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broadinstitute · Mar 14, 2019 · 5ca8d0b · 5ca8d0b
1 parent b3eac71
commit 5ca8d0b
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Showing 2 changed files with 14 additions and 23 deletions.
diff --git a/...n/java/org/broadinstitute/hellbender/tools/walkers/readorientation/CollectF1R2Counts.java b/...n/java/org/broadinstitute/hellbender/tools/walkers/readorientation/CollectF1R2Counts.java
@@ -5,7 +5,7 @@
 import htsjdk.samtools.util.Histogram;
 import org.broadinstitute.barclay.argparser.Argument;
 import org.broadinstitute.barclay.argparser.CommandLineProgramProperties;
-import org.broadinstitute.hellbender.cmdline.programgroups.ShortVariantDiscoveryProgramGroup;
+import org.broadinstitute.hellbender.cmdline.programgroups.CoverageAnalysisProgramGroup;
 import org.broadinstitute.hellbender.engine.*;
 import org.broadinstitute.hellbender.engine.filters.ReadFilter;
 import org.broadinstitute.hellbender.exceptions.UserException;
@@ -44,16 +44,13 @@
 @CommandLineProgramProperties(
         summary = "Collect F1R2 read counts for the Mutect2 orientation bias mixture model filter",
         oneLineSummary = "Collect F1R2 read counts for the Mutect2 orientation bias mixture model filter",
-        programGroup = ShortVariantDiscoveryProgramGroup.class
+        programGroup = CoverageAnalysisProgramGroup.class
 )
 
 public class CollectF1R2Counts extends LocusWalker {
     public static final String ALT_DATA_TABLE_LONG_NAME = "alt-table";
-    public static final String ALT_DATA_TABLE_SHORT_NAME = "at";
     public static final String ALT_DEPTH1_HISTOGRAM_LONG_NAME = "alt-hist";
-    public static final String ALT_DEPTH1_HISTOGRAM_SHORT_NAME = "ah";
     public static final String REF_SITE_METRICS_LONG_NAME = "ref-hist";
-    public static final String REF_SITE_METRICS_SHORT_NAME = "rh";
     public static final String MIN_MEDIAN_MQ_LONG_NAME = "median-mq";
     public static final String MIN_BASE_QUALITY_LONG_NAME = "min-bq";
     public static final String MAX_DEPTH_LONG_NAME = "max-depth";
@@ -64,13 +61,13 @@ public class CollectF1R2Counts extends LocusWalker {
     @Argument(fullName = MIN_BASE_QUALITY_LONG_NAME, doc = "exclude bases below this quality from pileup", optional = true)
     private int MINIMUM_BASE_QUALITY = 20;
 
-    @Argument(shortName = ALT_DATA_TABLE_SHORT_NAME, fullName = ALT_DATA_TABLE_LONG_NAME, doc = "a tab-separated output table of pileup data over alt sites")
+    @Argument(fullName = ALT_DATA_TABLE_LONG_NAME, doc = "a tab-separated output table of pileup data over alt sites")
     private File altDataTable = null;
 
-    @Argument(shortName = REF_SITE_METRICS_SHORT_NAME, fullName = REF_SITE_METRICS_LONG_NAME, doc = "a metrics file with overall summary metrics and reference context-specific depth histograms")
+    @Argument(fullName = REF_SITE_METRICS_LONG_NAME, doc = "a metrics file with overall summary metrics and reference context-specific depth histograms")
     private File refMetricsOutput = null;
 
-    @Argument(shortName = ALT_DEPTH1_HISTOGRAM_SHORT_NAME, fullName = ALT_DEPTH1_HISTOGRAM_LONG_NAME, doc = "a histogram of alt sites with alt depth = 1")
+    @Argument(fullName = ALT_DEPTH1_HISTOGRAM_LONG_NAME, doc = "a histogram of alt sites with alt depth = 1")
     private File altMetricsOutput = null;
 
