purple tumor only mode

hartwigmedical · Oct 30, 2019 · 65aa394 · 65aa394
1 parent 449f3ee
commit 65aa394
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Showing 4 changed files with 10 additions and 3 deletions.
diff --git a/purity-ploidy-estimator/README.md b/purity-ploidy-estimator/README.md
@@ -973,6 +973,7 @@ Threads | Elapsed Time| CPU Time | Peak Mem
 ## Version History and Download Links
 - Upcoming
   - Driver catalog written to DB
+  - Tumor only mode (disables somatic fitting)
 - [2.34](https://github.com/hartwigmedical/hmftools/releases/tag/purple-v2.34)
   - Added driver catalog to file output
   - Purity sunrise plot now supports somatic inferred purity 

diff --git a/...-estimator/src/main/java/com/hartwig/hmftools/purple/PurityPloidyEstimateApplication.java b/...-estimator/src/main/java/com/hartwig/hmftools/purple/PurityPloidyEstimateApplication.java
@@ -137,7 +137,9 @@ private PurityPloidyEstimateApplication(final String... args)
             // Load structural and somatic variants
             final PurpleStructuralVariantSupplier structuralVariants = structuralVariants(configSupplier);
             final List<SomaticVariant> allSomatics = somaticVariants(configSupplier);
-            final List<SomaticVariant> snpSomatics = allSomatics.stream().filter(SomaticVariant::isSnp).collect(Collectors.toList());
+            final List<SomaticVariant> fittingSomatics = config.tumorOnly()
+                    ? Collections.emptyList()
+                    : allSomatics.stream().filter(SomaticVariant::isSnp).collect(Collectors.toList());
 
             LOGGER.info("Applying segmentation");
             final Segmentation segmentation = new Segmentation(configSupplier, cobaltGender);
@@ -146,8 +148,7 @@ private PurityPloidyEstimateApplication(final String... args)
             LOGGER.info("Fitting purity");
             final FitScoreConfig fitScoreConfig = configSupplier.fitScoreConfig();
             final FittedRegionFactory fittedRegionFactory = createFittedRegionFactory(averageTumorDepth, cobaltGender, fitScoreConfig);
-            final BestFit bestFit =
-                    fitPurity(executorService, configSupplier, cobaltGender, snpSomatics, observedRegions, fittedRegionFactory);
+            final BestFit bestFit = fitPurity(executorService, configSupplier, cobaltGender, fittingSomatics, observedRegions, fittedRegionFactory);
             final FittedPurity fittedPurity = bestFit.fit();
             final PurityAdjuster purityAdjuster = new PurityAdjuster(cobaltGender, fittedPurity);
 

diff --git a/purity-ploidy-estimator/src/main/java/com/hartwig/hmftools/purple/config/CommonConfig.java b/purity-ploidy-estimator/src/main/java/com/hartwig/hmftools/purple/config/CommonConfig.java
@@ -31,6 +31,8 @@ public interface CommonConfig {
     @NotNull
     String version();
 
+    boolean tumorOnly();
+
     default int windowSize() {
         return WINDOW_SIZE;
     }

diff --git a/purity-ploidy-estimator/src/main/java/com/hartwig/hmftools/purple/config/ConfigSupplier.java b/purity-ploidy-estimator/src/main/java/com/hartwig/hmftools/purple/config/ConfigSupplier.java
@@ -24,6 +24,7 @@ public class ConfigSupplier {
     private static final String GC_PROFILE = "gc_profile";
     private static final String AMBER = "amber";
     private static final String COBALT = "cobalt";
+    private static final String TUMOR_ONLY = "tumor_only";
 
     private static final String MIN_DIPLOID_TUMOR_RATIO_COUNT = "min_diploid_tumor_ratio_count";
     private static final int MIN_DIPLOID_TUMOR_RATIO_COUNT_DEFAULT = 30;
@@ -32,6 +33,7 @@ public class ConfigSupplier {
     private static final int MIN_DIPLOID_TUMOR_RATIO_COUNT_AT_CENTROMERE_DEFAULT = 50;
 
     public static void addOptions(@NotNull Options options) {
+        options.addOption(TUMOR_ONLY, false, "Tumor only mode. Disables somatic fitting.");
         options.addOption(REF_SAMPLE, true, "Name of the reference sample. This should correspond to the value used in AMBER and COBALT.");
         options.addOption(TUMOR_SAMPLE, true, "Name of the tumor sample. This should correspond to the value used in AMBER and COBALT.");
 
@@ -106,6 +108,7 @@ public ConfigSupplier(@NotNull final String version, @NotNull CommandLine cmd, @
                 .amberDirectory(amberDirectory)
                 .cobaltDirectory(cobaltDirectory)
                 .gcProfile(gcProfile)
+                .tumorOnly(cmd.hasOption(TUMOR_ONLY))
                 .build();
 
         LOGGER.info("Reference Sample: {}, Tumor Sample: {}", commonConfig.refSample(), commonConfig.tumorSample());