Commit 702b9276 authored by Peter van 't Hof's avatar Peter van 't Hof
Browse files

Fixing PR comments

parent 96d882f0
......@@ -172,7 +172,7 @@ object FastqSync extends ToolCommand {
val commandArgs: Args = parseArgs(args)
val subFixes = findR1R2Subfixes(commandArgs.refFastq1, commandArgs.refFastq2)
idSufixes = findR1R2Subfixes(commandArgs.refFastq1, commandArgs.refFastq2)
val refReader = new FastqReader(commandArgs.refFastq1)
val AReader = new FastqReader(commandArgs.inputFastq1)
......@@ -194,6 +194,13 @@ object FastqSync extends ToolCommand {
}
}
/**
* This method will look up the unique suffix for R1 and R2
*
* @param fastqR1 input R1 file
* @param fastqR2 Input R2 file
* @return subfix for (R1, R2)
*/
def findR1R2Subfixes(fastqR1: File, fastqR2: File): (String, String) = {
val refReader1 = new FastqReader(fastqR1)
val refReader2 = new FastqReader(fastqR2)
......@@ -208,6 +215,6 @@ object FastqSync extends ToolCommand {
}
/** Regex for capturing read ID ~ taking into account its read pair mark (if present) */
var idSufixes: (String, String) = _
private var idSufixes: (String, String) = _
}
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