update readme

This reverts commit adebe1542e.

readme.md

@@ -96,7 +96,7 @@ These files are often generated in sequence. When entering filenames, it is not
 (.csv or .ser). When reading or writing files, the program will automatically add the correct extension to any filename 
 without one.
 
-To save file I/O time, the most recent instance of each of these four
+To save file I/O time when using the interactive interface, the most recent instance of each of these four
 files either generated or read from disk can be cached in program memory. When caching is active, subsequent uses of the 
 same data file won't need to be read in again until another file of that type is used or generated,
 or caching is turned off for that file type. The program checks whether it needs to update its cached data by comparing
@@ -160,7 +160,7 @@ Options when making a Sample Plate file:
     * Number of sections on plate
     * Number of T cells per well
       * per section, if more than one section
-* Dropout rate
+* Sequence dropout rate
 
 Files are in CSV format. There are no header labels. Every row represents a well. 
 Every value represents an individual cell, containing four sequences, depicted as an array string:
@@ -204,6 +204,7 @@ Options for creating a Graph/Data file:
   * The read depth (number of times each sequence is read)
   * The read error rate (probability a sequence is misread)
   * The error collision rate (probability two misreads produce the same spurious sequence)
+  * The real sequence collision rate (probability that a misread will produce a different, real sequence from the sample plate. Only applies to new misreads; once an error of this type has occurred, it's likelihood of ocurring again is dominated by the error collision probability.)
 
 These files do not have a human-readable structure, and are not portable to other programs.
 
@@ -211,8 +212,8 @@ These files do not have a human-readable structure, and are not portable to othe
 
 For portability of graph data to other software, turn on [GraphML](http://graphml.graphdrawing.org/index.html) output 
 in the Options menu in interactive mode, or use the `-graphml`command line argument. This will produce a .graphml file 
-for the weighted graph, with vertex attributes for sequence, type, and occupancy data. This graph contains all the data 
-necessary for the BiGpairSEQ matching algorithm. It does not include the data to measure pairing accuracy; for that, 
+for the weighted graph, with vertex attributes for sequence, type, total occupancy, total read count, and the read count for every individual occupied well.
+This graph contains all the data necessary for the BiGpairSEQ matching algorithm. It does not include the data to measure pairing accuracy; for that, 
 compare the matching results to the original Cell Sample .csv file.
 
 ---
@@ -361,8 +362,10 @@ roughly as though it had a constant well population equal to the plate's average
 * ~~Add read depth simulation options to CLI~~ DONE
 * ~~Update graphml output to reflect current Vertex class attributes~~ DONE
   * Individual well data from the SequenceRecords could be included, if there's ever a reason for it
+* ~~Implement simulation of sequences being misread as other real sequence~~ DONE
 * Update matching metadata output options in CLI
 * Update performance data in this readme
+* Add section to ReadMe describing data filtering methods.
 * Re-implement CDR1 matching method
 * Refactor simulator code to collect all needed data in a single scan of the plate
   * Currently it scans once for the vertices and then again for the edge weights. This made simulating read depth awkward, and incompatible with caching of plate files.

src/main/java/CommandLineInterface.java

@@ -150,16 +150,21 @@ public class CommandLineInterface {
                 Integer readDepth = 1;
                 Double readErrorRate = 0.0;
                 Double errorCollisionRate = 0.0;
+                Double realSequenceCollisionRate = 0.0;
                 if (line.hasOption("rd")) {
                     readDepth = Integer.parseInt(line.getOptionValue("rd"));
                 }
                 if (line.hasOption("err")) {
                     readErrorRate = Double.parseDouble(line.getOptionValue("err"));
                 }
-                if (line.hasOption("coll")) {
-                    errorCollisionRate = Double.parseDouble(line.getOptionValue("coll"));
+                if (line.hasOption("errcoll")) {
+                    errorCollisionRate = Double.parseDouble(line.getOptionValue("errcoll"));
                 }
-                graph = Simulator.makeCDR3Graph(cells, plate, readDepth, readErrorRate, errorCollisionRate, false);
+                if (line.hasOption("realcoll")) {
+                    realSequenceCollisionRate = Double.parseDouble(line.getOptionValue("realcoll"));
+                }
+                graph = Simulator.makeCDR3Graph(cells, plate, readDepth, readErrorRate, errorCollisionRate,
+                        realSequenceCollisionRate, false);
                 if (!line.hasOption("no-binary")) { //output binary file unless told not to
                     GraphDataObjectWriter writer = new GraphDataObjectWriter(outputFilename, graph, false);
                     writer.writeDataToFile();
@@ -413,12 +418,20 @@ public class CommandLineInterface {
                 .hasArg()
                 .argName("prob")
                 .build();
-        Option errorCollisionProb = Option.builder("coll")
+        Option errorCollisionProb = Option.builder("errcoll")
                 .longOpt("error-collision-prob")
                 .desc("(Optional) The probability that two misreads will produce the same spurious sequence. (0.0 - 1.0)")
                 .hasArg()
                 .argName("prob")
                 .build();
+        Option realSequenceCollisionProb = Option.builder("realcoll")
+                .longOpt("real-collision-prob")
+                .desc("(Optional) The probability that a sequence will be misread " +
+                        "as another real sequence. (Only applies to unique misreads; after this has happened once, " +
+                        "future error collisions could produce the real sequence again) (0.0 - 1.0)")
+                .hasArg()
+                .argName("prob")
+                .build();
         graphOptions.addOption(cellFilename);
         graphOptions.addOption(plateFilename);
         graphOptions.addOption(outputFileOption());
@@ -427,6 +440,7 @@ public class CommandLineInterface {
         graphOptions.addOption(readDepth);
         graphOptions.addOption(readErrorProb);
         graphOptions.addOption(errorCollisionProb);
+        graphOptions.addOption(realSequenceCollisionProb);
         return graphOptions;
     }
 

