efischer/BiGpairSEQ
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Clear plate in memory when simulating read depth

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eugenefischer
2022-09-26 23:17:10 -05:00
parent db99c74810
commit 077af3b46e
1 changed files with 3 additions and 0 deletions
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3
src/main/java/InteractiveInterface.java
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@@ -264,6 +264,7 @@ public class InteractiveInterface {
System.out.print("\nPlease enter name of an existing sample plate file: "); System.out.print("\nPlease enter name of an existing sample plate file: ");
plateFile = sc.next(); plateFile = sc.next();
System.out.println("\nEnable simulation of sequence read depth and sequence read errors? (y/n)"); 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(); String ans = sc.next();
Pattern pattern = Pattern.compile("(?:yes|y)", Pattern.CASE_INSENSITIVE); Pattern pattern = Pattern.compile("(?:yes|y)", Pattern.CASE_INSENSITIVE);
Matcher matcher = pattern.matcher(ans); Matcher matcher = pattern.matcher(ans);
@@ -271,6 +272,8 @@ public class InteractiveInterface {
simulateReadDepth = true; simulateReadDepth = true;
} }
if (simulateReadDepth) { if (simulateReadDepth) {
BiGpairSEQ.setCachePlate(false);
BiGpairSEQ.clearPlateInMemory();
System.out.print("\nPlease enter read depth (the integer number of reads per sequence): "); System.out.print("\nPlease enter read depth (the integer number of reads per sequence): ");
readDepth = sc.nextInt(); readDepth = sc.nextInt();
if(readDepth < 1) { if(readDepth < 1) {