Commit c5f4ca8b authored by Peter van 't Hof's avatar Peter van 't Hof
Browse files

Fix compile errors

parent 038301cc
......@@ -16,7 +16,7 @@ import nl.lumc.sasc.biopet.core.config.Configurable
* Written based on cufflinks version v2.2.1.
*/
class Cufflinks(val root: Configurable) extends BiopetCommandLineFunction {
/** default executable */
executable = config("exe", default = "cufflinks")
......@@ -31,7 +31,7 @@ class Cufflinks(val root: Configurable) extends BiopetCommandLineFunction {
if (input == null || output_dir == null)
throw new RuntimeException("Unexpected error when trying to set cufflinks GTF output")
// cufflinks always outputs a transcripts.gtf file in the output directory
output_dir.getCanonicalPath() + File.pathSeparator + "transcripts.gtf"
new File(output_dir + File.pathSeparator + "transcripts.gtf")
}
@Output(doc = "Output isoform FPKM file")
......@@ -39,7 +39,7 @@ class Cufflinks(val root: Configurable) extends BiopetCommandLineFunction {
if (input == null || output_dir == null)
throw new RuntimeException("Unexpected error when trying to set cufflinks isoform FPKM output")
// cufflinks always outputs a isoforms.fpkm_tracking file in the output directory
output_dir.getCanonicalPath() + File.pathSeparator + "isoforms.fpkm_tracking"
new File(output_dir + File.pathSeparator + "isoforms.fpkm_tracking")
}
@Output(doc = "Output GTF file")
......@@ -47,11 +47,11 @@ class Cufflinks(val root: Configurable) extends BiopetCommandLineFunction {
if (input == null || output_dir == null)
throw new RuntimeException("Unexpected error when trying to set cufflinks genes FPKM output")
// cufflinks always outputs a genes.fpkm_tracking file in the output directory
output_dir.getCanonicalPath() + File.pathSeparator + "genes.fpkm_tracking"
new File(output_dir + File.pathSeparator + "genes.fpkm_tracking")
}
/** write all output files to this directory [./] */
var output_dir: String = config("output_dir", required = true)
var output_dir: String = _
/** number of threads used during analysis [1] */
var num_threads: Option[Int] = config("num_threads")
......@@ -72,7 +72,7 @@ class Cufflinks(val root: Configurable) extends BiopetCommandLineFunction {
var frag_bias_correct: String = config("frag_bias_correct")
/** use 'rescue method' for multi-reads (more accurate) [FALSE] */
var multi_read_correct: Bool = config("multi_read_correct")
var multi_read_correct: Boolean = config("multi_read_correct")
/** library prep used for input reads [below] */
var library_type: String = config("library_type")
......@@ -90,10 +90,10 @@ class Cufflinks(val root: Configurable) extends BiopetCommandLineFunction {
var max_mle_iterations: Option[Int] = config("max_mle_iterations")
/** count hits compatible with reference RNAs only [FALSE] */
var compatible_hits_norm: Bool = config("compatible_hits_norm")
var compatible_hits_norm: Boolean = config("compatible_hits_norm")
/** count all hits for normalization [TRUE] */
var total_hits_norm: Bool = config("total_hits_norm")
var total_hits_norm: Boolean = config("total_hits_norm")
/** Number of fragment generation samples [100] */
var num_frag_count_draws: Option[Int] = config("num_frag_count_draws")
......@@ -105,10 +105,10 @@ class Cufflinks(val root: Configurable) extends BiopetCommandLineFunction {
var max_frag_multihits: String = config("max_frag_multihits")
/** No effective length correction [FALSE] */
var no_effective_length_correction: Bool = config("no_effective_length_correction")
var no_effective_length_correction: Boolean = config("no_effective_length_correction")
/** No length correction [FALSE] */
var no_length_correction: Bool = config("no_length_correction")
var no_length_correction: Boolean = config("no_length_correction")
/** assembled transcripts have this ID prefix [CUFF] */
var label: String = config("label")
......@@ -156,7 +156,7 @@ class Cufflinks(val root: Configurable) extends BiopetCommandLineFunction {
var overlap_radius: Option[Int] = config("overlap_radius")
/** disable tiling by faux reads [FALSE] */
var no_faux_reads: Bool = config("no_faux_reads")
var no_faux_reads: Boolean = config("no_faux_reads")
/** overhang allowed on 3' end when merging with reference [600] */
var flag_3_overhang_tolerance: Option[Int] = config("flag_3_overhang_tolerance")
......@@ -165,13 +165,13 @@ class Cufflinks(val root: Configurable) extends BiopetCommandLineFunction {
var intron_overhang_tolerance: Option[Int] = config("intron_overhang_tolerance")
/** log-friendly verbose processing (no progress bar) [FALSE] */
var verbose: Bool = config("verbose")
var verbose: Boolean = config("verbose")
/** log-friendly quiet processing (no progress bar) [FALSE] */
var quiet: Bool = config("quiet")
var quiet: Boolean = config("quiet")
/** do not contact server to check for update availability [FALSE] */
var no_update_check: Bool = config("no_update_check")
var no_update_check: Boolean = config("no_update_check")
override val versionRegex = """cufflinks v(.*)""".r
override def versionCommand = executable
......
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