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Implement read count for vertices

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eugenefischer
2022-09-26 19:42:19 -05:00
parent 19a2a35f07
commit 199c81f983
6 changed files with 93 additions and 15 deletions
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5
src/main/java/InteractiveInterface.java
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@@ -273,6 +273,9 @@ public class InteractiveInterface {
if (simulateReadDepth) {
System.out.print("\nPlease enter read depth (the integer number of reads per sequence): ");
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): ");
readErrorRate = sc.nextDouble();
if(readErrorRate < 0.0 || readErrorRate > 1.0) {
@@ -332,7 +335,7 @@ public class InteractiveInterface {
System.out.println("Returning to main menu.");
}
else{
GraphWithMapData data = Simulator.makeGraph(cellSample, plate, true);
GraphWithMapData data = Simulator.makeGraph(cellSample, plate, readDepth, readErrorRate, errorCollisionRate, true);
assert filename != null;
if(BiGpairSEQ.outputBinary()) {
GraphDataObjectWriter dataWriter = new GraphDataObjectWriter(filename, data);