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Ultima.flow annotations.fix #8442

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merged 6 commits into from
Nov 13, 2023
Merged

Ultima.flow annotations.fix #8442

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7852871
hmer ondel must have mon length
dror27 Jun 25, 2023
d659028
Revert "hmer ondel must have mon length"
dror27 Jul 16, 2023
86dfd3d
remove superfluous variant type condition
dror27 Jul 16, 2023
d191821
fix error message to actually reflect missing argument
dror27 Jul 31, 2023
44ece89
fixed unittest to include variant type
dror27 Nov 11, 2023
51bd318
Remove conflict
dror27 Nov 11, 2023
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7 changes: 2 additions & 5 deletions ...in/java/org/broadinstitute/hellbender/tools/walkers/annotator/flow/FlowAnnotatorBase.java
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Original file line number Diff line number Diff line change
Expand Up @@ -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;
Expand Down Expand Up @@ -149,7 +150,7 @@
// 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");

Check warning on line 153 in src/main/java/org/broadinstitute/hellbender/tools/walkers/annotator/flow/FlowAnnotatorBase.java

View check run for this annotation

Codecov / codecov/patch

src/main/java/org/broadinstitute/hellbender/tools/walkers/annotator/flow/FlowAnnotatorBase.java#L153 

Added line #L153 was not covered by tests
}

return FlowBasedRead.DEFAULT_FLOW_ORDER;
Expand Down Expand Up @@ -204,10 +205,6 @@
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){
Expand Down
7 changes: 4 additions & 3 deletions ...ava/org/broadinstitute/hellbender/tools/walkers/annotator/flow/FlowAnnotatorUnitTest.java
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Expand Up @@ -27,7 +27,8 @@ public class FlowAnnotatorUnitTest extends GATKBaseTest {
new HmerIndelNuc(),
new HmerMotifs(),
new GcContent(),
new CycleSkipStatus()
new CycleSkipStatus(),
new VariantType()
};

@DataProvider(name = "testData")
Expand Down Expand Up @@ -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
Expand Down Expand Up @@ -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;
Expand Down