", "-CT 1-5,11-15", "be4fcad5b666a5540028b774169cbad7", "7dc5da735c437b6523e0823a1ed0e981"); }
 
-    @Test public void testClipSeq() { testClipper("clipSeqX", "-X CCCCC", "db199bd06561c9f2122f6ffb07941fbc", "a9cf540e4ed2514061248a878e09a09c"); }
-    @Test public void testClipSeqFile() { testClipper("clipSeqXF", "-XF " + privateTestDir + "seqsToClip.fasta", "22cd33dbd06cc425ce3626360367bfca", "906871df304dd966682e5798d59fc86b"); }
+    @Test public void testClipSeq() { testClipper("clipSeqX", "-X CCCCC", "db199bd06561c9f2122f6ffb07941fbc", "daa41acd8c9f1a75c8107d0fd0db8cf0"); }
+    @Test public void testClipSeqFile() { testClipper("clipSeqXF", "-XF " + privateTestDir + "seqsToClip.fasta", "22cd33dbd06cc425ce3626360367bfca", "b1812de69c967059362139a269044362"); }
 
-    @Test public void testClipMulti() { testClipper("clipSeqMulti", "-QT 10 -CT 1-5 -XF " + privateTestDir + "seqsToClip.fasta -X CCCCC", "e4a88276a6f76ccc2b05a06c76305a1c", "b41995fea04034ca0427c4a71504ef83"); }
+    @Test public void testClipMulti() { testClipper("clipSeqMulti", "-QT 10 -CT 1-5 -XF " + privateTestDir + "seqsToClip.fasta -X CCCCC", "e4a88276a6f76ccc2b05a06c76305a1c", "9f999ed70684fdfb8dba019ff71741fe"); }
 
-    @Test public void testClipNs() { testClipper("testClipNs", "-QT 10 -CR WRITE_NS", Q10ClipOutput, "27847d330b962e60650df23b6efc8c3c"); }
-    @Test public void testClipQ0s() { testClipper("testClipQs", "-QT 10 -CR WRITE_Q0S", Q10ClipOutput, "195b8bdfc0186fdca742764aa9b06363"); }
-    @Test public void testClipSoft() { testClipper("testClipSoft", "-QT 10 -CR SOFTCLIP_BASES", Q10ClipOutput, "08d16051be0b3fa3453eb1e6ca48b098"); }
+    @Test public void testClipNs() { testClipper("testClipNs", "-QT 10 -CR WRITE_NS", Q10ClipOutput, "1b0d2317dfd1fd5a4d14eea3f560ac17"); }
+    @Test public void testClipQ0s() { testClipper("testClipQs", "-QT 10 -CR WRITE_Q0S", Q10ClipOutput, "b7ce95f277d5f66b7f5a60ffbf9692cf"); }
+    @Test public void testClipSoft() { testClipper("testClipSoft", "-QT 10 -CR SOFTCLIP_BASES", Q10ClipOutput, "55c9d86c18c5a59a98429e8a5076e871"); }
 
