Commit 5571a0d7 authored by Peter van 't Hof's avatar Peter van 't Hof
Browse files

Added more options for bowtie

parent 2df385bf
...@@ -27,13 +27,27 @@ class Bowtie(val root: Configurable) extends BiopetCommandLineFunction { ...@@ -27,13 +27,27 @@ class Bowtie(val root: Configurable) extends BiopetCommandLineFunction {
override val defaultThreads = 8 override val defaultThreads = 8
var sam: Boolean = config("sam", default = true) var sam: Boolean = config("sam", default = true)
var sam_RG: String = _ var sam_RG: String = config("sam-RG")
var seedlen: Option[Int] = config("seedlen")
var k: Option[Int] = config("k")
var m: Option[Int] = config("m")
var best: Boolean = config("best")
var maxbts: Option[Int] = config("maxbts")
var strata: Boolean = config("strata")
var maqerr: Option[Int] = config("maqerr")
def cmdLine = { def cmdLine = {
required(executable) + required(executable) +
optional("--threads", nCoresRequest) + optional("--threads", nCoresRequest) +
conditional(sam, "--sam") + conditional(sam, "--sam") +
required("--sam-RG", sam_RG) + conditional(best, "--best") +
conditional(strata, "--strata") +
optional("--sam-RG", sam_RG) +
optional("--seedlen", seedlen) +
optional("--k", k) +
optional("--m", m) +
optional("--maxbts", maxbts) +
optional("--maqerr", maqerr) +
required(reference) + required(reference) +
required(R1) + required(R1) +
optional(R2) + optional(R2) +
......
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