src/main/java/GraphMLFileWriter.java

@@ -5,7 +5,6 @@ import org.jgrapht.nio.AttributeType;
 import org.jgrapht.nio.DefaultAttribute;
 import org.jgrapht.nio.graphml.GraphMLExporter;
 import org.jgrapht.nio.graphml.GraphMLExporter.AttributeCategory;
-import org.w3c.dom.Attr;
 
 import java.io.BufferedWriter;
 import java.io.IOException;
@@ -13,6 +12,7 @@ import java.nio.file.Files;
 import java.nio.file.Path;
 import java.nio.file.StandardOpenOption;
 import java.util.HashMap;
+import java.util.Iterator;
 import java.util.Map;
 
 public class GraphMLFileWriter {
@@ -41,11 +41,11 @@ public class GraphMLFileWriter {
     }
 
     private Map<String, Attribute> createGraphAttributes(){
-        Map<String, Attribute> ga = new HashMap<>();
+        Map<String, Attribute> attributes = new HashMap<>();
         //Sample plate filename
-        ga.put("sample plate filename", DefaultAttribute.createAttribute(data.getSourceFilename()));
+        attributes.put("sample plate filename", DefaultAttribute.createAttribute(data.getSourceFilename()));
         // Number of wells
-        ga.put("well count", DefaultAttribute.createAttribute(data.getNumWells().toString()));
+        attributes.put("well count", DefaultAttribute.createAttribute(data.getNumWells().toString()));
         //Well populations
         Integer[] wellPopulations = data.getWellPopulations();
         StringBuilder populationsStringBuilder = new StringBuilder();
@@ -55,11 +55,37 @@ public class GraphMLFileWriter {
             populationsStringBuilder.append(wellPopulations[i].toString());
         }
         String wellPopulationsString = populationsStringBuilder.toString();
-        ga.put("well populations", DefaultAttribute.createAttribute(wellPopulationsString));
-        ga.put("read depth", DefaultAttribute.createAttribute(data.getReadDepth().toString()));
-        ga.put("read error rate", DefaultAttribute.createAttribute(data.getReadErrorRate().toString()));
-        ga.put("error collision rate", DefaultAttribute.createAttribute(data.getErrorCollisionRate().toString()));
-        return ga;
+        attributes.put("well populations", DefaultAttribute.createAttribute(wellPopulationsString));
+        attributes.put("read depth", DefaultAttribute.createAttribute(data.getReadDepth().toString()));
+        attributes.put("read error rate", DefaultAttribute.createAttribute(data.getReadErrorRate().toString()));
+        attributes.put("error collision rate", DefaultAttribute.createAttribute(data.getErrorCollisionRate().toString()));
+        attributes.put("real sequence collision rate", DefaultAttribute.createAttribute(data.getRealSequenceCollisionRate()));
+        return attributes;
+    }
+
+    private Map<String, Attribute> createVertexAttributes(Vertex v){
+        Map<String, Attribute> attributes = new HashMap<>();
+        //sequence type
+        attributes.put("type", DefaultAttribute.createAttribute(v.getType().name()));
+        //sequence
+        attributes.put("sequence", DefaultAttribute.createAttribute(v.getSequence()));
+        //number of wells the sequence appears in
+        attributes.put("occupancy", DefaultAttribute.createAttribute(v.getOccupancy()));
+        //total number of times the sequence was read
+        attributes.put("total read count", DefaultAttribute.createAttribute(v.getReadCount()));
+        StringBuilder wellsAndReadCountsBuilder = new StringBuilder();
+        Iterator<Map.Entry<Integer, Integer>> wellOccupancies = v.getWellOccupancies().entrySet().iterator();
+        while (wellOccupancies.hasNext()) {
+            Map.Entry<Integer, Integer> entry = wellOccupancies.next();
+            wellsAndReadCountsBuilder.append(entry.getKey() + ":" + entry.getValue());
+            if (wellOccupancies.hasNext()) {
+                wellsAndReadCountsBuilder.append(", ");
+            }
+        }
+        String wellsAndReadCounts = wellsAndReadCountsBuilder.toString();
+        //the wells the sequence appears in and the read counts in those wells
+        attributes.put("wells:read counts", DefaultAttribute.createAttribute(wellsAndReadCounts));
+        return attributes;
     }
 
