Commit b0608696 authored by Peter van 't Hof's avatar Peter van 't Hof
Browse files

Fixed style

parent f7e873b0
...@@ -66,7 +66,7 @@ object VcfToTsv extends ToolCommand { ...@@ -66,7 +66,7 @@ object VcfToTsv extends ToolCommand {
opt[String]("list_separator") maxOccurs (1) action { (x, c) => opt[String]("list_separator") maxOccurs (1) action { (x, c) =>
c.copy(listSeparator = x) c.copy(listSeparator = x)
} text ("Optional list separator. By default, lists are separated by a comma") } 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) c.copy(maxDecimals = x)
} text ("Number of decimal places for numbers. Default is 2") } text ("Number of decimal places for numbers. Default is 2")
} }
...@@ -79,7 +79,7 @@ object VcfToTsv extends ToolCommand { ...@@ -79,7 +79,7 @@ object VcfToTsv extends ToolCommand {
// Throw exception if separator and listSeparator are identical // Throw exception if separator and listSeparator are identical
if (commandArgs.separator == commandArgs.listSeparator) throw new IllegalArgumentException( if (commandArgs.separator == commandArgs.listSeparator) throw new IllegalArgumentException(
"Separator and list_separator should not be identical" "Separator and list_separator should not be identical"
) )
val formatter = createFormatter(commandArgs.maxDecimals) val formatter = createFormatter(commandArgs.maxDecimals)
...@@ -101,7 +101,6 @@ object VcfToTsv extends ToolCommand { ...@@ -101,7 +101,6 @@ object VcfToTsv extends ToolCommand {
buffer.toSet[String] buffer.toSet[String]
} }
val sortedFields = sortFields(fields, samples.toList) val sortedFields = sortFields(fields, samples.toList)
val writer = if (commandArgs.outputFile != null) new PrintStream(commandArgs.outputFile) val writer = if (commandArgs.outputFile != null) new PrintStream(commandArgs.outputFile)
...@@ -137,10 +136,10 @@ object VcfToTsv extends ToolCommand { ...@@ -137,10 +136,10 @@ object VcfToTsv extends ToolCommand {
val l = for (g <- genotype.getAlleles) yield vcfRecord.getAlleleIndex(g) val l = for (g <- genotype.getAlleles) yield vcfRecord.getAlleleIndex(g)
l.map(x => if (x < 0) "." else x).mkString("/") l.map(x => if (x < 0) "." else x).mkString("/")
} }
if (genotype.hasAD) values += sample + "-AD" -> List(genotype.getAD: _*).mkString(commandArgs.listSeparator) if (genotype.hasAD) values += sample + "-AD" -> List(genotype.getAD: _*).mkString(commandArgs.listSeparator)
if (genotype.hasDP) values += sample + "-DP" -> genotype.getDP if (genotype.hasDP) values += sample + "-DP" -> genotype.getDP
if (genotype.hasGQ) values += sample + "-GQ" -> genotype.getGQ if (genotype.hasGQ) values += sample + "-GQ" -> genotype.getGQ
if (genotype.hasPL) values += sample + "-PL" -> List(genotype.getPL: _*).mkString(commandArgs.listSeparator) if (genotype.hasPL) values += sample + "-PL" -> List(genotype.getPL: _*).mkString(commandArgs.listSeparator)
for ((field, content) <- genotype.getExtendedAttributes) { for ((field, content) <- genotype.getExtendedAttributes) {
values += sample + "-" + field -> content values += sample + "-" + field -> content
} }
...@@ -164,7 +163,6 @@ object VcfToTsv extends ToolCommand { ...@@ -164,7 +163,6 @@ object VcfToTsv extends ToolCommand {
new DecimalFormat(patternString) new DecimalFormat(patternString)
} }
/** /**
* This fields sorts fields, such that non-info and non-sample specific fields (e.g. general ones) are on front * This fields sorts fields, such that non-info and non-sample specific fields (e.g. general ones) are on front
* followed by info fields * followed by info fields
...@@ -182,7 +180,7 @@ object VcfToTsv extends ToolCommand { ...@@ -182,7 +180,7 @@ object VcfToTsv extends ToolCommand {
fields.toList.sortWith((a, b) => { fields.toList.sortWith((a, b) => {
(fieldType(a), fieldType(b)) match { (fieldType(a), fieldType(b)) match {
case ('g','g') => { case ('g', 'g') => {
val ai = defaultFields.indexOf(a) val ai = defaultFields.indexOf(a)
val bi = defaultFields.indexOf(b) val bi = defaultFields.indexOf(b)
if (bi < 0) true else ai <= bi if (bi < 0) true else ai <= bi
...@@ -191,16 +189,16 @@ object VcfToTsv extends ToolCommand { ...@@ -191,16 +189,16 @@ object VcfToTsv extends ToolCommand {
val sampleA = a.split("-").head val sampleA = a.split("-").head
val sampleB = b.split("-").head val sampleB = b.split("-").head
sampleA.compareTo(sampleB) match { sampleA.compareTo(sampleB) match {
case 0 => !(a.compareTo(b) > 0) case 0 => !(a.compareTo(b) > 0)
case i if (i > 0) => false case i if (i > 0) => false
case _ => true case _ => true
} }
} }
case ('g', _) => true case ('g', _) => true
case (_, 'g') => false case (_, 'g') => false
case (a, b) if a == b => !(a.compareTo(b) > 0) case (a, b) if a == b => !(a.compareTo(b) > 0)
case ('i', _) => true case ('i', _) => true
case _ => false case _ => false
} }
}) })
} }
......
...@@ -64,7 +64,7 @@ class VcfToTsvTest extends TestNGSuite with MockitoSugar with Matchers { ...@@ -64,7 +64,7 @@ class VcfToTsvTest extends TestNGSuite with MockitoSugar with Matchers {
val sorted = sortFields(unsortedFields, samples) val sorted = sortFields(unsortedFields, samples)
sorted should be(List("WeirdField", "INFO-AlleleScoreSomething", "INFO-ScoreSomething", "INFO-Something", sorted should be(List("WeirdField", "INFO-AlleleScoreSomething", "INFO-ScoreSomething", "INFO-Something",
"Child01-GT", "Father03-GT", "Mother02-GT")) "Child01-GT", "Father03-GT", "Mother02-GT"))
} }
} }
Markdown is supported
0% or .
You are about to add 0 people to the discussion. Proceed with caution.
Finish editing this message first!
Please register or to comment