Commit 7930bcb4 authored by bow's avatar bow
Browse files

Add functions to main

parent b91de099
......@@ -223,5 +223,17 @@ object ExtractAlignedFastq extends ToolCommand {
val commandArgs: Args = new OptParser()
.parse(args, Args())
.getOrElse(sys.exit(1))
val memFunc = makeMembershipFunction(
iv = makeFeatureFromString(commandArgs.intervals),
inAln = commandArgs.inputBam,
minMapQ = commandArgs.minMapQ,
commonSuffixLength = commandArgs.commonSuffixLength)
selectFastqReads(memFunc,
inputFastq1 = commandArgs.inputFastq1,
inputFastq2 = commandArgs.inputFastq2,
outputFastq1 = commandArgs.outputFastq1,
outputFastq2 = commandArgs.outputFastq2)
}
}
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