Commit 217f72ff authored by Peter van 't Hof's avatar Peter van 't Hof
Browse files

Added seedmms option

parent 6d77359f
......@@ -29,6 +29,7 @@ class Bowtie(val root: Configurable) extends BiopetCommandLineFunction {
var sam: Boolean = config("sam", default = true)
var sam_RG: String = config("sam-RG")
var seedlen: Option[Int] = config("seedlen")
var seedmms: Option[Int] = config("seedmms")
var k: Option[Int] = config("k")
var m: Option[Int] = config("m")
var best: Boolean = config("best")
......@@ -44,8 +45,9 @@ class Bowtie(val root: Configurable) extends BiopetCommandLineFunction {
conditional(strata, "--strata") +
optional("--sam-RG", sam_RG) +
optional("--seedlen", seedlen) +
optional("--k", k) +
optional("--m", m) +
optional("--seedmms", seedmms) +
optional("-k", k) +
optional("-m", m) +
optional("--maxbts", maxbts) +
optional("--maqerr", maqerr) +
required(reference) +
......
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