     public void writeGraphToFile() {
@@ -72,15 +98,7 @@ public class GraphMLFileWriter {
             //Set graph attributes
             exporter.setGraphAttributeProvider( () -> graphAttributes);
             //set type, sequence, and occupancy attributes for each vertex
-            //NEED TO ADD NEW FIELD FOR READ COUNT
-            exporter.setVertexAttributeProvider( v -> {
-                Map<String, Attribute> attributes = new HashMap<>();
-                attributes.put("type", DefaultAttribute.createAttribute(v.getType().name()));
-                attributes.put("sequence", DefaultAttribute.createAttribute(v.getSequence()));
-                attributes.put("occupancy", DefaultAttribute.createAttribute(v.getOccupancy()));
-                attributes.put("read count", DefaultAttribute.createAttribute(v.getReadCount()));
-                return attributes;
-            });
+            exporter.setVertexAttributeProvider(this::createVertexAttributes);
             //register the attributes
             for(String s : graphAttributes.keySet()) {
                 exporter.registerAttribute(s, AttributeCategory.GRAPH, AttributeType.STRING);
@@ -88,7 +106,8 @@ public class GraphMLFileWriter {
             exporter.registerAttribute("type", AttributeCategory.NODE, AttributeType.STRING);
             exporter.registerAttribute("sequence", AttributeCategory.NODE, AttributeType.STRING);
             exporter.registerAttribute("occupancy", AttributeCategory.NODE, AttributeType.STRING);
-            exporter.registerAttribute("read count", AttributeCategory.NODE, AttributeType.STRING);
+            exporter.registerAttribute("total read count", AttributeCategory.NODE, AttributeType.STRING);
+            exporter.registerAttribute("wells:read counts", AttributeCategory.NODE, AttributeType.STRING);
             //export the graph
             exporter.exportGraph(graph, writer);
         } catch(IOException ex){

src/main/java/GraphWithMapData.java

@@ -11,13 +11,14 @@ public class GraphWithMapData implements java.io.Serializable {
 
     private String sourceFilename;
     private final SimpleWeightedGraph graph;
-    private Integer numWells;
-    private Integer[] wellPopulations;
-    private Integer alphaCount;
-    private Integer betaCount;
-    private int readDepth;
-    private double readErrorRate;
-    private double errorCollisionRate;
+    private final int numWells;
+    private final Integer[] wellPopulations;
+    private final int alphaCount;
+    private final int betaCount;
+    private final int readDepth;
+    private final double readErrorRate;
+    private final double errorCollisionRate;
+    private final double realSequenceCollisionRate;
     private final Map<String, String> distCellsMapAlphaKey;
 //    private final Map<Integer, Integer> plateVtoAMap;
 //    private final Map<Integer, Integer> plateVtoBMap;
@@ -29,7 +30,8 @@ public class GraphWithMapData implements java.io.Serializable {
 
     public GraphWithMapData(SimpleWeightedGraph graph, Integer numWells, Integer[] wellConcentrations,
                             Map<String, String> distCellsMapAlphaKey, Integer alphaCount, Integer betaCount,
-                            Integer readDepth, Double readErrorRate, Double errorCollisionRate, Duration time){
+                            Integer readDepth, Double readErrorRate, Double errorCollisionRate,
+                            Double realSequenceCollisionRate, Duration time){
 
