Merge branch 'patch-picard_summary' into 'develop'

Fix Picard metrics parsing to use the correct types

Work in progress: don't merge yet.

This merge request is for #151. I implemented a general utility function that should be able to handle arbitrarily large numbers. The trade off is that it loses the type information. Maybe there is some clever way to retain it, based on the return types of the supplied conversion function(s). But for now, this should be sufficient for the fix of issue #151 (there, we pattern match to check the actual type).

There are still some todos:

- [x] Update Picard parsing to handle this
- [x] Add unit tests for the conversion functions
- [ ] Add BigInt and BigDecimal support for the `anyToJson` function (this is optional, I think)

See merge request !148

public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/extensions/picard/CollectAlignmentSummaryMetrics.scala

@@ -70,7 +70,7 @@ class CollectAlignmentSummaryMetrics(val root: Configurable) extends Picard with
     case None => Map()
     case Some((header, content)) =>
       (for (category <- 0 until content.size) yield {
-        content(category)(0) -> (
+        content(category)(0).toString -> (
           for (
             i <- 1 until header.size if i < content(category).size
           ) yield {

public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/extensions/picard/MarkDuplicates.scala

@@ -103,7 +103,7 @@ class MarkDuplicates(val root: Configurable) extends Picard with Summarizable {
     case None => Map()
     case Some((header, content)) =>
       (for (category <- 0 until content.size) yield {
-        content(category)(0) -> (
+        content(category)(0).toString -> (
           for (
             i <- 1 until header.size if i < content(category).size
           ) yield {

public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/extensions/picard/Picard.scala

@@ -16,11 +16,12 @@
 package nl.lumc.sasc.biopet.extensions.picard
 
 import java.io.File
+import scala.io.Source
 
-import nl.lumc.sasc.biopet.core.BiopetJavaCommandLineFunction
-import org.broadinstitute.gatk.utils.commandline.{ Argument }
+import org.broadinstitute.gatk.utils.commandline.Argument
 
-import scala.io.Source
+import nl.lumc.sasc.biopet.core.BiopetJavaCommandLineFunction
+import nl.lumc.sasc.biopet.utils.tryToParseNumber
 
 /**
  * General picard extension
@@ -80,7 +81,7 @@ object Picard {
    * @param file input metrics file
    * @return (header, content)
    */
-  def getMetrics(file: File): Option[(Array[String], List[Array[String]])] =
+  def getMetrics(file: File): Option[(Array[String], List[Array[Any]])] =
     if (file.exists) {
       val lines = Source.fromFile(file).getLines().toArray
 
@@ -88,9 +89,10 @@ object Picard {
       val end = lines.indexOf("", start)
 
       val header = lines(start).split("\t")
-      val content = (for (i <- (start + 1) until end) yield lines(i).split("\t")).toList
+      val content = (for (i <- (start + 1) until end) yield lines(i).split("\t"))
+        .map(row => row.map(col => tryToParseNumber(col, true).getOrElse(col)))
 
-      Option((header, content))
+      Option((header, content.toList))
     } else {
       None
     }

public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/utils/package.scala

+package nl.lumc.sasc.biopet
+
+import scala.util.{ Failure, Success, Try }
+
+/**
+ * General utility functions.
+ *
+ * @author Wibowo Arindrarto <w.arindrarto@lumc.nl>
+ */
+package object utils {
+
+  /** Regular expression for matching entire integer numbers (numbers without decimals / fractions) */
+  val isInteger = """^([-+]?\d+)L?$""".r
+
+  /** Regular expression for matching entire decimal numbers (compatible with the scientific notation) */
+  val isDecimal = """^([-+]?\d*\.?\d+(?:[eE][-+]?[0-9]+)?)$""".r
+
+  /**
+   * Tries to convert the given string with the given conversion functions recursively.
+   *
+   * If conversion is successful, the converted object is returned within as a [[Success]] type. Otherwise, a [[Failure]]
+   * is returned. The order of conversion functions is the same as the order they are specified.
+   *
+   * @param raw the string to convert.
+   * @param funcs one or more conversion functions to apply.
+   * @return a [[Try]] object encapsulating the conversion result.
+   */
+  def tryToConvert(raw: String, funcs: (String => Any)*): Try[Any] = {
+    if (funcs.isEmpty) Try(throw new Exception(s"Can not extract value from string $raw"))
+    else Try(funcs.head(raw))
+      .transform(s => Success(s), f => tryToConvert(raw, funcs.tail: _*))
+  }
+
+  /**
+   * Tries to convert the given string into the appropriate number representation.
+   *
+   * The given string must be whole numbers without any preceeding or succeeding whitespace. This function takes
+   * into account the maximum values of the number object to use. For example, if the raw string represents a bigger
+   * number than the maximum [[Int]] value, then a [[Long]] will be used. If the number is still bigger than a [[Long]],
+   * the [[BigInt]] class will be used. The same is applied for decimal numbers, where the conversion order is first
+   * a [[Double]], then a [[BigDecimal]].
+   *
+   * @param raw the string to convert.
+   * @param fallBack Allows also to return the string itself when converting fails, default false.
+   * @return a [[Try]] object encapsulating the conversion result.
+   */
+  def tryToParseNumber(raw: String, fallBack: Boolean = false) = raw match {
+    case isInteger(i)  => tryToConvert(i, x => x.toInt, x => x.toLong, x => BigInt(x))
+    case isDecimal(f)  => tryToConvert(f, x => x.toDouble, x => BigDecimal(x))
+    case _ if fallBack => Try(raw)
+    case _             => Try(throw new Exception(s"Can not extract number from string $raw"))
+  }
+}

public/biopet-framework/src/test/scala/nl/lumc/sasc/biopet/utils/PackageTest.scala

+package nl.lumc.sasc.biopet.utils
+
+import org.scalatest.Matchers
+import org.scalatest.testng.TestNGSuite
+import org.testng.annotations.Test
+
+import scala.util.Try
+
+/**
+ * Created by pjvan_thof on 4/14/15.
+ */
+class PackageTest extends TestNGSuite with Matchers {
+
+  @Test def testConvert: Unit = {
+    tryToParseNumber("4") shouldBe Try(4)
+    tryToParseNumber("13.37") shouldBe Try(13.37)
+    tryToParseNumber("I'm not a number") should not be Try("I'm not a number")
+
+    tryToParseNumber("4", true) shouldBe Try(4)
+    tryToParseNumber("13.37", true) shouldBe Try(13.37)
+    tryToParseNumber("I'm not a number", true) shouldBe Try("I'm not a number")
+  }
+}