add maxScore

adam-core/src/main/scala/org/bdgenomics/adam/algorithms/smithwaterman/SmithWaterman.scala

@@ -24,7 +24,8 @@ abstract class SmithWaterman(xSequence: String, ySequence: String) extends Seria
 
  lazy val (scoringMatrix, moveMatrix) = buildScoringMatrix()
  lazy val (cigarX, cigarY, xStart, yStart) = trackback(scoringMatrix, moveMatrix)
-
+ lazy val maxScore=maxScores(scoringMatrix)
+
  /**
  * Builds Smith-Waterman scoring matrix.
  *
@@ -48,38 +49,47 @@ abstract class SmithWaterman(xSequence: String, ySequence: String) extends Seria
  * @return Tuple of (i, j) coordinates.
  */
  private[smithwaterman] final def maxCoordinates(matrix: Array[Array[Double]]): (Int, Int) = {
- def maxInCol(col: Array[Double]): (Double, Int) = {
- def takeMax(a: (Double, Int), b: (Double, Int)): (Double, Int) = {
- if (a._1 > b._1) {
- a
- } else {
- b
+ var xMax = 0
+ var yMax = 0
+ var max = Double.MinValue
+ var x = 0
+ while (x < matrix.length) {
+ var y = 0
+ while (y < matrix(x).length) {
+ if (matrix(x)(y) >= max) {
+ max = matrix(x)(y)
+ xMax = x
+ yMax = y
  }
+ y += 1
  }
-
- val c: Array[(Double, Int)] = col.zipWithIndex
-
- c.reduce(takeMax)
+ x += 1
  }
+ (yMax, xMax)
+ }
 
- def maxCol(cols: Array[(Double, Int)]): (Int, Int) = {
- def takeMax(a: (Double, Int, Int), b: (Double, Int, Int)): (Double, Int, Int) = {
- if (a._1 > b._1) {
- a
- } else {
- b
+ /**
+ * Finds max Score of a matrix with highest value.
+ *
+ * @param matrix Matrix to score.
+ * @return maxScore: max score in Matrix.
+ */
+ private[smithwaterman] final def maxScores(matrix: Array[Array[Double]]):Double = {
+
+ var maxScoreReturn = 0
+ var max = Double.MinValue
+ var x = 0
+ while (x < matrix.length) {
+ var y = 0
+ while (y < matrix(x).length) {
+ if (matrix(x)(y) >= max) {
+ max = matrix(x)(y)
  }
+ y += 1
  }
-
- val c: Array[((Double, Int), Int)] = cols.zipWithIndex
-
- val m: (Double, Int, Int) = c.map(kv => (kv._1._1, kv._1._2, kv._2))
- .reduce(takeMax)
-
- (m._2, m._3)
+ x += 1
  }
-
- maxCol(matrix.map(maxInCol))
+ max
  }
 
  /**
@@ -130,11 +140,12 @@ abstract class SmithWaterman(xSequence: String, ySequence: String) extends Seria
  *
  * @see buildScoringMatrix
  */
- @tailrec private[smithwaterman] final def move(matrix: Array[Array[Char]],
- i: Int,
- j: Int,
- cX: String,
- cY: String): (String, String, Int, Int) = {
+ @tailrec private[smithwaterman] final def move(
+ matrix: Array[Array[Char]],
+ i: Int,
+ j: Int,
+ cX: String,
+ cY: String): (String, String, Int, Int) = {
  if (matrix(i)(j) == 'T') {
  // return if told to terminate
  (cigarFromRNNCigar(cX), cigarFromRNNCigar(cY), i, j)
@@ -160,8 +171,9 @@ abstract class SmithWaterman(xSequence: String, ySequence: String) extends Seria
  * @param moveMatrix Move matrix to track back on.
  * @return Tuple of Cigar for X, Y.
  */
- private[smithwaterman] def trackback(scoreMatrix: Array[Array[Double]],
- moveMatrix: Array[Array[Char]]): (Cigar, Cigar, Int, Int) = {
+ private[smithwaterman] def trackback(
+ scoreMatrix: Array[Array[Double]],
+ moveMatrix: Array[Array[Char]]): (Cigar, Cigar, Int, Int) = {
  assert(scoreMatrix.length == xSequence.length + 1)
  assert(scoreMatrix.forall(_.length == ySequence.length + 1))
  assert(moveMatrix.length == xSequence.length + 1)

adam-core/src/test/scala/org/bdgenomics/adam/rdd/read/MarkDuplicatesSuite.scala

@@ -172,7 +172,7 @@ class MarkDuplicatesSuite extends ADAMFunSuite {
  assert(dups.size == 10 && dups.forall(p => p.getReadName.startsWith("fragment")))
  }
 
- test("quality scores") {
+ sparkTest("quality scores") {
  // The ascii value 53 is equal to a phred score of 20
  val qual = 53.toChar.toString * 100
  val record = AlignmentRecord.newBuilder().setQual(qual).build()