Purge old code
This commit is contained in:
eugenefischer
@@ -148,37 +148,7 @@ public class Plate {
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return wells;
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}
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// //returns a map of the counts of the sequence at cell index sIndex, in all wells
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// public void assayWellsSequenceS(Map<String, Integer> sequences, int... sIndices){
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// this.assayWellsSequenceS(sequences, 0, size, sIndices);
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// }
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//
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// //returns a map of the counts of the sequence at cell index sIndex, in a specific well
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// public void assayWellsSequenceS(Map<String, Integer> sequences, int n, int... sIndices) {
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// this.assayWellsSequenceS(sequences, n, n+1, sIndices);
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// }
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//
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// //returns a map of the counts of the sequence at cell index sIndex, in a range of wells
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// public void assayWellsSequenceS(Map<String, Integer> sequences, int start, int end, int... sIndices) {
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// for(int sIndex: sIndices){
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// for(int i = start; i < end; i++){
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// countSequences(sequences, wells.get(i), sIndex);
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// }
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// }
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// }
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// //For the sequences at cell indices sIndices, counts number of unique sequences in the given well into the given map
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// private void countSequences(Map<String, Integer> wellMap, List<String[]> well, int... sIndices) {
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// for(String[] cell : well) {
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// for(int sIndex: sIndices){
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// //skip dropout sequences, which have value -1
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// if(!"-1".equals(cell[sIndex])){
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// wellMap.merge(cell[sIndex], 1, (oldValue, newValue) -> oldValue + newValue);
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// }
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// }
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// }
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// }
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//For the sequences at cell indices sIndices, counts number of unique sequences in all well into the given map
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//For the sequences at cell indices sIndices, counts number of unique sequences in all wells into the given map
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public Map<String, SequenceRecord> countSequences(Integer readDepth, Double readErrorRate,
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Double errorCollisionRate, int... sIndices) {
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SequenceType[] sequenceTypes = EnumSet.allOf(SequenceType.class).toArray(new SequenceType[0]);
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@@ -231,98 +201,6 @@ public class Plate {
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return sequenceMap;
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}
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// //returns a map of the counts of the sequence at cell index sIndex, in all wells
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// //Simulates read depth and read errors, counts the number of reads of a unique sequence into the given map.
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// public void assayWellsSequenceSWithReadDepth(Map<String, Integer> misreadCounts, Map<String, Integer> occupancyMap, Map<String, Integer> readCountMap,
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// int readDepth, double readErrorProb, double errorCollisionProb, int... sIndices) {
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// this.assayWellsSequenceSWithReadDepth(misreadCounts, occupancyMap, readCountMap, readDepth, readErrorProb, errorCollisionProb, 0, size, sIndices);
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// }
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// //returns a map of the counts of the sequence at cell index sIndex, in a specific of wells
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// //Simulates read depth and read errors, counts the number of reads of a unique sequence into the given map.
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// public void assayWellsSequenceSWithReadDepth(Map<String, Integer> misreadCounts, Map<String, Integer> occupancyMap, Map<String, Integer> readCountMap,
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// int readDepth, double readErrorProb, double errorCollisionProb,
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// int n, int... sIndices) {
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// this.assayWellsSequenceSWithReadDepth(misreadCounts, occupancyMap, readCountMap, readDepth, readErrorProb, errorCollisionProb, n, n+1, sIndices);
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// }
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//
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// //returns a map of the counts of the sequence at cell index sIndex, in a range of wells
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// //Simulates read depth and read errors, counts the number of reads of a unique sequence into the given map.
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// public void assayWellsSequenceSWithReadDepth(Map<String, Integer> misreadCounts, Map<String, Integer> occupancyMap, Map<String, Integer> readCountMap,
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// int readDepth, double readErrorProb, double errorCollisionProb,
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// int start, int end, int... sIndices) {
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// for(int sIndex: sIndices){
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// for(int i = start; i < end; i++){
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// countSequencesWithReadDepth(misreadCounts, occupancyMap, readCountMap, readDepth, readErrorProb, errorCollisionProb, wells.get(i), sIndex);
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// }
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// }
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// }
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//
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// //For the sequences at cell indices sIndices, counts number of unique sequences in the given well into the given map
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// //Simulates read depth and read errors, counts the number of reads of a unique sequence into the given map.
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// //NOTE: this function changes the content of the well, adding spurious cells to contain the misread sequences
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// //(this is necessary because, in the simulation, the plate is read multiple times, but random misreads can only
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// //be simulated once).
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// //(Possibly I should refactor all of this to only require a single plate assay, to speed things up. Or at least
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// //to see if it would speed things up.)
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// private void countSequencesWithReadDepth(Map<String, Integer> distinctMisreadCounts, Map<String, Integer> occupancyMap, Map<String, Integer> readCountMap,
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// int readDepth, double readErrorProb, double errorCollisionProb,
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// List<String[]> well, int... sIndices) {
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// //list of spurious cells to add to well after counting
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// List<String[]> spuriousCells = new ArrayList<>();
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// for(String[] cell : well) {
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// //new potential spurious cell for each cell that gets read
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// String[] spuriousCell = new String[SequenceType.values().length];
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// //initialize spurious cell with all dropout sequences
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// Arrays.fill(spuriousCell, "-1");
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// //has a read error occurred?
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// boolean readError = false;
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// for(int sIndex: sIndices){
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// //skip dropout sequences, which have value "-1"
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// if(!"-1".equals(cell[sIndex])){
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// Map<String, Integer> sequencesWithReadCounts = new LinkedHashMap<>();
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// for(int i = 0; i < readDepth; i++) {
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// if (rand.nextDouble() <= readErrorProb) {
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// readError = true;
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// //Read errors are represented by appending "*"s to the end of the sequence some number of times
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// StringBuilder spurious = new StringBuilder(cell[sIndex]);
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// //if this sequence hasn't been misread before, or the read error is unique,
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// //append one more "*" than has been appended before
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// if (!distinctMisreadCounts.containsKey(cell[sIndex]) || rand.nextDouble() > errorCollisionProb) {
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// distinctMisreadCounts.merge(cell[sIndex], 1, (oldValue, newValue) -> oldValue + newValue);
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// for (int j = 0; j < distinctMisreadCounts.get(cell[sIndex]); j++) {
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// spurious.append("*");
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// }
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// }
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// //if this is a read error collision, randomly choose a number of "*"s that has been appended before
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// else {
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// int starCount = rand.nextInt(distinctMisreadCounts.get(cell[sIndex]));
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// for (int j = 0; j < starCount; j++) {
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// spurious.append("*");
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// }
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// }
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// sequencesWithReadCounts.merge(spurious.toString(), 1, (oldValue, newValue) -> oldValue + newValue);
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// //add spurious sequence to spurious cell
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// spuriousCell[sIndex] = spurious.toString();
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// }
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// else {
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// sequencesWithReadCounts.merge(cell[sIndex], 1, (oldValue, newValue) -> oldValue + newValue);
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// }
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// }
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// for(String seq : sequencesWithReadCounts.keySet()) {
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// occupancyMap.merge(seq, 1, (oldValue, newValue) -> oldValue + newValue);
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// readCountMap.merge(seq, sequencesWithReadCounts.get(seq), (oldValue, newValue) -> oldValue + newValue);
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// }
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// }
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// }
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// if (readError) { //only add a new spurious cell if there was a read error
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// spuriousCells.add(spuriousCell);
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// }
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// }
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// //add all spurious cells to the well
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// well.addAll(spuriousCells);
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// }
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public String getSourceFileName() {
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return sourceFile;
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}
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