 //                            Map<Integer, Integer> plateVtoAMap,
 //                            Map<Integer,Integer> plateVtoBMap, Map<Integer, Integer> plateAtoVMap,
@@ -50,6 +52,7 @@ public class GraphWithMapData implements java.io.Serializable {
         this.readDepth = readDepth;
         this.readErrorRate = readErrorRate;
         this.errorCollisionRate = errorCollisionRate;
+        this.realSequenceCollisionRate = realSequenceCollisionRate;
         this.time = time;
     }
 
@@ -122,4 +125,6 @@ public class GraphWithMapData implements java.io.Serializable {
     public Double getErrorCollisionRate() {
         return errorCollisionRate;
     }
+
+    public Double getRealSequenceCollisionRate() { return realSequenceCollisionRate; }
 }

src/main/java/InteractiveInterface.java

@@ -255,6 +255,7 @@ public class InteractiveInterface {
         int readDepth = 1;
         double readErrorRate = 0.0;
         double errorCollisionRate = 0.0;
+        double realSequenceCollisionRate = 0.0;
         try {
             String str = "\nGenerating bipartite weighted graph encoding occupancy overlap data ";
             str = str.concat("\nrequires a cell sample file and a sample plate file.");
@@ -264,7 +265,6 @@ public class InteractiveInterface {
             System.out.print("\nPlease enter name of an existing sample plate file: ");
             plateFile = sc.next();
             System.out.println("\nEnable simulation of sequence read depth and sequence read errors? (y/n)");
-            System.out.println("NOTE: sample plate data cannot be cached when simulating read errors");
             String ans = sc.next();
             Pattern pattern = Pattern.compile("(?:yes|y)", Pattern.CASE_INSENSITIVE);
             Matcher matcher = pattern.matcher(ans);
@@ -272,25 +272,29 @@ public class InteractiveInterface {
                 simulateReadDepth = true;
             }
             if (simulateReadDepth) {
-                BiGpairSEQ.setCachePlate(false);
-                BiGpairSEQ.clearPlateInMemory();
-                System.out.print("\nPlease enter read depth (the integer number of reads per sequence): ");
+                System.out.print("\nPlease enter the read depth (the integer number of times a sequence is read): ");
                 readDepth = sc.nextInt();
                 if(readDepth < 1) {
                     throw new InputMismatchException("The read depth must be an integer >= 1");
                 }
-                System.out.print("\nPlease enter probability of a sequence read error (0.0 to 1.0): ");
+                System.out.println("\nPlease enter the read error probability (0.0 to 1.0)");
+                System.out.print("(The probability that a sequence will be misread): ");
                 readErrorRate = sc.nextDouble();
                 if(readErrorRate < 0.0 || readErrorRate > 1.0) {
-                    throw new InputMismatchException("The read error rate must be in the range [0.0, 1.0]");
+                    throw new InputMismatchException("The read error probability must be in the range [0.0, 1.0]");
                 }
-                System.out.println("\nPlease enter the probability of read error collision");
-                System.out.println("(the likelihood that two read errors produce the same spurious sequence)");
-                System.out.print("(0.0 to 1.0): ");
+                System.out.println("\nPlease enter the error collision probability (0.0 to 1.0)");
+                System.out.print("(The probability of a sequence being misread in a way it has been misread before): ");
                 errorCollisionRate = sc.nextDouble();
                 if(errorCollisionRate < 0.0 || errorCollisionRate > 1.0) {
                     throw new InputMismatchException("The error collision probability must be an in the range [0.0, 1.0]");
                 }
+                System.out.println("\nPlease enter the real sequence collision probability (0.0 to 1.0)");
+                System.out.print("(The probability that a (non-collision) misread produces a different, real sequence): ");
+                realSequenceCollisionRate = sc.nextDouble();
+                if(realSequenceCollisionRate < 0.0 || realSequenceCollisionRate > 1.0) {
+                    throw new InputMismatchException("The real sequence collision probability must be an in the range [0.0, 1.0]");
+                }
             }
             System.out.println("\nThe graph and occupancy data will be written to a file.");
             System.out.print("Please enter a name for the output file: ");
@@ -338,7 +342,8 @@ public class InteractiveInterface {
             System.out.println("Returning to main menu.");
         }
         else{
-            GraphWithMapData data = Simulator.makeCDR3Graph(cellSample, plate, readDepth, readErrorRate, errorCollisionRate, true);
+            GraphWithMapData data = Simulator.makeCDR3Graph(cellSample, plate, readDepth, readErrorRate,
+                    errorCollisionRate, realSequenceCollisionRate, true);
             assert filename != null;
             if(BiGpairSEQ.outputBinary()) {
                 GraphDataObjectWriter dataWriter = new GraphDataObjectWriter(filename, data);

