efischer/BiGpairSEQ
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Bug fix, add comments

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eugenefischer
2022-09-28 18:09:47 -05:00
parent 34dc2a5721
commit e5803defa3
1 changed files with 11 additions and 6 deletions
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17
src/main/java/Plate.java
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@@ -162,15 +162,18 @@ public class Plate {
public Map<String, SequenceRecord> countSequences(Integer readDepth, Double readErrorRate, public Map<String, SequenceRecord> countSequences(Integer readDepth, Double readErrorRate,
Double errorCollisionRate, Double realSequenceCollisionRate, int... sIndices) { Double errorCollisionRate, Double realSequenceCollisionRate, int... sIndices) {
SequenceType[] sequenceTypes = EnumSet.allOf(SequenceType.class).toArray(new SequenceType[0]); SequenceType[] sequenceTypes = EnumSet.allOf(SequenceType.class).toArray(new SequenceType[0]);
//Map of all sequences read. Keys are sequences, values are ways sequence has been misread. //Map of all real sequences read. Keys are sequences, values are ways sequence has been misread.
Map<String, List<String>> sequencesAndMisreads = new HashMap<>(); 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<>(); Map<String, SequenceRecord> sequenceMap = new LinkedHashMap<>();
for (int well = 0; well < size; well++) { for (int well = 0; well < size; well++) {
for (String[] cell : wells.get(well)) { for (String[] cell: wells.get(well)) {
for (int sIndex : sIndices) { for (int sIndex: sIndices) {
//the sequence being read
String currentSequence = cell[sIndex]; String currentSequence = cell[sIndex];
//skip dropout sequences, which have value -1 //skip dropout sequences, which have value -1
if (!"-1".equals(currentSequence)) { if (!"-1".equals(currentSequence)) {
//keep rereading the sequence until the read depth is reached
for (int j = 0; j < readDepth; j++) { for (int j = 0; j < readDepth; j++) {
//The sequence is misread //The sequence is misread
if (rand.nextDouble() < readErrorRate) { if (rand.nextDouble() < readErrorRate) {
@@ -180,7 +183,7 @@ public class Plate {
} }
//The specific misread hasn't happened before //The specific misread hasn't happened before
if (rand.nextDouble() >= errorCollisionRate || sequencesAndMisreads.get(currentSequence).size() == 0) { if (rand.nextDouble() >= errorCollisionRate || sequencesAndMisreads.get(currentSequence).size() == 0) {
//The misread doesn't collide with a real sequence already on the plate //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()){ if(rand.nextDouble() >= realSequenceCollisionRate || !sequenceMap.isEmpty()){
StringBuilder spurious = new StringBuilder(currentSequence); StringBuilder spurious = new StringBuilder(currentSequence);
for (int k = 0; k <= sequencesAndMisreads.get(currentSequence).size(); k++) { for (int k = 0; k <= sequencesAndMisreads.get(currentSequence).size(); k++) {
@@ -202,9 +205,11 @@ public class Plate {
wrongSequence = sequencesAndMisreads.keySet().toArray(new String[0])[index]; wrongSequence = sequencesAndMisreads.keySet().toArray(new String[0])[index];
//make sure it's not accidentally the *right* sequence //make sure it's not accidentally the *right* sequence
//Also that it's not a wrong sequence already in the misread list //Also that it's not a wrong sequence already in the misread list
} while(cell[sIndex].equals(wrongSequence) || sequencesAndMisreads.get(currentSequence).contains(wrongSequence)); } while(currentSequence.equals(wrongSequence) || sequencesAndMisreads.get(currentSequence).contains(wrongSequence));
//update the SequenceRecord for wrongSequence
sequenceMap.get(wrongSequence).addRead(well); sequenceMap.get(wrongSequence).addRead(well);
//add wrongSequence to the misreads for currentSequence
sequencesAndMisreads.get(currentSequence).add(wrongSequence);
} }
} }
} }