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Add code to simulate read depth

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eugenefischer
2022-09-26 16:52:56 -05:00
parent 1ddac63b0a
commit 36c628cde5
2 changed files with 62 additions and 6 deletions
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8
src/main/java/InteractiveInterface.java
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@@ -252,9 +252,9 @@ public class InteractiveInterface {
String plateFile = null;
Boolean simulateReadDepth = false;
//number of times to read each sequence in a well
Integer readDepth = 1;
Double readErrorRate = 0.0;
Double errorCollisionRate = 0.0;
int readDepth = 1;
double readErrorRate = 0.0;
double errorCollisionRate = 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.");
@@ -283,7 +283,7 @@ public class InteractiveInterface {
System.out.print("(0.0 to 1.0): ");
errorCollisionRate = sc.nextDouble();
if(errorCollisionRate < 0.0 || errorCollisionRate > 1.0) {
throw new InputMismatchException("The error collision rate must be in the range [0.0, 1.0]");
throw new InputMismatchException("The error 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.");