src/main/java/Plate.java

@@ -2,6 +2,13 @@
 
 /*
 TODO: Implement exponential distribution using inversion method - DONE
+TODO: Implement collisions with real sequences by having the counting function keep a map of all sequences it's read,
+with values of all misreads. Can then have a spurious/real collision rate, which will have count randomly select a sequence
+it's already read at least once, and put that into the list of spurious sequences for the given real sequence. Will let me get rid
+of the distinctMisreadCount map, and use this new map instead. Doing it this way, once a sequence has been misread as another
+sequence once, it is more likely to be misread that way again, as future read error collisions can also be real sequence collisions
+Prob A: a read error occurs. Prob B: it's a new error (otherwise it's a repeated error). Prob C: if new error, prob that it's
+a real sequence collision (otherwise it's a new spurious sequence) - DONE
 TODO: Implement discrete frequency distributions using Vose's Alias Method
  */
 
@@ -148,79 +155,83 @@ public class Plate {
         return wells;
     }
 
-//    //returns a map of the counts of the sequence at cell index sIndex, in all wells
-//    public void assayWellsSequenceS(Map<String, Integer> sequences, int... sIndices){
-//        this.assayWellsSequenceS(sequences, 0, size, sIndices);
-//    }
-//
-//    //returns a map of the counts of the sequence at cell index sIndex, in a specific well
-//    public void assayWellsSequenceS(Map<String, Integer> sequences, int n, int... sIndices) {
-//        this.assayWellsSequenceS(sequences, n, n+1, sIndices);
-//    }
-//
-//    //returns a map of the counts of the sequence at cell index sIndex, in a range of wells
-//    public void assayWellsSequenceS(Map<String, Integer> sequences, int start, int end, int... sIndices) {
-//        for(int sIndex: sIndices){
-//            for(int i = start; i < end; i++){
-//                countSequences(sequences, wells.get(i), sIndex);
-//            }
-//        }
-//    }
-//    //For the sequences at cell indices sIndices, counts number of unique sequences in the given well into the given map
-//    private void countSequences(Map<String, Integer> wellMap, List<String[]> well, int... sIndices) {
-//        for(String[] cell : well) {
-//            for(int sIndex: sIndices){
-//                //skip dropout sequences, which have value -1
-//                if(!"-1".equals(cell[sIndex])){
-//                    wellMap.merge(cell[sIndex], 1, (oldValue, newValue) -> oldValue + newValue);
-//                }
-//            }
-//        }
-//    }
-
-    //For the sequences at cell indices sIndices, counts number of unique sequences in all well into the given map
+    //For the sequences at cell indices sIndices, counts number of unique sequences in all wells.
+    //Also simulates sequence read errors with given probabilities.
+    //Returns a map of SequenceRecords containing plate data for all sequences read.
+    //TODO actually implement usage of misreadSequences - DONE
     public Map<String, SequenceRecord> countSequences(Integer readDepth, Double readErrorRate,
-                                                       Double errorCollisionRate, int... sIndices) {
+                                                       Double errorCollisionRate, Double realSequenceCollisionRate, int... sIndices) {
         SequenceType[] sequenceTypes = EnumSet.allOf(SequenceType.class).toArray(new SequenceType[0]);
-        Map<String, Integer> distinctMisreadCounts = new HashMap<>();
+        //Map of all real sequences read. Keys are sequences, values are ways sequence has been misread.
+        Map<String, List<String>> sequencesAndMisreads = new HashMap<>();
+        //Map of all sequences read. Keys are sequences, values are associated SequenceRecords
         Map<String, SequenceRecord> sequenceMap = new LinkedHashMap<>();
+        //get list of all distinct, real sequences
+        String[] realSequences = assayWells(sIndices).toArray(new String[0]);
         for (int well = 0; well < size; well++) {
-            for (String[] cell : wells.get(well)) {
-                for (int sIndex : sIndices) {
+            for (String[] cell: wells.get(well)) {
+                for (int sIndex: sIndices) {
+                    //the sequence being read
+                    String currentSequence = cell[sIndex];
                     //skip dropout sequences, which have value -1
-                    if (!"-1".equals(cell[sIndex])) {
+                    if (!"-1".equals(currentSequence)) {
+                        //keep rereading the sequence until the read depth is reached
                         for (int j = 0; j < readDepth; j++) {
-                            //Misread sequence
+                            //The sequence is misread
                             if (rand.nextDouble() < readErrorRate) {
-                                StringBuilder spurious = new StringBuilder(cell[sIndex]);
-                                //if this sequence hasn't been misread before, or the read error is unique,
-                                //append one more "*" than has been appended before
-                                if (rand.nextDouble() > errorCollisionRate || !distinctMisreadCounts.containsKey(cell[sIndex])) {
-                                    distinctMisreadCounts.merge(cell[sIndex], 1, (oldValue, newValue) -> oldValue + newValue);
-                                    for (int k = 0; k < distinctMisreadCounts.get(cell[sIndex]); k++) {
