fix(reporter): add call-only tsv reporter

src/main/java/org/pharmgkb/pharmcat/BaseConfig.java

@@ -48,9 +48,11 @@ public class BaseConfig {
   List<PrescribingGuidanceSource> reporterSources;
   boolean reporterJson;
   boolean reporterHtml = true;
+  boolean reporterCallsOnlyTsv = false;
   Path outputDir;
   String baseFilename;
   boolean deleteIntermediateFiles;
+  boolean verbose;
   SortedSet<String> samples = new TreeSet<>();
 
 
@@ -125,13 +127,15 @@ public class BaseConfig {
       reporterTitle = cliHelper.getValue("rt");
       reporterCompact = !cliHelper.hasOption("re");
       reporterJson = cliHelper.hasOption("reporterJson");
+      reporterCallsOnlyTsv = cliHelper.hasOption("reporterCallsOnly");
 
       if (researchMode) {
-        System.out.println("WARNING: REPORTER MODULE NOT AVAILABLE IN RESEARCH MODE");
-        if (!reporterJson) {
+        System.out.println("WARNING: FULL REPORTER OUTPUT NOT AVAILABLE IN RESEARCH MODE");
+        if (!reporterCallsOnlyTsv) {
           runReporter = false;
         }
         reporterHtml = false;
+        reporterJson = false;
       }
 
       if (cliHelper.hasOption("rs")) {
@@ -166,6 +170,7 @@ public class BaseConfig {
     }
     baseFilename = cliHelper.getValue("bf");
     deleteIntermediateFiles = cliHelper.hasOption("del");
+    verbose = cliHelper.isVerbose();
   }
 
 

src/main/java/org/pharmgkb/pharmcat/BatchPharmCAT.java

@@ -65,6 +65,7 @@ public static void main(String[] args) {
           .addOption("rs", "reporter-sources", "Comma-separated list of sources to limit recommendations to: [CPIC, DPWG, FDA]", false, "sources")
           .addOption("re", "reporter-extended", "Write an extended report (includes all possible genes and drugs, even if no data is available)")
           .addOption("reporterJson", "reporter-save-json", "Save reporter results as JSON")
+          .addOption("reporterCallsOnly", "reporter-save-calls-only", "Save calls only as TSV")
 
           // outputs
           .addOption("o", "output-dir", "Directory to output to (optional, default is input file directory)", false, "directory")
@@ -396,7 +397,8 @@ public Pipeline build(Env env, int index, int totalTasks) throws ReportableExcep
           m_config.topCandidateOnly, m_config.callCyp2d6, m_config.findCombinations, m_config.matcherHtml,
           m_runPhenotyper, m_piFile, m_poFile,
           m_runReporter, m_riFile, m_config.reporterTitle,
-          m_config.reporterSources, m_config.reporterCompact, m_config.reporterJson, m_config.reporterHtml,
+          m_config.reporterSources, m_config.reporterCompact,
+          m_config.reporterJson, m_config.reporterHtml, m_config.reporterCallsOnlyTsv,
           m_config.outputDir, m_config.baseFilename, m_config.deleteIntermediateFiles,
           mode, (index + "/" + totalTasks), m_verbose);
     }

src/main/java/org/pharmgkb/pharmcat/PharmCAT.java

@@ -47,6 +47,7 @@ public static void main(String[] args) {
           .addOption("rs", "reporter-sources", "Comma-separated list of sources to limit recommendations to: [CPIC, DPWG, FDA]", false, "sources")
           .addOption("re", "reporter-extended", "Write an extended report (includes all possible genes and drugs, even if no data is available)")
           .addOption("reporterJson", "reporter-save-json", "Save reporter results as JSON")
+          .addOption("reporterCallsOnly", "reporter-save-calls-only", "Save calls only as TSV")
 
           // outputs
           .addOption("o", "output-dir", "Directory to output to (optional, default is input file directory)", false, "directory")
@@ -163,14 +164,8 @@ Please specify a VCF file (-vcf)"""
           if (config.samples.size() > 1) {
             System.out.println(x + " / " + config.samples.size() + " - " + sampleId);
           }
-          Pipeline pipeline = new Pipeline(env,
-              config.runMatcher, vcfFile, sampleId, singleSample,
-              config.topCandidateOnly, config.callCyp2d6, config.findCombinations, config.matcherHtml,
-              config.runPhenotyper, phenotyperInputFile, phenotyperOutsideCallsFiles,
-              config.runReporter, reporterInputFile, config.reporterTitle,
-              config.reporterSources, config.reporterCompact, config.reporterJson, config.reporterHtml,
-              config.outputDir, config.baseFilename, config.deleteIntermediateFiles,
-              Pipeline.Mode.CLI, null, cliHelper.isVerbose());
+          Pipeline pipeline = new Pipeline(env, config, vcfFile, sampleId, singleSample,
+              phenotyperInputFile, phenotyperOutsideCallsFiles, reporterInputFile);
           if (pipeline.call().getStatus() == PipelineResult.Status.NOOP) {
             failIfNotTest();
             blankRuns.add(sampleId);
@@ -187,14 +182,8 @@ Please specify a VCF file (-vcf)"""
         }
 
