DEV-950: Refactor a bunch of things in gene disruption factory

hartwigmedical · Oct 31, 2019 · eb6819a · eb6819a
1 parent 0f546ad
commit eb6819a
Showing 1 changed file with 7 additions and 6 deletions.
diff --git a/...java/com/hartwig/hmftools/patientreporter/structural/ReportableGeneDisruptionFactory.java b/...java/com/hartwig/hmftools/patientreporter/structural/ReportableGeneDisruptionFactory.java
@@ -6,6 +6,7 @@
 
 import com.google.common.collect.Lists;
 import com.google.common.collect.Maps;
+import com.hartwig.hmftools.common.numeric.Doubles;
 import com.hartwig.hmftools.common.variant.structural.annotation.ReportableDisruption;
 
 import org.apache.commons.lang3.tuple.Pair;
@@ -34,16 +35,17 @@ static List<ReportableGeneDisruption> convert(@NotNull List<ReportableDisruption
                         Math.min(primaryDisruptionLeft.undisruptedCopyNumber(), primaryDisruptionRight.undisruptedCopyNumber());
 
                 Double ploidyLeft = primaryDisruptionLeft.ploidy();
-                if (ploidyLeft != null && !ploidyLeft.equals(primaryDisruptionRight.ploidy())) {
+                Double ploidyRight = primaryDisruptionRight.ploidy();
+                if (ploidyLeft != null && ploidyRight != null && !Doubles.equal(ploidyLeft, ploidyRight)) {
                     LOGGER.warn("The disrupted copy number of a paired sv is not the same on {}", primaryDisruptionLeft.gene());
                 }
                 reportableDisruptions.add(ImmutableReportableGeneDisruption.builder()
                         .location(primaryDisruptionLeft.chromosome() + primaryDisruptionLeft.chrBand())
                         .gene(primaryDisruptionLeft.gene())
                         .type(primaryDisruptionLeft.type())
                         .range(rangeField(pairedDisruption))
-                        .ploidy(primaryDisruptionLeft.ploidy() >= 0 ? primaryDisruptionLeft.ploidy() : 0)
-                        .undisruptedCopyNumber(lowestUndisruptedCopyNumber >= 0 ? lowestUndisruptedCopyNumber : 0)
+                        .ploidy(primaryDisruptionLeft.ploidy())
+                        .undisruptedCopyNumber(Math.max(0, lowestUndisruptedCopyNumber))
                         .firstAffectedExon(primaryDisruptionLeft.exonUp())
                         .build());
             } else {
@@ -52,9 +54,8 @@ static List<ReportableGeneDisruption> convert(@NotNull List<ReportableDisruption
                         .gene(primaryDisruptionLeft.gene())
                         .type(primaryDisruptionLeft.type())
                         .range(rangeField(pairedDisruption))
-                        .ploidy(primaryDisruptionLeft.ploidy() >= 0 ? primaryDisruptionLeft.ploidy() : 0)
-                        .undisruptedCopyNumber(
-                                primaryDisruptionLeft.undisruptedCopyNumber() >= 0 ? primaryDisruptionLeft.undisruptedCopyNumber() : 0)
+                        .ploidy(primaryDisruptionLeft.ploidy())
+                        .undisruptedCopyNumber(Math.max(0, primaryDisruptionLeft.undisruptedCopyNumber()))
                         .firstAffectedExon(primaryDisruptionLeft.exonUp())
                         .build());
             }