     @Test
     public void testUseOriginalQuals() {
@@ -74,7 +74,7 @@ public void testUseOriginalQuals() {
                         " -OQ -QT 4 -CR WRITE_Q0S" +
                         " -o %s -os %s",
                 2,
-                Arrays.asList("a2819d54b2110150e38511f5a55db91d", "55c01ccc2e84481b22d3632cdb06c8ba"));
+                Arrays.asList("0e4c116fa07c3d8190eefe6968a0b819", "55c01ccc2e84481b22d3632cdb06c8ba"));
         executeTest("clipOriginalQuals", spec);
     }
 }
diff --git a/.../test/java/org/broadinstitute/gatk/tools/walkers/readutils/PrintReadsIntegrationTest.java b/.../test/java/org/broadinstitute/gatk/tools/walkers/readutils/PrintReadsIntegrationTest.java
@@ -59,27 +59,27 @@ public String toString() {
     @DataProvider(name = "PRTest")
     public Object[][] createPrintReadsTestData() {
         return new Object[][]{
-                {new PRTest(hg18Reference, new String[]{"HiSeq.1mb.bam"}, "", "0aa3505ba61e05663e629011dd54e423")},
+                {new PRTest(hg18Reference, new String[]{"HiSeq.1mb.bam"}, "", "83d1454dc01cd2e7458dad4012695f64")},
                 {new PRTest(hg18Reference, new String[]{"HiSeq.1mb.bam"}, " -compress 0", "0aec10d19e0dbdfe1d0cbb3eddaf623a")},
-                {new PRTest(hg18Reference, new String[]{"HiSeq.1mb.bam"}, " -simplifyBAM", "c565d9cd4838a313e7bdb30530c0cf71")},
-                {new PRTest(hg18Reference, new String[]{"HiSeq.1mb.bam"}, " -n 10", "917440a38aba707ec0e012168590981a")},
+                {new PRTest(hg18Reference, new String[]{"HiSeq.1mb.bam"}, " -simplifyBAM", "60255a68df1b8f2fbba373d75274f0de")},
+                {new PRTest(hg18Reference, new String[]{"HiSeq.1mb.bam"}, " -n 10", "eb7c6bacca5fee09b8df50880eb81ee6")},
                 // See: GATKBAMIndex.getStartOfLastLinearBin(), BAMScheduler.advance(), IntervalOverlapFilteringIterator.advance()
-                {new PRTest(b37KGReference, new String[]{"unmappedFlagReadsInLastLinearBin.bam"}, "", "0b58c903f54e8543a8b2ce1439aa769b")},
-                {new PRTest(b37KGReference, new String[]{"unmappedFlagReadsInLastLinearBin.bam"}, " -L 1", "5b1154cc81dba6bcfe76188e4df8d79c")},
-                {new PRTest(b37KGReference, new String[]{"unmappedFlagReadsInLastLinearBin.cram"}, " -L 1:10001 -L GL000192.1:500204", "a84efdc3d4a8d6329b5f0b494dd280d2")},
-                {new PRTest(b37KGReference, new String[]{"unmappedFlagReadsInLastLinearBin.bam"}, " -L unmapped", "cbd3d1d50c8674f79033aa8c36aa3cd1")},
-                {new PRTest(b37KGReference, new String[]{"unmappedFlagReadsInLastLinearBin.bam"}, " -L 1 -L unmapped", "5b1154cc81dba6bcfe76188e4df8d79c")},
-                {new PRTest(b37KGReference, new String[]{"oneReadAllInsertion.bam"}, "",  "e212d1799ae797e781b17e630656a9a1")},
-                {new PRTest(b37KGReference, new String[]{"NA12878.1_10mb_2_10mb.bam"}, "",  "0387c61303140d8899fcbfdd3e72ed80")},
+                {new PRTest(b37KGReference, new String[]{"unmappedFlagReadsInLastLinearBin.bam"}, "", "3d67c398ce2ac1deeddbccbd850380a7")},
+                {new PRTest(b37KGReference, new String[]{"unmappedFlagReadsInLastLinearBin.bam"}, " -L 1", "37cdd8871843693f2650d7b48c8ae1d4")},
+                {new PRTest(b37KGReference, new String[]{"unmappedFlagReadsInLastLinearBin.cram"}, " -L 1:10001 -L GL000192.1:500204", "4d63fd6e977a53e5d9590bd030b40bd0")},
+                {new PRTest(b37KGReference, new String[]{"unmappedFlagReadsInLastLinearBin.bam"}, " -L unmapped", "a834400e3bd69045eb8a9e94131633f5")},
+                {new PRTest(b37KGReference, new String[]{"unmappedFlagReadsInLastLinearBin.bam"}, " -L 1 -L unmapped", "37cdd8871843693f2650d7b48c8ae1d4")},
+                {new PRTest(b37KGReference, new String[]{"oneReadAllInsertion.bam"}, "",  "6c04aac25e2136fee395897aac96bea8")},
+                {new PRTest(b37KGReference, new String[]{"NA12878.1_10mb_2_10mb.bam"}, "",  "57a9bc1f7dd4e7717ee796c484bcf45a")},
                 // Tests for filtering options
                 {new PRTest(b37KGReference, new String[]{"NA12878.1_10mb_2_10mb.bam", "NA20313.highCoverageRegion.bam"},
-                        "",  "ad56da66be0bdab5a8992de9617ae6a5")},
+                        "",  "e691d61df10f7614d73c8ecb46c75ee1")},
                 {new PRTest(b37KGReference, new String[]{"NA12878.1_10mb_2_10mb.bam", "NA20313.highCoverageRegion.bam"},
-                        " -readGroup SRR359098",  "c3bfe28722a665e666098dbb7048a9f1")},
+                        " -readGroup SRR359098",  "7644eab114bf537411218f782d75a6a6")},
                 {new PRTest(b37KGReference, new String[]{"NA12878.1_10mb_2_10mb.bam", "NA20313.highCoverageRegion.bam"},
-                        " -readGroup 20FUK.3 -sn NA12878",  "8191f8d635d00b1f4d0993b785cc46c5")},
+                        " -readGroup 20FUK.3 -sn NA12878",  "351d5da29874033e50d29c5c36575a6c")},
                 {new PRTest(b37KGReference, new String[]{"NA12878.1_10mb_2_10mb.bam", "NA20313.highCoverageRegion.bam"},
-                        " -sn na12878",  "92a85b4223ec45e114f12a1fe6ebbaeb")},
+                        " -sn na12878",  "9056d852418dd2083f38e3eac1551fcd")},
         };
     }
 