       } else {
-        Pipeline pipeline = new Pipeline(env,
-            false, null, null, true,
-            config.topCandidateOnly, config.callCyp2d6, config.findCombinations, config.matcherHtml,
-            config.runPhenotyper, phenotyperInputFile, phenotyperOutsideCallsFiles,
-            config.runReporter, reporterInputFile, config.reporterTitle,
-            config.reporterSources, config.reporterCompact, config.reporterJson, config.reporterHtml,
-            config.outputDir, config.baseFilename, config.deleteIntermediateFiles,
-            Pipeline.Mode.CLI, null, cliHelper.isVerbose());
+        Pipeline pipeline = new Pipeline(env, config, null, null, true,
+            phenotyperInputFile, phenotyperOutsideCallsFiles, reporterInputFile);
         if (pipeline.call().getStatus() == PipelineResult.Status.NOOP) {
           cliHelper.printHelp();
           System.out.println("Nothing to do.");

src/main/java/org/pharmgkb/pharmcat/Pipeline.java

@@ -26,6 +26,7 @@
 import org.pharmgkb.pharmcat.phenotype.Phenotyper;
 import org.pharmgkb.pharmcat.phenotype.model.OutsideCall;
 import org.pharmgkb.pharmcat.reporter.ReportContext;
+import org.pharmgkb.pharmcat.reporter.format.CallsOnlyFormat;
 import org.pharmgkb.pharmcat.reporter.format.HtmlFormat;
 import org.pharmgkb.pharmcat.reporter.format.JsonFormat;
 import org.pharmgkb.pharmcat.reporter.model.PrescribingGuidanceSource;
@@ -72,6 +73,7 @@ public enum Mode {
   private List<PrescribingGuidanceSource> m_reporterSources;
   private Path m_reporterJsonFile;
   private Path m_reporterHtmlFile;
+  private Path m_reporterCallsOnlyFile;
   private ReportContext m_reportContext;
 
   private final boolean m_deleteIntermediateFiles;
@@ -83,12 +85,28 @@ public enum Mode {
   private final String m_displayCount;
 
 
+  public Pipeline(Env env, BaseConfig config, @Nullable VcfFile vcfFile,
+      @Nullable String sampleId, boolean singleSample,
+      @Nullable Path phenotyperInputFile, @Nullable List<Path> phenotyperOutsideCallsFiles,
+      @Nullable Path reporterInputFile) throws ReportableException {
+    this(env, config.runMatcher, vcfFile, sampleId, singleSample,
+        config.topCandidateOnly, config.callCyp2d6, config.findCombinations, config.matcherHtml,
+        config.runPhenotyper, phenotyperInputFile, phenotyperOutsideCallsFiles,
+        config.runReporter, reporterInputFile, config.reporterTitle,
+        config.reporterSources, config.reporterCompact,
+        config.reporterJson, config.reporterHtml, config.reporterCallsOnlyTsv,
+        config.outputDir, config.baseFilename, config.deleteIntermediateFiles,
+        Pipeline.Mode.CLI, null, config.verbose);
+  }
+
+
   public Pipeline(Env env,
       boolean runMatcher, @Nullable VcfFile vcfFile, @Nullable String sampleId, boolean singleSample,
       boolean topCandidateOnly, boolean callCyp2d6, boolean findCombinations, boolean matcherHtml,
       boolean runPhenotyper, @Nullable Path phenotyperInputFile, @Nullable List<Path> phenotyperOutsideCallsFile,
       boolean runReporter, @Nullable Path reporterInputFile, @Nullable String reporterTitle,
-      @Nullable List<PrescribingGuidanceSource> reporterSources, boolean reporterCompact, boolean reporterJson, boolean reporterHtml,
+      @Nullable List<PrescribingGuidanceSource> reporterSources, boolean reporterCompact,
+      boolean reporterJson, boolean reporterHtml, boolean reporterCallsOnlyTsv,
       @Nullable Path outputDir, @Nullable String baseFilename, boolean deleteIntermediateFiles,
       Mode mode, @Nullable String displayCount, boolean verbose) throws ReportableException {
     m_env = env;
@@ -151,6 +169,9 @@ public Pipeline(Env env,
       if (reporterJson) {
         m_reporterJsonFile = m_baseDir.resolve(m_basename + BaseConfig.REPORTER_SUFFIX + ".json");
       }
+      if (reporterCallsOnlyTsv) {
+        m_reporterCallsOnlyFile = m_baseDir.resolve(m_basename + BaseConfig.REPORTER_SUFFIX + ".tsv");
+      }
       m_reporterTitle = reporterTitle;
       if (m_reporterTitle == null) {
         m_reporterTitle = m_basename;
@@ -348,6 +369,16 @@ public PipelineResult call() throws IOException {
           new JsonFormat(m_reporterJsonFile, m_env)
               .write(m_reportContext);
         }
+        if (m_reporterCallsOnlyFile != null) {
+          if (!batchDisplayMode) {
+            output.add("Saving calls-only TSV results to " + m_reporterCallsOnlyFile);
+          }
+          CallsOnlyFormat caf = new CallsOnlyFormat(m_reporterCallsOnlyFile, m_env);
+          if (!m_topCandidateOnly) {
+            caf.showMatchScores();
+          }
+          caf.write(m_reportContext);
+        }
         didSomething = true;
       }
 

