Commit 19236e6f authored by Peter van 't Hof's avatar Peter van 't Hof
Browse files

Added piping to freebayes

parent cf10ac0c
......@@ -149,7 +149,6 @@ class Freebayes(val root: Configurable) extends BiopetCommandLineFunction with R
optional("--contamination-estimates", contamination_estimates) +
optional("--variant-input", variant_input) +
optional("--haplotype-basis-alleles", haplotype_basis_alleles) +
optional("--vcf", outputVcf) +
optional("--pvar", pvar) +
optional("--theta", theta) +
optional("--ploidy", ploidy) +
......@@ -202,5 +201,7 @@ class Freebayes(val root: Configurable) extends BiopetCommandLineFunction with R
conditional(harmonic_indel_quality, "--harmonic-indel-quality") +
conditional(genotype_qualities, "--genotype-qualities") +
conditional(debug, "--debug") +
optional("--haplotype-length", haplotypeLength)
optional("--haplotype-length", haplotypeLength) +
(if (inputAsStdin) required("--stdin") else "") +
(if (outputAsStsout) "" else optional("--vcf", outputVcf))
}
......@@ -14,15 +14,9 @@ class Freebayes(val root: Configurable) extends Variantcaller {
val fb = new nl.lumc.sasc.biopet.extensions.Freebayes(this)
fb.bamfiles = inputBams.values.toList
fb.outputVcf = new File(outputDir, namePrefix + ".freebayes.vcf")
fb.isIntermediate = true
add(fb)
//fb.isIntermediate = true
add(fb | new Bgzip(this) > outputFile)
//TODO: need piping for this, see also issue #114
val bz = new Bgzip(this)
bz.input = List(fb.outputVcf)
bz.output = outputFile
add(bz)
add(Tabix.apply(this, bz.output))
add(Tabix.apply(this, outputFile))
}
}
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