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**feat(genomics): Add coverage expectation profiles with confidence evaluation**
- Introduced `coverage_expectation_profile` table with schema for per-test-type variant calling confidence thresholds. - Added seed data for test types like `WGS`, `BIG_Y_700`, `MT_FULL_SEQUENCE`, and others. - Created `CoverageExpectationProfile` model, repository, and service for CRUD operations and confidence assessment. - Implemented `CoverageExpectationService` for evaluating variant calling confidence and coverage adequacy. - Wrote unit tests to validate confidence tier logic, metrics inputs, and service behavior.
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‎app/models/dal/DatabaseSchema.scala‎

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@@ -82,6 +82,7 @@ object DatabaseSchema {
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val validationServices = TableQuery[ValidationServicesTable]
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val testTypeDefinition = TableQuery[TestTypeTable]
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val testTypeTargetRegions = TableQuery[TestTypeTargetRegionTable]
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val coverageExpectationProfiles = TableQuery[CoverageExpectationProfileTable]
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// Consolidated variant schema (replaces variant + variant_alias)
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val variantsV2 = TableQuery[VariantV2Table]

‎app/models/dal/domain/genomics/CoverageExpectationProfileTable.scala‎

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package models.dal.domain.genomics
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import models.dal.MyPostgresProfile
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import models.dal.MyPostgresProfile.api.*
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import models.domain.genomics.CoverageExpectationProfile
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import slick.lifted.{ProvenShape, Tag}
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import java.time.LocalDateTime
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class CoverageExpectationProfileTable(tag: Tag)
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extends MyPostgresProfile.api.Table[CoverageExpectationProfile](tag, "coverage_expectation_profile") {
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def id = column[Int]("id", O.PrimaryKey, O.AutoInc)
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def testTypeId = column[Int]("test_type_id")
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def contigName = column[String]("contig_name")
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def variantClass = column[String]("variant_class")
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def minDepthHigh = column[Double]("min_depth_high")
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def minDepthMedium = column[Double]("min_depth_medium")
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def minDepthLow = column[Double]("min_depth_low")
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def minCoveragePct = column[Option[Double]]("min_coverage_pct")
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def minMappingQuality = column[Option[Double]]("min_mapping_quality")
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def minCallablePct = column[Option[Double]]("min_callable_pct")
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def notes = column[Option[String]]("notes")
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def createdAt = column[LocalDateTime]("created_at")
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def updatedAt = column[LocalDateTime]("updated_at")
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override def * : ProvenShape[CoverageExpectationProfile] = (
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id.?,
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testTypeId,
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contigName,
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variantClass,
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minDepthHigh,
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minDepthMedium,
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minDepthLow,
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minCoveragePct,
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minMappingQuality,
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minCallablePct,
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notes,
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createdAt,
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updatedAt
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).mapTo[CoverageExpectationProfile]
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}

‎app/models/domain/genomics/CoverageExpectationProfile.scala‎

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package models.domain.genomics
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import play.api.libs.json.{Json, OFormat}
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import java.time.LocalDateTime
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case class CoverageExpectationProfile(
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id: Option[Int] = None,
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testTypeId: Int,
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contigName: String,
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variantClass: String = "SNP",
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minDepthHigh: Double,
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minDepthMedium: Double,
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minDepthLow: Double,
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minCoveragePct: Option[Double] = None,
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minMappingQuality: Option[Double] = None,
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minCallablePct: Option[Double] = None,
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notes: Option[String] = None,
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createdAt: LocalDateTime = LocalDateTime.now(),
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updatedAt: LocalDateTime = LocalDateTime.now()
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) {
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def confidenceForDepth(actualDepth: Double): String = {
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if (actualDepth >= minDepthHigh) "high"
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else if (actualDepth >= minDepthMedium) "medium"
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else if (actualDepth >= minDepthLow) "low"
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else "insufficient"
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}
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}
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object CoverageExpectationProfile {
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implicit val format: OFormat[CoverageExpectationProfile] = Json.format[CoverageExpectationProfile]
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}
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sealed trait VariantClass {
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def dbValue: String
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}
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object VariantClass {
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case object SNP extends VariantClass { val dbValue = "SNP" }
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case object STR extends VariantClass { val dbValue = "STR" }
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case object INDEL extends VariantClass { val dbValue = "INDEL" }
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def fromString(s: String): Option[VariantClass] = s.toUpperCase match {
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case "SNP" => Some(SNP)
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case "STR" => Some(STR)
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case "INDEL" => Some(INDEL)
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case _ => None
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}
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}
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case class VariantCallingConfidence(
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contigName: String,
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variantClass: String,
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depthConfidence: String,
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coverageAdequate: Boolean,
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mappingQualityAdequate: Boolean,
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callableBasesAdequate: Boolean,
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overallConfidence: String,
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details: Map[String, String] = Map.empty
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)
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object VariantCallingConfidence {
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implicit val format: OFormat[VariantCallingConfidence] = Json.format[VariantCallingConfidence]
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val HIGH = "high"
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val MEDIUM = "medium"
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val LOW = "low"
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val INSUFFICIENT = "insufficient"
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}
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case class SampleCoverageAssessment(
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testTypeCode: String,
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testTypeDisplayName: String,
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isChipBased: Boolean,
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confidences: Seq[VariantCallingConfidence],
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overallConfidence: String
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)
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object SampleCoverageAssessment {
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implicit val format: OFormat[SampleCoverageAssessment] = Json.format[SampleCoverageAssessment]
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}

