Merge baba084 into b29d204

bigdatagenomics · Mar 2, 2016 · 8cc5c6d · 8cc5c6d
2 parents b29d204 + baba084
commit 8cc5c6d
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Showing 3 changed files with 32 additions and 33 deletions.
diff --git a/adam-core/src/main/scala/org/bdgenomics/adam/algorithms/smithwaterman/SmithWaterman.scala b/adam-core/src/main/scala/org/bdgenomics/adam/algorithms/smithwaterman/SmithWaterman.scala
@@ -47,41 +47,26 @@ abstract class SmithWaterman(xSequence: String, ySequence: String) extends Seria
    * @param matrix Matrix to score.
    * @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
+    private[smithwaterman] final def maxCoordinates(matrix: Array[Array[Double]]): (Int, Int) = {
+      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
         }
+        x += 1
       }
-
-      val c: Array[(Double, Int)] = col.zipWithIndex
-
-      c.reduce(takeMax)
+      (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
-        }
-      }
-
-      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)
-    }
-
-    maxCol(matrix.map(maxInCol))
-  }
-
   /**
    * Converts a reversed non-numeric CIGAR into a normal CIGAR.
    *

diff --git a/...in/scala/org/bdgenomics/adam/algorithms/smithwaterman/SmithWatermanGapScoringFromFn.scala b/...in/scala/org/bdgenomics/adam/algorithms/smithwaterman/SmithWatermanGapScoringFromFn.scala
@@ -46,8 +46,10 @@ abstract class SmithWatermanGapScoringFromFn(
     }
 
     // score matrix
-    for (i <- 1 to x) {
-      for (j <- 1 to y) {
+    var i = 1
+    while (i <= x) {
+      var j = 1
+      while (j <= y) {
         val m = scoreMatrix(i - 1)(j - 1) + scoreFn(i, j, xSequence(i - 1), ySequence(j - 1))
         val d = scoreMatrix(i - 1)(j) + scoreFn(i, j, xSequence(i - 1), '_')
         val in = scoreMatrix(i)(j - 1) + scoreFn(i, j, '_', ySequence(j - 1))
@@ -64,7 +66,9 @@ abstract class SmithWatermanGapScoringFromFn(
 
         scoreMatrix(i)(j) = scoreUpdate
         moveMatrix(i)(j) = moveUpdate
+        j += 1
       }
+      i += 1
     }
 
     (scoreMatrix, moveMatrix)

diff --git a/...core/src/test/scala/org/bdgenomics/adam/algorithms/smithwaterman/SmithWatermanSuite.scala b/...core/src/test/scala/org/bdgenomics/adam/algorithms/smithwaterman/SmithWatermanSuite.scala
@@ -19,6 +19,7 @@ package org.bdgenomics.adam.algorithms.smithwaterman
 
 import org.scalatest.FunSuite
 import scala.math.abs
+import scala.util.Random
 
 class SmithWatermanSuite extends FunSuite {
 
@@ -237,4 +238,13 @@ class SmithWatermanSuite extends FunSuite {
     assert(sw.xStart === 8)
   }
 
+  test("smithWaterman - simple alignment") {
+    val sw = new SmithWatermanConstantGapScoring("AAA",
+      "AAT",
+      1.0, 0.0, -0.333, -0.333)
+    assert(sw.cigarX.toString === "3M")
+    assert(sw.cigarY.toString === "3M")
+    assert(sw.xStart === 0)
+  }
+
 }