src/main/java/org/pharmgkb/pharmcat/definition/model/NamedAllele.java

@@ -58,6 +58,8 @@ public class NamedAllele implements Comparable<NamedAllele> {
   private HashMap<VariantLocus, String> m_alleleMap;
   private HashMap<VariantLocus, String> m_cpicAlleleMap;
   private List<Integer> m_wobblePositions;
+  @Expose
+  @SerializedName("score")
   private int m_score;
   private transient Pattern m_permutations;
   // generated by combinations code

src/main/java/org/pharmgkb/pharmcat/reporter/DiplotypeFactory.java

@@ -61,7 +61,7 @@ public List<Diplotype> makeComponentDiplotypes(GeneCall geneCall, DataSource sou
       }
     }
     for (NamedAllele na : haps) {
-      dips.add(new Diplotype(m_gene, na.getName(), null, m_env, source));
+      dips.add(new Diplotype(m_gene, na.getName(), null, m_env, source, na.getScore()));
     }
     return dips;
   }
@@ -79,8 +79,7 @@ public List<Diplotype> makeDiplotypes(Collection<DiplotypeMatch> matches, DataSo
           if (h2 != null) {
             h2Name = h2.getName();
           }
-
-          Diplotype diplotype = new Diplotype(m_gene, h1.getName(), h2Name, m_env, source);
+          Diplotype diplotype = new Diplotype(m_gene, h1.getName(), h2Name, m_env, source, dm.getScore());
           diplotype.setCombination(h1 instanceof CombinationMatch || h2 instanceof CombinationMatch);
           return diplotype;
         })
@@ -92,7 +91,7 @@ public List<Diplotype> makeDiplotypesFromHaplotypeMatches(Collection<HaplotypeMa
       return ImmutableList.of(makeUnknownDiplotype(m_gene, m_env, source));
     }
     return matches.stream()
-        .map((hm) -> new Diplotype(m_gene, hm.getName(), null, m_env, source))
+        .map((hm) -> new Diplotype(m_gene, hm.getName(), null, m_env, source, 0))
         .toList();
   }
 

src/main/java/org/pharmgkb/pharmcat/reporter/caller/Slco1b1CustomCaller.java

@@ -51,7 +51,7 @@ public static SortedSet<Diplotype> inferDiplotypes(GeneReport report, Env env,
     List<VariantReport> variants = report.getVariantReports().stream()
         .filter(v -> sf_callPosition.equals(v.getDbSnpId()))
         .toList();
-    if (variants.size() == 0) {
+    if (variants.isEmpty()) {
       return report.getSourceDiplotypes();
     }
     if (variants.size() > 1) {
@@ -64,13 +64,13 @@ public static SortedSet<Diplotype> inferDiplotypes(GeneReport report, Env env,
       return report.getSourceDiplotypes();
     }
 
-    Diplotype diplotype = new Diplotype(GENE, haps[0], haps[1], env, source);
+    Diplotype diplotype = new Diplotype(GENE, haps[0], haps[1], env, source, 0);
     diplotype.setVariant(variant);
     diplotype.setInferred(true);
 
     String[] alleles = Objects.requireNonNull(splitVariant(variant));
     diplotype.setInferredSourceDiplotype(new Diplotype(GENE,
-        sf_callPosition + " " + alleles[0], sf_callPosition + " " + alleles[1], env, source));
+        sf_callPosition + " " + alleles[0], sf_callPosition + " " + alleles[1], env, source, 0));
 
     SortedSet<Diplotype> dips = new TreeSet<>();
     dips.add(diplotype);