From 7852871f7d144a5f622777cebdc4b0c3cc22b3b2 Mon Sep 17 00:00:00 2001 From: Dror Kessler Date: Sun, 25 Jun 2023 23:14:47 +0300 Subject: [PATCH 1/6] hmer ondel must have mon length --- .../tools/walkers/annotator/flow/FlowAnnotatorBase.java | 2 +- .../tools/walkers/annotator/flow/FlowAnnotatorUnitTest.java | 2 +- 2 files changed, 2 insertions(+), 2 deletions(-) diff --git a/src/main/java/org/broadinstitute/hellbender/tools/walkers/annotator/flow/FlowAnnotatorBase.java b/src/main/java/org/broadinstitute/hellbender/tools/walkers/annotator/flow/FlowAnnotatorBase.java index 30531f9b153..e575547daf4 100644 --- a/src/main/java/org/broadinstitute/hellbender/tools/walkers/annotator/flow/FlowAnnotatorBase.java +++ b/src/main/java/org/broadinstitute/hellbender/tools/walkers/annotator/flow/FlowAnnotatorBase.java @@ -295,7 +295,7 @@ protected void isHmerIndel(final VariantContext vc, final LocalContext localCont if ( diffIndex < 0 ) { continue; } - if ( Math.max(refKey[diffIndex], altKey[diffIndex]) == 0 ) { + if ( Math.min(refKey[diffIndex], altKey[diffIndex]) == 0 ) { continue; } diff --git a/src/test/java/org/broadinstitute/hellbender/tools/walkers/annotator/flow/FlowAnnotatorUnitTest.java b/src/test/java/org/broadinstitute/hellbender/tools/walkers/annotator/flow/FlowAnnotatorUnitTest.java index 6a71d8c82aa..be0e16cbc64 100644 --- a/src/test/java/org/broadinstitute/hellbender/tools/walkers/annotator/flow/FlowAnnotatorUnitTest.java +++ b/src/test/java/org/broadinstitute/hellbender/tools/walkers/annotator/flow/FlowAnnotatorUnitTest.java @@ -57,7 +57,7 @@ public Object[][] getTestData() { { // not hmer indel "TATCT CA TTGACCAA", "C", - "del", "1", "1", "A", "ATCTC", "TTGAC", "0.3", "NA", "non-h-indel" + "del", "1", "0", "", "ATCTC", "TTGAC", "0.3", "NA", "non-h-indel" }, { // del hmer indel From d6590283394ad9c9242b3ee08190b8aadaba8d92 Mon Sep 17 00:00:00 2001 From: Dror Kessler Date: Sun, 16 Jul 2023 12:18:02 +0300 Subject: [PATCH 2/6] Revert "hmer ondel must have mon length" This reverts commit 7852871f7d144a5f622777cebdc4b0c3cc22b3b2. --- .../tools/walkers/annotator/flow/FlowAnnotatorBase.java | 2 +- .../tools/walkers/annotator/flow/FlowAnnotatorUnitTest.java | 2 +- 2 files changed, 2 insertions(+), 2 deletions(-) diff --git a/src/main/java/org/broadinstitute/hellbender/tools/walkers/annotator/flow/FlowAnnotatorBase.java b/src/main/java/org/broadinstitute/hellbender/tools/walkers/annotator/flow/FlowAnnotatorBase.java index e575547daf4..30531f9b153 100644 --- a/src/main/java/org/broadinstitute/hellbender/tools/walkers/annotator/flow/FlowAnnotatorBase.java +++ b/src/main/java/org/broadinstitute/hellbender/tools/walkers/annotator/flow/FlowAnnotatorBase.java @@ -295,7 +295,7 @@ protected void isHmerIndel(final VariantContext vc, final LocalContext localCont if ( diffIndex < 0 ) { continue; } - if ( Math.min(refKey[diffIndex], altKey[diffIndex]) == 0 ) { + if ( Math.max(refKey[diffIndex], altKey[diffIndex]) == 0 ) { continue; } diff --git a/src/test/java/org/broadinstitute/hellbender/tools/walkers/annotator/flow/FlowAnnotatorUnitTest.java