     @Argument(fullName = MAX_DEPTH_LONG_NAME, doc = "sites with depth higher than this value will be grouped", optional = true)

diff --git a/...rg/broadinstitute/hellbender/tools/walkers/readorientation/LearnReadOrientationModel.java b/...rg/broadinstitute/hellbender/tools/walkers/readorientation/LearnReadOrientationModel.java
@@ -47,19 +47,13 @@ public class LearnReadOrientationModel extends CommandLineProgram {
     public static final String MAX_EM_ITERATIONS_LONG_NAME = "num-em-iterations";
     public static final String MAX_DEPTH_LONG_NAME = "max-depth";
 
-    @Argument(fullName = CollectF1R2Counts.REF_SITE_METRICS_LONG_NAME,
-            shortName = CollectF1R2Counts.REF_SITE_METRICS_SHORT_NAME,
-            doc = "histograms of depths over ref sites for each reference context")
+    @Argument(fullName = CollectF1R2Counts.REF_SITE_METRICS_LONG_NAME, doc = "histograms of depths over ref sites for each reference context")
     private List<File> refHistogramFiles;
 
-    @Argument(fullName = CollectF1R2Counts.ALT_DATA_TABLE_LONG_NAME,
-            shortName = CollectF1R2Counts.ALT_DATA_TABLE_SHORT_NAME,
-            doc = "a table of F1R2 and depth counts")
+    @Argument(fullName = CollectF1R2Counts.ALT_DATA_TABLE_LONG_NAME, doc = "a table of F1R2 and depth counts")
     private List<File> altDataTables;
 
-    @Argument(fullName = CollectF1R2Counts.ALT_DEPTH1_HISTOGRAM_LONG_NAME,
-            shortName = CollectF1R2Counts.ALT_DEPTH1_HISTOGRAM_SHORT_NAME,
-            doc = "histograms of depth 1 alt sites", optional = true)
+    @Argument(fullName = CollectF1R2Counts.ALT_DEPTH1_HISTOGRAM_LONG_NAME, doc = "histograms of depth 1 alt sites", optional = true)
     private List<File> altHistogramFiles = null;
 
     @Argument(fullName = StandardArgumentDefinitions.OUTPUT_LONG_NAME, shortName = StandardArgumentDefinitions.OUTPUT_SHORT_NAME, doc = "table of artifact priors")
@@ -80,6 +74,10 @@ public class LearnReadOrientationModel extends CommandLineProgram {
 
     @Override
     protected void onStartup(){
+        Utils.validate(refHistogramFiles.size() == altDataTables.size() && altDataTables.size() == altHistogramFiles.size(),
+                "The numbers of ref histograms, alt histograms, and alt table files must all be the same");
+        START HERE CHECK HEADER
+
         refHistograms = sumHistogramsFromFiles(refHistogramFiles);
 
         if (altHistogramFiles != null) {
@@ -269,9 +267,7 @@ public static List<Histogram<Integer>> sumHistogramsFromFiles(final List<File> f
             for (final Histogram<Integer> jthHistogram : ithHistograms){
                 final String refContext = jthHistogram.getValueLabel();
                 final Optional<Histogram<Integer>> hist = histogramList.stream().filter(h -> h.getValueLabel().equals(refContext)).findAny();
-                if (! hist.isPresent()){
-                    throw new IllegalStateException("Reference histogram is empty, which violates the invariant enforced by CollectF1R2Counts");
-                }
+                Utils.validate(hist.isPresent(),"Reference histogram is empty, which violates the invariant enforced by CollectF1R2Counts");
 
                 hist.get().addHistogram(jthHistogram);
             }
@@ -296,7 +292,5 @@ public static Pair<String, List<AltSiteRecord>> gatherAltSiteRecords(final List<
         }
 
         return new ImmutablePair<>(sample, records);
-
     }
-
-}
+}