diff --git a/src/main/java/InteractiveInterface.java b/src/main/java/InteractiveInterface.java index f367a0a..5c1f14f 100644 --- a/src/main/java/InteractiveInterface.java +++ b/src/main/java/InteractiveInterface.java @@ -264,7 +264,6 @@ public class InteractiveInterface { System.out.print("\nPlease enter name of an existing sample plate file: "); plateFile = sc.next(); System.out.println("\nEnable simulation of sequence read depth and sequence read errors? (y/n)"); - System.out.println("NOTE: sample plate data cannot be cached when simulating read errors"); String ans = sc.next(); Pattern pattern = Pattern.compile("(?:yes|y)", Pattern.CASE_INSENSITIVE); Matcher matcher = pattern.matcher(ans); @@ -272,8 +271,6 @@ public class InteractiveInterface { simulateReadDepth = true; } if (simulateReadDepth) { - BiGpairSEQ.setCachePlate(false); - BiGpairSEQ.clearPlateInMemory(); System.out.print("\nPlease enter read depth (the integer number of reads per sequence): "); readDepth = sc.nextInt(); if(readDepth < 1) { @@ -282,11 +279,10 @@ public class InteractiveInterface { 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) { - throw new InputMismatchException("The read error rate must be in the range [0.0, 1.0]"); + throw new InputMismatchException("The read error probability must be in the range [0.0, 1.0]"); } - System.out.println("\nPlease enter the probability of read error collision"); - System.out.println("(the likelihood that two read errors produce the same spurious sequence)"); - System.out.print("(0.0 to 1.0): "); + System.out.println("\nPlease enter the probability of read error collision (0.0 to 1.0)"); + System.out.print("(The probability that two misreads produce the same spurious sequence): "); errorCollisionRate = sc.nextDouble(); if(errorCollisionRate < 0.0 || errorCollisionRate > 1.0) { throw new InputMismatchException("The error collision probability must be an in the range [0.0, 1.0]");