b/src/test/java/org/broadinstitute/hellbender/tools/walkers/annotator/flow/FlowAnnotatorUnitTest.java index be0e16cbc64..6a71d8c82aa 100644 --- a/src/test/java/org/broadinstitute/hellbender/tools/walkers/annotator/flow/FlowAnnotatorUnitTest.java +++ b/src/test/java/org/broadinstitute/hellbender/tools/walkers/annotator/flow/FlowAnnotatorUnitTest.java @@ -57,7 +57,7 @@ public Object[][] getTestData() { { // not hmer indel "TATCT CA TTGACCAA", "C", - "del", "1", "0", "", "ATCTC", "TTGAC", "0.3", "NA", "non-h-indel" + "del", "1", "1", "A", "ATCTC", "TTGAC", "0.3", "NA", "non-h-indel" }, { // del hmer indel From 86dfd3d6a5bd05dca0e5a220beb1a7fbd25c5ef8 Mon Sep 17 00:00:00 2001 From: Dror Kessler Date: Sun, 16 Jul 2023 12:21:36 +0300 Subject: [PATCH 3/6] remove superfluous variant type condition --- .../tools/walkers/annotator/flow/FlowAnnotatorBase.java | 4 ---- 1 file changed, 4 deletions(-) diff --git a/src/main/java/org/broadinstitute/hellbender/tools/walkers/annotator/flow/FlowAnnotatorBase.java b/src/main/java/org/broadinstitute/hellbender/tools/walkers/annotator/flow/FlowAnnotatorBase.java index 30531f9b153..0c4a07f015a 100644 --- a/src/main/java/org/broadinstitute/hellbender/tools/walkers/annotator/flow/FlowAnnotatorBase.java +++ b/src/main/java/org/broadinstitute/hellbender/tools/walkers/annotator/flow/FlowAnnotatorBase.java @@ -204,10 +204,6 @@ protected void variantType(final VariantContext vc, final LocalContext localCont if ((localContext.hmerIndelLength.get(i)==null) || (localContext.hmerIndelLength.get(i)==0)){ isHmer=false; } - if ((localContext.hmerIndelLength.get(i)==1) && (localContext.indel.equals(C_DELETE))){ // new definition 1->0 has hmer indel 1 - isHmer=false; - } - } if (isHmer){ From d1918210e8483c0e3a87ff01008f28749ff8098e Mon Sep 17 00:00:00 2001 From: Dror Kessler Date: Mon, 31 Jul 2023 13:22:16 +0100 Subject: [PATCH 4/6] fix error message to actually reflect missing argument --- .../tools/walkers/annotator/flow/FlowAnnotatorBase.java | 3 ++- 1 file changed, 2 insertions(+), 1 deletion(-) diff --git a/src/main/java/org/broadinstitute/hellbender/tools/walkers/annotator/flow/FlowAnnotatorBase.java b/src/main/java/org/broadinstitute/hellbender/tools/walkers/annotator/flow/FlowAnnotatorBase.java index 0c4a07f015a..acf1c74bf9c 100644 --- a/src/main/java/org/broadinstitute/hellbender/tools/walkers/annotator/flow/FlowAnnotatorBase.java +++ b/src/main/java/org/broadinstitute/hellbender/tools/walkers/annotator/flow/FlowAnnotatorBase.java @@ -4,6 +4,7 @@ import htsjdk.variant.variantcontext.VariantContext; import org.apache.logging.log4j.LogManager; import org.apache.logging.log4j.Logger; +import org.broadinstitute.hellbender.cmdline.StandardArgumentDefinitions; import org.broadinstitute.hellbender.engine.ReferenceContext; import org.broadinstitute.hellbender.exceptions.GATKException; import org.broadinstitute.hellbender.tools.walkers.annotator.InfoFieldAnnotation; @@ -149,7 +150,7 @@ private String establishReadGroupFlowOrder(final LocalContext localContext, fina // if here, no flow order was found. may we use a default? if ( isActualFlowOrderRequired() ) { localContext.generateAnnotation = false; - flowMissingOneShotLogger.warn("this.getClass().getSimpleName() + \" annotation will not be calculated, no '\" + StandardArgumentDefinitions.FLOW_ORDER_FOR_ANNOTATIONS + \"' argument provided\""); + flowMissingOneShotLogger.warn(this.getClass().getSimpleName() + " annotation will not be calculated, no '" + StandardArgumentDefinitions.FLOW_ORDER_FOR_ANNOTATIONS + "' argument provided"); } return FlowBasedRead.DEFAULT_FLOW_ORDER; From 44ece892a6a1cd35f64295779a9acfb4dda57de3 Mon Sep 17 00:00:00 2001 From: Dror Kessler Date: Sat, 11 Nov 2023 12:36:34 +0200 Subject: [PATCH 5/6] fixed unittest to include variant type --- .../walkers/annotator/flow/FlowAnnotatorUnitTest.java | 7 ++++--- 1 file changed, 4 insertions(+), 3 deletions(-) diff --git a/src/test/java/org/broadinstitute/hellbender/tools/walkers/annotator/flow/FlowAnnotatorUnitTest.java b/src/test/java/org/broadinstitute/hellbender/tools/walkers/annotator/flow/FlowAnnotatorUnitTest.java index 6a71d8c82aa..054f833c54e 100644 --- a/src/test/java/org/broadinstitute/hellbender/tools/walkers/annotator/flow/FlowAnnotatorUnitTest.java +++ b/src/test/java/org/broadinstitute/hellbender/tools/walkers/annotator/flow/FlowAnnotatorUnitTest.java @@ -27,7 +27,8 @@ public class FlowAnnotatorUnitTest extends GATKBaseTest { new HmerIndelNuc(), new HmerMotifs(), new GcContent(), - new CycleSkipStatus() + new CycleSkipStatus(), + new VariantType(), }; @DataProvider(name = "testData") @@ -57,7 +58,7 @@ public Object[][] getTestData() { { // not hmer indel "TATCT CA TTGACCAA", "C", - "del", "1", "1", "A", "ATCTC", "TTGAC", "0.3", "NA", "non-h-indel" + "del", "1", "1", "A", "ATCTC", "TTGAC", "0.3", "NA", "h-indel" }, { // del hmer indel @@ -99,7 +100,7 @@ public void testBasic(final String refBases, final String altAllele, // check that all expected attributes are there String[] testResults = {indelClass, indelLength, hmerIndelLength, hmerIndelNuc, leftMotif, rightMotif, gcContent, cycleskipStatus, variantType}; - for ( int n = 0 ; n < 8 ; n++ ) { + for ( int n = 0 ; n < 9 ; n++ ) { String key = expectedAttrs.get(n); String elem = testResults[n]; String keyMsg = "on " + key + " " + msg; From 51bd318e27eae81a3e6990a717b63573137f80ec Mon Sep 17 00:00:00 2001 From: Dror Kessler Date: Sat, 11 Nov 2023 12:40:09 +0200 Subject: [PATCH 6/6] Remove conflict --- .../tools/walkers/annotator/flow/FlowAnnotatorUnitTest.java | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/src/test/java/org/broadinstitute/hellbender/tools/walkers/annotator/flow/FlowAnnotatorUnitTest.java b/src/test/java/org/broadinstitute/hellbender/tools/walkers/annotator/flow/FlowAnnotatorUnitTest.java index 054f833c54e..5e399ea662c 100644 --- a/src/test/java/org/broadinstitute/hellbender/tools/walkers/annotator/flow/FlowAnnotatorUnitTest.java +++ b/src/test/java/org/broadinstitute/hellbender/tools/walkers/annotator/flow/FlowAnnotatorUnitTest.java @@ -28,7 +28,7 @@ public class FlowAnnotatorUnitTest extends GATKBaseTest { new HmerMotifs(), new GcContent(), new CycleSkipStatus(), - new VariantType(), + new VariantType() }; @DataProvider(name = "testData")