Commit 6e1f2a48 authored by akaljuvee's avatar akaljuvee
Browse files

added logging about the parameter ''mate_inner_dist'

parent f99febca
......@@ -281,6 +281,9 @@ class Tophat(val parent: Configurable)
.filter(_.startsWith(new File(bowtieIndex).getName))
.exists(_.endsWith(".bt2")))
throw new IllegalArgumentException("No bowtie2 index found for tophat")
if (R2.nonEmpty && mateInnerDist.isEmpty) {
logger.warn("The parameter 'mate_inner_dist' is not set in the configuration, TopHat will use it's default value - 50bp, please check if this value for inner mate distance is correct for the current data.")
}
}
def cmdLine: String =
......
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