Commit 51d189aa authored by Peter van 't Hof's avatar Peter van 't Hof
Browse files

Adding placeholder for RNA and Target stats

parent 0c9b920b
#{ //TODO: Need content }#
Todo
\ No newline at end of file
package nl.lumc.sasc.biopet.pipelines.bammetrics
import nl.lumc.sasc.biopet.core.report.{ReportBuilder, ReportPage, ReportSection}
import nl.lumc.sasc.biopet.core.report.{ ReportBuilder, ReportPage, ReportSection }
/**
* Created by pjvan_thof on 3/30/15.
......@@ -22,6 +22,8 @@ object BammetricsReport extends ReportBuilder {
"Summary" -> ReportSection("/nl/lumc/sasc/biopet/pipelines/bammetrics/alignmentSummary.ssp"),
"Bam Stats" -> ReportSection("/nl/lumc/sasc/biopet/pipelines/bammetrics/bamStats.ssp"),
"Insert Size" -> ReportSection("/nl/lumc/sasc/biopet/pipelines/bammetrics/insertSize.ssp"),
"RNA (optional)" -> ReportSection("/nl/lumc/sasc/biopet/pipelines/bammetrics/rna.ssp"),
"Target (optional)" -> ReportSection("/nl/lumc/sasc/biopet/pipelines/bammetrics/target.ssp"),
"GC Bias" -> ReportSection("/nl/lumc/sasc/biopet/pipelines/bammetrics/gcBias.ssp")
),
Map()
......
......@@ -66,7 +66,7 @@ object VcfToTsv extends ToolCommand {
opt[String]("list_separator") maxOccurs (1) action { (x, c) =>
c.copy(listSeparator = x)
} text ("Optional list separator. By default, lists are separated by a comma")
opt[Int]("max_decimals") maxOccurs(1) action { (x, c) =>
opt[Int]("max_decimals") maxOccurs (1) action { (x, c) =>
c.copy(maxDecimals = x)
} text ("Number of decimal places for numbers. Default is 2")
}
......@@ -101,7 +101,6 @@ object VcfToTsv extends ToolCommand {
buffer.toSet[String]
}
val sortedFields = sortFields(fields, samples.toList)
val writer = if (commandArgs.outputFile != null) new PrintStream(commandArgs.outputFile)
......@@ -164,7 +163,6 @@ object VcfToTsv extends ToolCommand {
new DecimalFormat(patternString)
}
/**
* This fields sorts fields, such that non-info and non-sample specific fields (e.g. general ones) are on front
* followed by info fields
......@@ -182,7 +180,7 @@ object VcfToTsv extends ToolCommand {
fields.toList.sortWith((a, b) => {
(fieldType(a), fieldType(b)) match {
case ('g','g') => {
case ('g', 'g') => {
val ai = defaultFields.indexOf(a)
val bi = defaultFields.indexOf(b)
if (bi < 0) true else ai <= bi
......
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