Commit 6b69a6d5 authored by Peter van 't Hof's avatar Peter van 't Hof
Browse files

Added -s and -S option

parent 1f6b6d87
......@@ -16,6 +16,12 @@ class BedtoolsCoverage(val root: Configurable) extends Bedtools {
@Argument(doc = "dept", required = false)
var depth: Boolean = false
@Argument(doc = "sameStrand", required = false)
var sameStrand: Boolean = false
@Argument(doc = "diffStrand", required = false)
var diffStrand: Boolean = false
var inputTag = "-a"
......@@ -27,17 +33,21 @@ class BedtoolsCoverage(val root: Configurable) extends Bedtools {
required(inputTag, input) +
required("-b", intersectFile) +
conditional(depth, "-d") +
conditional(sameStrand, "-s") +
conditional(diffStrand, "-S") +
" > " + required(output)
}
object BedtoolsCoverage {
def apply(root: Configurable, input: File, intersect: File, output: File,
depth: Boolean = true): BedtoolsCoverage = {
depth: Boolean = true, sameStrand: Boolean = false, diffStrand: Boolean = false): BedtoolsCoverage = {
val bedtoolsCoverage = new BedtoolsCoverage(root)
bedtoolsCoverage.input = input
bedtoolsCoverage.intersectFile = intersect
bedtoolsCoverage.output = output
bedtoolsCoverage.depth = depth
bedtoolsCoverage.sameStrand = sameStrand
bedtoolsCoverage.diffStrand = diffStrand
return bedtoolsCoverage
}
}
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