add per-strand alignment aggregation

weng-lab · Nov 21, 2020 · 65db8a2 · 65db8a2
1 parent f3ac213
commit 65db8a2
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Showing 3 changed files with 28 additions and 4 deletions.
diff --git a/build.gradle.kts b/build.gradle.kts
@@ -9,7 +9,7 @@ plugins {
 }
 
 group = "com.genomealmanac"
-version = "0.6.1"
+version = "0.7.0"
 val artifactID = "bam-aggregate-task"
 
 repositories {

diff --git a/src/main/kotlin/app/Matrix.kt b/src/main/kotlin/app/Matrix.kt
@@ -33,9 +33,10 @@ class Matrix : CliktCommand() {
         .int().default(0)
     private val reverseShift by option("--reverse-shift", help = "if set, shifts reverse strand reads by the given number of basepairs")
         .int().default(0)
+    private val strand by option("--strand", help = "if set, aggregates reads on the given strand only; may be one of 'forward' or 'reverse'")
 
     override fun run() {
-        runTask(regionFiles, alignments, expansionSize, outputDir, randomAccess, batchSize, forwardShift, reverseShift)
+        runTask(regionFiles, alignments, expansionSize, outputDir, randomAccess, batchSize, forwardShift, reverseShift, strand)
     }
 
 }
@@ -48,7 +49,10 @@ class Matrix : CliktCommand() {
  * @param expansionSize number of basepairs by which to expand each region around its center
  * @param outputDir path to directory for writing output files
  */
-private fun runTask(regionFiles: List<Path>, alignments: Path, expansionSize: Int, outputDir: Path, randomAccess: Boolean, batchSize: Int, forwardShift: Int, reverseShift: Int) {
+private fun runTask(
+    regionFiles: List<Path>, alignments: Path, expansionSize: Int, outputDir: Path, randomAccess: Boolean, batchSize: Int, forwardShift: Int, reverseShift: Int,
+    strand: String?
+) {
 
     regionFiles.forEach {
 
@@ -63,7 +67,7 @@ private fun runTask(regionFiles: List<Path>, alignments: Path, expansionSize: In
                 )
             else
                 writeJSONMatrix(
-                    matrix(resizeRegions(regions, expansionSize / 2), alignments, forwardShift, reverseShift),
+                    matrix(resizeRegions(regions, expansionSize / 2), alignments, forwardShift, reverseShift, strand),
                     outputDir.resolve("$combinedOutPrefix$AGGREGATE_TSV_SUFFIX")
                 )
         }

diff --git a/src/test/kotlin/MatrixTests.kt b/src/test/kotlin/MatrixTests.kt
@@ -46,6 +46,26 @@ class MatrixTests {
         assertThat(values).isEqualTo(listOf(listOf(0, 1), listOf(0, 0)))
     }
 
+    @Test
+    fun `Run aggregation on regions with reads on the forward strand only`() {
+        val regions = listOf(
+            Region("chr22", 10602488, 10602489, "", 0, '+'),
+            Region("chr22", 10667451, 10667452, "", 0, '-')
+        )
+        val values = matrix(regions, TEST_BAM_PATH, 0, 0, "forward")
+        assertThat(values).isEqualTo(listOf(listOf(1, 0), listOf(0, 0)))
+    }
+
+    @Test
+    fun `Run aggregation on regions with reads on the reverse strand only`() {
+        val regions = listOf(
+            Region("chr22", 10602488, 10602489, "", 0, '-'),
+            Region("chr22", 10667451, 10667452, "", 0, '+')
+        )
+        val values = matrix(regions, TEST_BAM_PATH, 0, 0, "reverse")
+        assertThat(values).isEqualTo(listOf(listOf(0, 1), listOf(0, 0)))
+    }
+
     @Test
     fun `Run aggregation and write a random access matrix`() {
         val regions = listOf(