+                                //The sequence hasn't been read or misread before
+                                if (!sequencesAndMisreads.containsKey(currentSequence)) {
+                                    sequencesAndMisreads.put(currentSequence, new ArrayList<>());
+                                }
+                                //The specific misread hasn't happened before
+                                if (rand.nextDouble() >= errorCollisionRate || sequencesAndMisreads.get(currentSequence).size() == 0) {
+                                    //The misread doesn't collide with a real sequence already on the plate and some sequences have already been read
+                                    if(rand.nextDouble() >= realSequenceCollisionRate || !sequenceMap.isEmpty()){
+                                        StringBuilder spurious = new StringBuilder(currentSequence);
+                                        for (int k = 0; k <= sequencesAndMisreads.get(currentSequence).size(); k++) {
                                             spurious.append("*");
                                         }
+                                        //New sequence record for the spurious sequence
                                         SequenceRecord tmp = new SequenceRecord(spurious.toString(), sequenceTypes[sIndex]);
                                         tmp.addRead(well);
                                         sequenceMap.put(spurious.toString(), tmp);
+                                        //add spurious sequence to list of misreads for the real sequence
+                                        sequencesAndMisreads.get(currentSequence).add(spurious.toString());
                                     }
-                                //if this is a read error collision, randomly choose a number of "*"s that has been appended before
+                                    //The misread collides with a real sequence already read from plate
                                     else {
-                                    int starCount = rand.nextInt(distinctMisreadCounts.get(cell[sIndex]));
-                                    for (int k = 0; k < starCount; k++) {
-                                        spurious.append("*");
-                                    }
-                                    sequenceMap.get(spurious.toString()).addRead(well);
+                                        String wrongSequence;
+                                        do{
+                                            //get a random real sequence that's been read from the plate before
+                                            int index = rand.nextInt(realSequences.length);
+                                            wrongSequence = realSequences[index];
+                                            //make sure it's not accidentally the *right* sequence
+                                            //Also that it's not a wrong sequence already in the misread list
+                                        } while(currentSequence.equals(wrongSequence) || sequencesAndMisreads.get(currentSequence).contains(wrongSequence));
+                                        //update the SequenceRecord for wrongSequence
+                                        sequenceMap.get(wrongSequence).addRead(well);
+                                        //add wrongSequence to the misreads for currentSequence
+                                        sequencesAndMisreads.get(currentSequence).add(wrongSequence);
                                     }
                                 }
-                            //sequence is read correctly
+                            }
+                            //The sequence is read correctly
                             else {
-                                if (!sequenceMap.containsKey(cell[sIndex])) {
-                                    SequenceRecord tmp = new SequenceRecord(cell[sIndex], sequenceTypes[sIndex]);
+                                //the sequence hasn't been read before
+                                if (!sequenceMap.containsKey(currentSequence)) {
+                                    //create new record for the sequence
+                                    SequenceRecord tmp = new SequenceRecord(currentSequence, sequenceTypes[sIndex]);
+                                    //add this read to the sequence record
                                     tmp.addRead(well);
-                                    sequenceMap.put(cell[sIndex], tmp);
-                                } else {
-                                    sequenceMap.get(cell[sIndex]).addRead(well);
+                                    //add the sequence and its record to the sequence map
+                                    sequenceMap.put(currentSequence, tmp);
+                                    //add the sequence to the sequences and misreads map
+                                    sequencesAndMisreads.put(currentSequence, new ArrayList<>());
+                                }
+                                //the sequence has been read before
+                                else {
+                                    //get the sequence's record and add this read to it
+                                    sequenceMap.get(currentSequence).addRead(well);
                                 }
                             }
                         }
@@ -231,97 +242,17 @@ public class Plate {
         return sequenceMap;
     }
 
