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

Add real sequence collision rate

Browse Source
This commit is contained in:
eugenefischer
2022-09-28 17:43:21 -05:00
parent 89687fa849
commit 9dacd8cd34
1 changed files with 14 additions and 5 deletions
Download Patch File Download Diff File Expand all files Collapse all files

19
src/main/java/InteractiveInterface.java
View File

@@ -255,6 +255,7 @@ public class InteractiveInterface {
int readDepth = 1; int readDepth = 1;
double readErrorRate = 0.0; double readErrorRate = 0.0;
double errorCollisionRate = 0.0; double errorCollisionRate = 0.0;
double realSequenceCollisionRate = 0.0;
try { try {
String str = "\nGenerating bipartite weighted graph encoding occupancy overlap data "; String str = "\nGenerating bipartite weighted graph encoding occupancy overlap data ";
str = str.concat("\nrequires a cell sample file and a sample plate file."); str = str.concat("\nrequires a cell sample file and a sample plate file.");
@@ -271,22 +272,29 @@ public class InteractiveInterface {
simulateReadDepth = true; simulateReadDepth = true;
} }
if (simulateReadDepth) { if (simulateReadDepth) {
System.out.print("\nPlease enter read depth (the integer number of reads per sequence): "); System.out.print("\nPlease enter the read depth (the integer number of times a sequence is read): ");
readDepth = sc.nextInt(); readDepth = sc.nextInt();
if(readDepth < 1) { if(readDepth < 1) {
throw new InputMismatchException("The read depth must be an integer >= 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): "); System.out.println("\nPlease enter the read error probability (0.0 to 1.0)");
System.out.print("(The probability that a sequence will be misread): ");
readErrorRate = sc.nextDouble(); readErrorRate = sc.nextDouble();
if(readErrorRate < 0.0 || readErrorRate > 1.0) { if(readErrorRate < 0.0 || readErrorRate > 1.0) {
throw new InputMismatchException("The read error probability 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 (0.0 to 1.0)"); System.out.println("\nPlease enter the error collision probability (0.0 to 1.0)");
System.out.print("(The probability that two misreads produce the same spurious sequence): "); System.out.print("(The probability of a sequence being misread in a way it has been misread before): ");
errorCollisionRate = sc.nextDouble(); errorCollisionRate = sc.nextDouble();
if(errorCollisionRate < 0.0 || errorCollisionRate > 1.0) { if(errorCollisionRate < 0.0 || errorCollisionRate > 1.0) {
throw new InputMismatchException("The error collision probability must be an 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("\nPlease enter the real sequence collision probability (0.0 to 1.0)");
System.out.print("(The probability that a (non-collision) misread produces a different, real sequence): ");
realSequenceCollisionRate = sc.nextDouble();
if(realSequenceCollisionRate < 0.0 || realSequenceCollisionRate > 1.0) {
throw new InputMismatchException("The real sequence 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."); System.out.println("\nThe graph and occupancy data will be written to a file.");
System.out.print("Please enter a name for the output file: "); System.out.print("Please enter a name for the output file: ");
@@ -334,7 +342,8 @@ public class InteractiveInterface {
System.out.println("Returning to main menu."); System.out.println("Returning to main menu.");
} }
else{ else{
GraphWithMapData data = Simulator.makeCDR3Graph(cellSample, plate, readDepth, readErrorRate, errorCollisionRate, true); GraphWithMapData data = Simulator.makeCDR3Graph(cellSample, plate, readDepth, readErrorRate,
errorCollisionRate, realSequenceCollisionRate, true);
assert filename != null; assert filename != null;
if(BiGpairSEQ.outputBinary()) { if(BiGpairSEQ.outputBinary()) {
GraphDataObjectWriter dataWriter = new GraphDataObjectWriter(filename, data); GraphDataObjectWriter dataWriter = new GraphDataObjectWriter(filename, data);