From f3ac213f598a28d357cf3bb3b292cba0324c1e61 Mon Sep 17 00:00:00 2001 From: hpratt Date: Wed, 11 Nov 2020 13:45:39 -0500 Subject: [PATCH] drop a couple unnecessary variables --- build.gradle.kts | 2 +- src/main/kotlin/step/BarcodeMap.kt | 4 ---- 2 files changed, 1 insertion(+), 5 deletions(-) diff --git a/build.gradle.kts b/build.gradle.kts index 9d2aced..d91929f 100644 --- a/build.gradle.kts +++ b/build.gradle.kts @@ -9,7 +9,7 @@ plugins { } group = "com.genomealmanac" -version = "0.6.0" +version = "0.6.1" val artifactID = "bam-aggregate-task" repositories { diff --git a/src/main/kotlin/step/BarcodeMap.kt b/src/main/kotlin/step/BarcodeMap.kt index 0ec3a54..946c54f 100644 --- a/src/main/kotlin/step/BarcodeMap.kt +++ b/src/main/kotlin/step/BarcodeMap.kt @@ -19,9 +19,6 @@ private val log = KotlinLogging.logger {} */ fun barcodeMap(regions: List, alignments: Path, forwardShift: Int = 0, reverseShift: Int = 0, strand: String? = null): Map> { - val values: List> = regions.map { - (it.start..it.end).map { 0 }.toMutableList() - } val queryExtension = max(abs(forwardShift), abs(reverseShift)) + 1 SamReaderFactory.makeDefault().validationStringency(ValidationStringency.SILENT).enable(SamReaderFactory.Option.INCLUDE_SOURCE_IN_RECORDS).open(alignments.toFile()).use { @@ -43,7 +40,6 @@ fun barcodeMap(regions: List, alignments: Path, forwardShift: Int = 0, r } val start = pileUpStart(alignment, forwardShift, reverseShift) if (start >= region.start && start <= region.end) { - val coordinate = if (region.strand == '+') start - region.start else region.end - start val barcode = alignment.getAttribute("CB")?.toString() if (barcode === null) return@forEach if (!results.containsKey(barcode)) results[barcode] = mutableMapOf()