Merge pull request #275 from maize-genetics/graph-constructor-dir

Graph constructor dir
maize-genetics · Jan 22, 2025 · 1ee20bf · 1ee20bf
2 parents 1571725 + 2edbeea
commit 1ee20bf
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diff --git a/src/main/kotlin/net/maizegenetics/phgv2/api/HaplotypeGraph.kt b/src/main/kotlin/net/maizegenetics/phgv2/api/HaplotypeGraph.kt
@@ -39,6 +39,20 @@ class HaplotypeGraph(hvcfFiles: List<String>) {
     // Map<ID (checksum), AltHeaderMetaData>
     private lateinit var altHeaderMap: Map<String, AltHeaderMetaData>
 
+    constructor(hvcfDirectory: String) : this(
+        File(hvcfDirectory)
+            .walk()
+            .filter {
+                it.isFile && (it.name.endsWith(".h.vcf") || it.name.endsWith(".h.vcf.gz") ||
+                        it.name.endsWith(".hvcf") || it.name.endsWith(".hvcf.gz"))
+            }
+            .map { it.absolutePath }
+            .toList()
+    ) {
+        require(File(hvcfDirectory).exists()) { "HVCF directory does not exist: $hvcfDirectory" }
+        require(File(hvcfDirectory).isDirectory) { "Provided path is not a directory: $hvcfDirectory" }
+    }
+
     init {
 
         getSampleNamesALTHeaders(hvcfFiles)

diff --git a/src/test/kotlin/net/maizegenetics/phgv2/api/HaplotypeGraphTest.kt b/src/test/kotlin/net/maizegenetics/phgv2/api/HaplotypeGraphTest.kt
@@ -1,15 +1,33 @@
 package net.maizegenetics.phgv2.api
 
 import net.maizegenetics.phgv2.cli.TestExtension
+import org.junit.jupiter.api.BeforeAll
 import org.junit.jupiter.api.Test
 import org.junit.jupiter.api.assertThrows
 import org.junit.jupiter.api.extension.ExtendWith
+import java.io.File
 import kotlin.test.assertEquals
 import kotlin.test.assertTrue
 
 @ExtendWith(TestExtension::class)
 class HaplotypeGraphTest {
 
+    companion object {
+
+        private val multiInputDir = "${TestExtension.tempDir}/graph-input-dir/"
+
+        @BeforeAll
+        @JvmStatic
+        fun setup() {
+            File(multiInputDir).mkdirs()
+
+            File(TestExtension.smallseqRefHvcfFile).copyTo(File(multiInputDir + File(TestExtension.smallseqRefHvcfFile).name))
+            File(TestExtension.smallseqLineAHvcfFile).copyTo(File(multiInputDir + File(TestExtension.smallseqLineAHvcfFile).name))
+            File(TestExtension.smallseqLineBHvcfFile).copyTo(File(multiInputDir + File(TestExtension.smallseqLineBHvcfFile).name))
+        }
+
+    }
+
     @Test
     fun testHaplotypeGraph() {
 
@@ -111,6 +129,81 @@ class HaplotypeGraphTest {
 
     }
 
+    @Test
+    fun testDirectoryHaplotypeGraph() {
+
+        val graph = HaplotypeGraph(multiInputDir)
+
+        assertTrue(
+            graph.checksum == "1e3d5c6ed7d43c1725542d826a515b16",
+            "checksum not 1e3d5c6ed7d43c1725542d826a515b16: ${graph.checksum}"
+        )
+
+        assertEquals(40, graph.numberOfRanges(), "numOfRanges not 40: ${graph.numberOfRanges()}")
+
+        assertEquals(3, graph.numberOfSamples(), "numOfSamples not 3: ${graph.numberOfSamples()}")
+
+        val ranges = graph.ranges()
+
+        assertTrue(ranges.isSorted(), "ranges not sorted")
+
+        assertEquals(graph.numberOfRanges(), ranges.size, "ranges size not equal to numberOfRanges")
+
+        // tests hapIdToSamples() method
+
+        var hapIdToSamples = graph.hapIdToSampleGametes(ranges[0])
+
+        assertEquals(3, hapIdToSamples.size, "hapIdToSamples size not 3: ${hapIdToSamples.size}")
+
+        var hapid = "12f0cec9102e84a161866e37072443b7"
+        var samples = hapIdToSamples[hapid]
+        assertEquals("LineA", samples?.get(0)?.name, "sample not LineA: ${samples?.get(0)?.name}")
+
+        hapid = "4fc7b8af32ddd74e07cb49d147ef1938"
+        samples = hapIdToSamples[hapid]
+        assertEquals("LineB", samples?.get(0)?.name, "sample not LineB: ${samples?.get(0)?.name}")
+
+        hapIdToSamples = graph.hapIdToSampleGametes(ranges[ranges.size - 2])
+        hapid = "0eb9029f3896313aebc69c8489923141"
+        samples = hapIdToSamples[hapid]
+        assertEquals("LineA", samples?.get(0)?.name, "sample not LineA: ${samples?.get(0)?.name}")
+
+        hapid = "5031218d4ac709dd51a946acd0550356"
+        samples = hapIdToSamples[hapid]
+        assertEquals("LineB", samples?.get(0)?.name, "sample not LineB: ${samples?.get(0)?.name}")
+
+        // tests for sampleToHapId() method
+
+        var checksum = graph.sampleToHapId(ranges[0], SampleGamete("LineA"))
+        assertEquals(
+            "12f0cec9102e84a161866e37072443b7",
+            checksum,
+            "sampleToHapId: checksum not 12f0cec9102e84a161866e37072443b7: $checksum"
+        )
+
+        checksum = graph.sampleToHapId(ranges[0], SampleGamete("LineB"))
+        assertEquals(
+            "4fc7b8af32ddd74e07cb49d147ef1938",
+            checksum,
+            "sampleToHapId: checksum not 4fc7b8af32ddd74e07cb49d147ef1938: $checksum"
+        )
+
+        checksum = graph.sampleToHapId(ranges[ranges.size - 2], SampleGamete("LineA"))
+        assertEquals(
+            "0eb9029f3896313aebc69c8489923141",
+            checksum,
+            "sampleToHapId: checksum not 0eb9029f3896313aebc69c8489923141: $checksum"
+        )
+
+        checksum = graph.sampleToHapId(ranges[ranges.size - 2], SampleGamete("LineB"))
+        assertEquals(
+            "5031218d4ac709dd51a946acd0550356",
+            checksum,
+            "sampleToHapId: checksum not 5031218d4ac709dd51a946acd0550356: $checksum"
+        )
+
+    }
+
     @Test
     fun testBadInputHaplotypeGraph() {
         // ALT tag does not contain sample name