-
-//    //returns a map of the counts of the sequence at cell index sIndex, in all wells
-//    //Simulates read depth and read errors, counts the number of reads of a unique sequence into the given map.
-//    public void assayWellsSequenceSWithReadDepth(Map<String, Integer> misreadCounts, Map<String, Integer> occupancyMap, Map<String, Integer> readCountMap,
-//                                                 int readDepth, double readErrorProb, double errorCollisionProb, int... sIndices) {
-//        this.assayWellsSequenceSWithReadDepth(misreadCounts, occupancyMap, readCountMap, readDepth, readErrorProb, errorCollisionProb, 0, size, sIndices);
-//    }
-//    //returns a map of the counts of the sequence at cell index sIndex, in a specific of wells
-//    //Simulates read depth and read errors, counts the number of reads of a unique sequence into the given map.
-//    public void assayWellsSequenceSWithReadDepth(Map<String, Integer> misreadCounts, Map<String, Integer> occupancyMap, Map<String, Integer> readCountMap,
-//                                                 int readDepth, double readErrorProb, double errorCollisionProb,
-//                                                 int n, int... sIndices) {
-//       this.assayWellsSequenceSWithReadDepth(misreadCounts, occupancyMap, readCountMap, readDepth, readErrorProb, errorCollisionProb, n, n+1, sIndices);
-//    }
-//
-//    //returns a map of the counts of the sequence at cell index sIndex, in a range of wells
-//    //Simulates read depth and read errors, counts the number of reads of a unique sequence into the given map.
-//    public void assayWellsSequenceSWithReadDepth(Map<String, Integer> misreadCounts, Map<String, Integer> occupancyMap, Map<String, Integer> readCountMap,
-//                                                 int readDepth, double readErrorProb, double errorCollisionProb,
-//                                                 int start, int end, int... sIndices) {
-//        for(int sIndex: sIndices){
-//            for(int i = start; i < end; i++){
-//                countSequencesWithReadDepth(misreadCounts, occupancyMap, readCountMap, readDepth, readErrorProb, errorCollisionProb, wells.get(i), sIndex);
-//            }
-//        }
-//    }
-//
-//    //For the sequences at cell indices sIndices, counts number of unique sequences in the given well into the given map
-//    //Simulates read depth and read errors, counts the number of reads of a unique sequence into the given map.
-//    //NOTE: this function changes the content of the well, adding spurious cells to contain the misread sequences
-//    //(this is necessary because, in the simulation, the plate is read multiple times, but random misreads can only
-//    //be simulated once).
-//    //(Possibly I should refactor all of this to only require a single plate assay, to speed things up. Or at least
-//    //to see if it would speed things up.)
-//    private void countSequencesWithReadDepth(Map<String, Integer> distinctMisreadCounts, Map<String, Integer> occupancyMap, Map<String, Integer> readCountMap,
-//                                             int readDepth, double readErrorProb, double errorCollisionProb,
-//                                             List<String[]> well, int... sIndices) {
-//        //list of spurious cells to add to well after counting
-//        List<String[]> spuriousCells = new ArrayList<>();
-//        for(String[] cell : well) {
-//            //new potential spurious cell for each cell that gets read
-//            String[] spuriousCell = new String[SequenceType.values().length];
-//            //initialize spurious cell with all dropout sequences
-//            Arrays.fill(spuriousCell, "-1");
-//            //has a read error occurred?
-//            boolean readError = false;
-//            for(int sIndex: sIndices){
-//                //skip dropout sequences, which have value "-1"
-//                if(!"-1".equals(cell[sIndex])){
-//                    Map<String, Integer> sequencesWithReadCounts = new LinkedHashMap<>();
-//                    for(int i = 0; i < readDepth; i++) {
-//                        if (rand.nextDouble() <= readErrorProb) {
-//                            readError = true;
-//                            //Read errors are represented by appending "*"s to the end of the sequence some number of times
-//                            StringBuilder spurious = new StringBuilder(cell[sIndex]);
-//                            //if this sequence hasn't been misread before, or the read error is unique,
-//                            //append one more "*" than has been appended before
-//                            if (!distinctMisreadCounts.containsKey(cell[sIndex]) || rand.nextDouble() > errorCollisionProb) {
-//                                distinctMisreadCounts.merge(cell[sIndex], 1, (oldValue, newValue) -> oldValue + newValue);
-//                                for (int j = 0; j < distinctMisreadCounts.get(cell[sIndex]); j++) {
-//                                    spurious.append("*");
-//                                }
-//                            }
-//                            //if this is a read error collision, randomly choose a number of "*"s that has been appended before
-//                            else {
-//                                int starCount = rand.nextInt(distinctMisreadCounts.get(cell[sIndex]));
-//                                for (int j = 0; j < starCount; j++) {
-//                                    spurious.append("*");
-//                                }
-//                            }
-//                            sequencesWithReadCounts.merge(spurious.toString(), 1, (oldValue, newValue) -> oldValue + newValue);
-//                            //add spurious sequence to spurious cell
-//                            spuriousCell[sIndex] = spurious.toString();
-//                        }
-//                        else {
-//                            sequencesWithReadCounts.merge(cell[sIndex], 1, (oldValue, newValue) -> oldValue + newValue);
-//                        }
-//                    }
-//                    for(String seq : sequencesWithReadCounts.keySet()) {
-//                        occupancyMap.merge(seq, 1, (oldValue, newValue) -> oldValue + newValue);
-//                        readCountMap.merge(seq, sequencesWithReadCounts.get(seq), (oldValue, newValue) -> oldValue + newValue);
-//                    }
-//                }
-//            }
-//            if (readError) { //only add a new spurious cell if there was a read error
-//                spuriousCells.add(spuriousCell);
-//            }
-//        }
-//        //add all spurious cells to the well
-//        well.addAll(spuriousCells);
-//    }
+    private HashSet<String> assayWells(int[] indices) {
+        HashSet<String> allSequences = new HashSet<>();
+        for (List<String[]> well: wells) {
+            for (String[] cell: well) {
+                for(int index: indices) {
+                    allSequences.add(cell[index]);
+                }
+            }
+        }
+        return allSequences;
+    }
 