diff --git a/...est/java/org/broadinstitute/gatk/tools/walkers/readutils/SplitSamFileIntegrationTest.java b/...est/java/org/broadinstitute/gatk/tools/walkers/readutils/SplitSamFileIntegrationTest.java
@@ -43,9 +43,9 @@ public void testSplitSamFile() {
                         " --outputRoot " + prefix,
                 Collections.<String>emptyList()
         );
-        addSplitOutput(spec, prefix, "NA12878", "3e28b666fb673be138eca9bd3db9520b");
-        addSplitOutput(spec, prefix, "NA12891", "af01069bc3da4252ce8417a03d11f48b");
-        addSplitOutput(spec, prefix, "NA12892", "cfa1cb6aaca03900160bd5627f4f698b");
+        addSplitOutput(spec, prefix, "NA12878", "356bddf614a44a0234f7b116f5cde998");
+        addSplitOutput(spec, prefix, "NA12891", "5dd92a0089e3f781e77d94010264b9fd");
+        addSplitOutput(spec, prefix, "NA12892", "ea8f16c18c89b49ce9d32d76c6af75f9");
         executeTest("testSplitSamFile", spec);
     }
 

diff --git a/...tk-utils/src/main/java/org/broadinstitute/gatk/utils/variant/GATKVariantContextUtils.java b/...tk-utils/src/main/java/org/broadinstitute/gatk/utils/variant/GATKVariantContextUtils.java
@@ -851,9 +851,13 @@ private static GenotypesContext createGenotypesWithSubsettedLikelihoods(final Ge
 
                 if ( newLikelihoods == null || (originalVC.getAttributeAsInt(VCFConstants.DEPTH_KEY, 0) == 0 && likelihoodsAreUninformative(newLikelihoods) )) {
                     gb.noPL();
+                    gb.noGQ();
                 } else {
                     gb.PL(newLikelihoods);
+                    final int PLindex = MathUtils.maxElementIndex(newLikelihoods);
+                    gb.log10PError(GenotypeLikelihoods.getGQLog10FromLikelihoods(PLindex, newLikelihoods));
                 }
+
             }
 
             // create the new strand allele counts array from the used alleles