efischer/BiGpairSEQ
1
0
Fork 0
Code Issues Pull Requests Projects Releases 13 Wiki Activity

Add menu option to activate simulation of read depth and sequence read errors

Browse Source
This commit is contained in:
eugenefischer
2022-09-26 13:47:19 -05:00
parent d81ab25a68
commit 86371668d5
2 changed files with 5 additions and 3 deletions
Download Patch File Download Diff File Expand all files Collapse all files

2
src/main/java/BiGpairSEQ.java
View File

@@ -176,7 +176,7 @@ public class BiGpairSEQ {
public static void setOutputGraphML(boolean b) {outputGraphML = b;} public static void setOutputGraphML(boolean b) {outputGraphML = b;}
public static String getVersion() { return version; } public static String getVersion() { return version; }
public static boolean getSimulateReadDepth() { public static boolean simulateReadDepth() {
return simulateReadDepth; return simulateReadDepth;
} }

6
src/main/java/InteractiveInterface.java
View File

@@ -505,7 +505,8 @@ public class InteractiveInterface {
System.out.println("3) Turn " + getOnOff(!BiGpairSEQ.cacheGraph()) + " graph/data file caching"); System.out.println("3) Turn " + getOnOff(!BiGpairSEQ.cacheGraph()) + " graph/data file caching");
System.out.println("4) Turn " + getOnOff(!BiGpairSEQ.outputBinary()) + " serialized binary graph output"); System.out.println("4) Turn " + getOnOff(!BiGpairSEQ.outputBinary()) + " serialized binary graph output");
System.out.println("5) Turn " + getOnOff(!BiGpairSEQ.outputGraphML()) + " GraphML graph output (for data portability to other programs)"); System.out.println("5) Turn " + getOnOff(!BiGpairSEQ.outputGraphML()) + " GraphML graph output (for data portability to other programs)");
System.out.println("6) Maximum weight matching algorithm options"); System.out.println("6) Turn " + getOnOff(!BiGpairSEQ.simulateReadDepth()) + " simulation of read depth and sequence read errors");
System.out.println("7) Maximum weight matching algorithm options");
System.out.println("0) Return to main menu"); System.out.println("0) Return to main menu");
try { try {
input = sc.nextInt(); input = sc.nextInt();
@@ -515,7 +516,8 @@ public class InteractiveInterface {
case 3 -> BiGpairSEQ.setCacheGraph(!BiGpairSEQ.cacheGraph()); case 3 -> BiGpairSEQ.setCacheGraph(!BiGpairSEQ.cacheGraph());
case 4 -> BiGpairSEQ.setOutputBinary(!BiGpairSEQ.outputBinary()); case 4 -> BiGpairSEQ.setOutputBinary(!BiGpairSEQ.outputBinary());
case 5 -> BiGpairSEQ.setOutputGraphML(!BiGpairSEQ.outputGraphML()); case 5 -> BiGpairSEQ.setOutputGraphML(!BiGpairSEQ.outputGraphML());
case 6 -> algorithmOptions(); case 6 -> BiGpairSEQ.setSimulateReadDepth(!BiGpairSEQ.simulateReadDepth());
case 7 -> algorithmOptions();
case 0 -> backToMain = true; case 0 -> backToMain = true;
default -> System.out.println("Invalid input"); default -> System.out.println("Invalid input");
} }