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Added metadata to MatchingResult to enable CLI options

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efischer
2022-02-22 18:36:30 -06:00
parent 90ae2ff474
commit 906c06062f
8 changed files with 417 additions and 370 deletions
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10
src/main/java/CommandLineInterface.java
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@@ -188,13 +188,14 @@ public class CommandLineInterface {
CommandLine line = parser.parse(mainOptions, args);
if(line.hasOption("match")){
//line = parser.parse(mainOptions, args);
String cellFile = line.getOptionValue("c");
//String cellFile = line.getOptionValue("c");
String graphFile = line.getOptionValue("g");
Integer lowThreshold = Integer.valueOf(line.getOptionValue(lowThresh));
Integer highThreshold = Integer.valueOf(line.getOptionValue(highThresh));
Integer occupancyDifference = Integer.valueOf(line.getOptionValue(occDiff));
Integer overlapPercent = Integer.valueOf(line.getOptionValue(overlapPer));
for(String plate: line.getOptionValues("p")) {
matchCDR3s(cellFile, plate, lowThreshold, highThreshold, occupancyDifference, overlapPercent);
matchCDR3s(graphFile, lowThreshold, highThreshold, occupancyDifference, overlapPercent);
}
}
else if(line.hasOption("cells")){
@@ -280,4 +281,9 @@ public class CommandLineInterface {
PlateFileWriter writer = new PlateFileWriter(filename, samplePlate);
writer.writePlateFile();
}
private static void matchCDR3s(String graphFile, Integer lowThreshold, Integer highThreshold,
Integer occupancyDifference, Integer overlapPercent) {
}
}