Commit d0768d9f authored by sajvanderzeeuw's avatar sajvanderzeeuw
Browse files

added all BWA options

parent 7ab284fd
......@@ -68,6 +68,29 @@ class Bwa(val root: Configurable) extends BiopetCommandLineFunction {
required(reference) +
required(R1) +
optional(R2) +
optional("-w", w) +
optional("-d", d) +
optional("-c", c) +
optional("-D", D) +
optional("-W", W) +
optional("-m", m) +
conditional(P, "-P") +
conditional(e, "-e") +
optional("-A", A) +
optional("-B", B) +
optional("-O", O) +
optional("-E", E) +
optional("-L", L) +
optional("-U", U) +
optional("-x", x) +
conditional(p, "-p") +
optional("-v", v) +
optional("-T", T) +
optional("-h", h) +
conditional(a, "-a") +
conditional(C, "-C") +
conditional(Y, "-Y") +
optional("-I", I) +
" > " + required(output)
}
}
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