Merge pull request #8 from PankratzLab/case_control_file

Add case/control output file

Author: jameeters

src/main/java/org/pankratzlab/internal/gwas/MatchMaker.java

@@ -4,15 +4,11 @@
 import java.io.File;
 import java.io.IOException;
 import java.io.PrintWriter;
-import java.nio.file.FileAlreadyExistsException;
 import java.nio.file.Files;
 import java.nio.file.Path;
 import java.nio.file.Paths;
 import java.util.ArrayList;
-import java.util.Arrays;
-import java.util.Collections;
 import java.util.HashMap;
-import java.util.HashSet;
 import java.util.LinkedHashMap;
 import java.util.LinkedHashSet;
 import java.util.List;
@@ -24,24 +20,24 @@
 import java.util.concurrent.ExecutionException;
 import java.util.logging.Logger;
 import java.util.stream.Collectors;
-import java.util.stream.Stream;
 
-import org.apache.commons.io.FileUtils;
 import org.pankratzlab.common.ArrayUtils;
 import org.pankratzlab.common.HashVec;
 import org.pankratzlab.common.Matrix;
 import org.pankratzlab.common.PSF;
-import org.pankratzlab.internal.gwas.FactorLoadings;
 import org.pankratzlab.kdmatch.KDMatch;
 import org.pankratzlab.kdmatch.KDTree;
 import org.pankratzlab.kdmatch.Match;
 import org.pankratzlab.kdmatch.Sample;
 import org.pankratzlab.kdmatch.SelectOptimizedNeighbors;
 
-import com.google.common.collect.Sets;
 import com.google.common.primitives.Ints;
 
 public class MatchMaker {
+  private static final String naiveMatchFileName = "match.naive.txt";
+  private static final String naiveStatusFileName = "status.naive.txt";
+  private static final String optimizedMatchFileName = "match.optimized.txt";
+  private static final String optimizedStatusFileName = "status.optimized.txt";
 
   private static List<Match> kdMatchMaker(Path baseDir, Path inputSamples, List<Sample> caseList,
                                           List<Sample> controlList,
@@ -63,9 +59,10 @@ private static List<Match> kdMatchMaker(Path baseDir, Path inputSamples, List<Sa
                                                                     initialNumSelect)
                                      .collect(Collectors.toList());
 
-    String outputBase = baseDir + File.separator + "match.naive.txt";
+    String outputBaseFileName = baseDir + File.separator + naiveMatchFileName;
+    String statusBaseFileName = baseDir + File.separator + naiveStatusFileName;
     log.info("reporting full baseline selection of " + initialNumSelect + " nearest neighbors to "
-             + outputBase);
+             + outputBaseFileName);
     LinkedHashSet<String> setConvert = new LinkedHashSet<String>();
 
     try {
@@ -75,9 +72,11 @@ private static List<Match> kdMatchMaker(Path baseDir, Path inputSamples, List<Sa
         setConvert.add(header[i]);
       }
       try {
-        KDMatch.writeToFile(naiveMatches.stream(), outputBase,
+        KDMatch.writeToFile(naiveMatches.stream(), outputBaseFileName,
                             setConvert.stream().toArray(String[]::new),
                             setConvert.stream().toArray(String[]::new), initialNumSelect);
+
+        KDMatch.writeSampleStatusFile(naiveMatches.stream(), statusBaseFileName, initialNumSelect);
       } catch (IOException e) {
         e.printStackTrace();
       }
@@ -86,8 +85,8 @@ private static List<Match> kdMatchMaker(Path baseDir, Path inputSamples, List<Sa
       System.exit(1);
     }
 
-    String outputOpt = baseDir + File.separator + "match.optimized.txt";
-
+    String outputOptFileName = baseDir + File.separator + optimizedMatchFileName;
+    String statusOptFileName = baseDir + File.separator + optimizedStatusFileName;
     log.info("selecting optimized nearest neighbors");
 
     List<Match> optimizedMatches = null;
@@ -96,10 +95,11 @@ private static List<Match> kdMatchMaker(Path baseDir, Path inputSamples, List<Sa
                                                                      threads, log)
                                                  .collect(Collectors.toList());
       log.info("reporting optimized selection of " + finalNumSelect + " nearest neighbors to "
-               + outputOpt);
-      KDMatch.writeToFile(optimizedMatches.stream(), outputOpt,
+               + outputOptFileName);
+      KDMatch.writeToFile(optimizedMatches.stream(), outputOptFileName,
                           setConvert.stream().toArray(String[]::new),
                           setConvert.stream().toArray(String[]::new), finalNumSelect);
+      KDMatch.writeSampleStatusFile(optimizedMatches.stream(), statusOptFileName, finalNumSelect);
     } catch (StackOverflowError s1) {
       s1.printStackTrace();
       log.info("To potentially prevent this StackOverflowError, try increasing the Thread Stack Size with the -Xss argument passed to the java virtual machine (i.e. java -Xss10m)");
@@ -577,9 +577,13 @@ public static void main(String[] args) {
     log.info("Starting sample match using k-d tree nearest neighbors.");
 
     try {
-      File naive = new File(d + "/match.naive.txt");
-      File optimized = new File(d + "/match.optimized.txt");
-      if (naive.exists() || optimized.exists()) {
+      List<String> fileNames = List.of(naiveMatchFileName, naiveStatusFileName,
+                                       optimizedMatchFileName, optimizedStatusFileName);
+      final Path finalD = d;
+      boolean outputExists = fileNames.stream()
+                                      .map(name -> new File(finalD + File.separator + name))
+                                      .anyMatch(File::exists);
+      if (outputExists) {
         log.info("Output already exists.");
         System.exit(0);
       }
@@ -597,7 +601,9 @@ public static void main(String[] args) {
           loadingIndicesForVis[s] = loadingIndicesForVis[s] - 1;
         }
         for (int i = 0; i < finalNumSelect; i++) {
-          buildVisHelpers(d, Paths.get(optimized.toString()), samples, i, log);
+          Path resultsFile = Paths.get(new File(d + File.separator
+                                                + optimizedMatchFileName).toString());
+          buildVisHelpers(d, resultsFile, samples, i, log);
           if (!onlyBuildVisFiles) {
             new MatchesVisualized(d.toString(), samples.toString(),
                                   d + "/visual_helpers/vis_helper_factors.temp",