diff --git a/src/main/java/Plate.java b/src/main/java/Plate.java index 0e8704b..75f3a86 100644 --- a/src/main/java/Plate.java +++ b/src/main/java/Plate.java @@ -184,18 +184,9 @@ public class Plate { SequenceType[] sequenceTypes = EnumSet.allOf(SequenceType.class).toArray(new SequenceType[0]); Map distinctMisreadCounts = new HashMap<>(); Map sequenceMap = new LinkedHashMap<>(); - //booleans for testing - Boolean first= false; - Boolean second = false; - Boolean third = false; - Boolean fourth = false; - for (int well = 0; well < size; well++) { - first = true; for (String[] cell : wells.get(well)) { - second = true; for (int sIndex : sIndices) { - third = true; //skip dropout sequences, which have value -1 if (!"-1".equals(cell[sIndex])) { for (int j = 0; j < readDepth; j++) { @@ -204,7 +195,7 @@ public class Plate { 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() > errorCollisionRate) { + 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++) { spurious.append("*"); @@ -224,7 +215,6 @@ public class Plate { } //sequence is read correctly else { - fourth = true; if (!sequenceMap.containsKey(cell[sIndex])) { SequenceRecord tmp = new SequenceRecord(cell[sIndex], sequenceTypes[sIndex]); tmp.addRead(well); @@ -238,11 +228,6 @@ public class Plate { } } } - System.out.println("First: " + first.toString()); - System.out.println("Second: " + second.toString()); - System.out.println("Third: " + third.toString()); - System.out.println("Fourth: " + fourth.toString()); - System.out.println(sequenceMap.size()); return sequenceMap; }