     public String getSourceFileName() {
         return sourceFile;

src/main/java/Simulator.java

@@ -27,7 +27,8 @@ public class Simulator implements GraphModificationFunctions {
 
 
     public static GraphWithMapData makeCDR3Graph(CellSample cellSample, Plate samplePlate, int readDepth,
-                                                 double readErrorRate, double errorCollisionRate, boolean verbose) {
+                                                 double readErrorRate, double errorCollisionRate,
+                                                 double realSequenceCollisionRate, boolean verbose) {
         //start timing
         Instant start = Instant.now();
         int[] alphaIndices = {SequenceType.CDR3_ALPHA.ordinal()};
@@ -44,11 +45,11 @@ public class Simulator implements GraphModificationFunctions {
         //Make linkedHashMap keyed to sequences, values are SequenceRecords reflecting plate statistics
         if(verbose){System.out.println("Making sample plate sequence maps");}
         Map<String, SequenceRecord> alphaSequences = samplePlate.countSequences(readDepth, readErrorRate,
-                errorCollisionRate, alphaIndices);
+                errorCollisionRate, realSequenceCollisionRate, alphaIndices);
         int alphaCount = alphaSequences.size();
         if(verbose){System.out.println("Alphas sequences read: " + alphaCount);}
         Map<String, SequenceRecord> betaSequences = samplePlate.countSequences(readDepth, readErrorRate,
-                errorCollisionRate, betaIndices);
+                errorCollisionRate, realSequenceCollisionRate, betaIndices);
         int betaCount = betaSequences.size();
         if(verbose){System.out.println("Betas sequences read: " + betaCount);}
         if(verbose){System.out.println("Sample plate sequence maps made");}
@@ -131,7 +132,7 @@ public class Simulator implements GraphModificationFunctions {
         Duration time = Duration.between(start, stop);
         //create GraphWithMapData object
         GraphWithMapData output = new GraphWithMapData(graph, numWells, samplePlate.getPopulations(), distCellsMapAlphaKey,
-                alphaCount, betaCount, readDepth, readErrorRate, errorCollisionRate, time);
+                alphaCount, betaCount, readDepth, readErrorRate, errorCollisionRate, realSequenceCollisionRate, time);
         //Set source file name in graph to name of sample plate
         output.setSourceFilename(samplePlate.getFilename());
         //return GraphWithMapData object
@@ -307,6 +308,7 @@ public class Simulator implements GraphModificationFunctions {
         metadata.put("sequence read depth", data.getReadDepth().toString());
         metadata.put("sequence read error rate", data.getReadErrorRate().toString());
         metadata.put("read error collision rate", data.getErrorCollisionRate().toString());
+        metadata.put("real sequence collision rate", data.getRealSequenceCollisionRate().toString());
         metadata.put("total alphas read from plate", data.getAlphaCount().toString());
         metadata.put("total betas read from plate", data.getBetaCount().toString());
         //HARD CODED, PARAMETERIZE LATER

src/main/java/Vertex.java

@@ -32,6 +32,8 @@ public class Vertex implements Serializable, Comparable<Vertex> {
 
     public Integer getReadCount() { return record.getReadCount(); }
 
+    public Integer getReadCount(Integer well) { return record.getReadCount(well); }
+
     public Map<Integer, Integer> getWellOccupancies() { return record.getWellOccupancies(); }
 
     @Override //adapted from JGraphT example code