‎app/modules/BaseModule.scala‎

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@@ -166,5 +166,9 @@ class BaseModule extends AbstractModule {
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bind(classOf[HaplogroupAncestralStrRepository])
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.to(classOf[HaplogroupAncestralStrRepositoryImpl])
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.asEagerSingleton()
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bind(classOf[CoverageExpectationProfileRepository])
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.to(classOf[CoverageExpectationProfileRepositoryImpl])
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.asEagerSingleton()
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}
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}

‎app/repositories/CoverageExpectationProfileRepository.scala‎

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package repositories
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import jakarta.inject.Inject
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import models.dal.DatabaseSchema
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import models.domain.genomics.CoverageExpectationProfile
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import play.api.Logging
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import play.api.db.slick.DatabaseConfigProvider
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import scala.concurrent.{ExecutionContext, Future}
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trait CoverageExpectationProfileRepository {
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def findByTestTypeId(testTypeId: Int): Future[Seq[CoverageExpectationProfile]]
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def findByTestTypeAndContig(testTypeId: Int, contigName: String): Future[Seq[CoverageExpectationProfile]]
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def findByTestTypeContigAndClass(testTypeId: Int, contigName: String, variantClass: String): Future[Option[CoverageExpectationProfile]]
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def create(profile: CoverageExpectationProfile): Future[CoverageExpectationProfile]
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def update(profile: CoverageExpectationProfile): Future[Boolean]
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def delete(id: Int): Future[Boolean]
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}
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class CoverageExpectationProfileRepositoryImpl @Inject()(
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dbConfigProvider: DatabaseConfigProvider
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)(implicit ec: ExecutionContext)
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extends BaseRepository(dbConfigProvider)
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with CoverageExpectationProfileRepository
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with Logging {
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import models.dal.MyPostgresProfile.api.*
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private val profiles = DatabaseSchema.domain.genomics.coverageExpectationProfiles
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override def findByTestTypeId(testTypeId: Int): Future[Seq[CoverageExpectationProfile]] =
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runQuery(profiles.filter(_.testTypeId === testTypeId).result)
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override def findByTestTypeAndContig(testTypeId: Int, contigName: String): Future[Seq[CoverageExpectationProfile]] =
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runQuery(profiles.filter(p => p.testTypeId === testTypeId && p.contigName === contigName).result)
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override def findByTestTypeContigAndClass(testTypeId: Int, contigName: String, variantClass: String): Future[Option[CoverageExpectationProfile]] =
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runQuery(profiles.filter(p =>
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p.testTypeId === testTypeId && p.contigName === contigName && p.variantClass === variantClass
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).result.headOption)
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override def create(profile: CoverageExpectationProfile): Future[CoverageExpectationProfile] =
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runQuery(
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(profiles returning profiles.map(_.id) into ((p, id) => p.copy(id = Some(id)))) += profile
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)
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override def update(profile: CoverageExpectationProfile): Future[Boolean] = profile.id match {
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case None => Future.successful(false)
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case Some(id) =>
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runQuery(
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profiles.filter(_.id === id)
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.map(p => (p.minDepthHigh, p.minDepthMedium, p.minDepthLow, p.minCoveragePct, p.minMappingQuality, p.minCallablePct, p.notes))
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.update((profile.minDepthHigh, profile.minDepthMedium, profile.minDepthLow, profile.minCoveragePct, profile.minMappingQuality, profile.minCallablePct, profile.notes))
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).map(_ > 0)
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}
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override def delete(id: Int): Future[Boolean] =
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runQuery(profiles.filter(_.id === id).delete).map(_ > 0)
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}

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