From d7db9edabb9972bc0af2122f6227677093fd8617 Mon Sep 17 00:00:00 2001 From: gnefedev Date: Thu, 18 Jan 2024 18:06:27 +0100 Subject: [PATCH] update version --- build.gradle.kts | 2 +- changelogs/v4.6.1.md | 8 ++++++-- .../com/milaboratory/mixcr/cli/CommandFindAlleles.kt | 4 ++-- 3 files changed, 9 insertions(+), 5 deletions(-) diff --git a/build.gradle.kts b/build.gradle.kts index 4ebe07bec..1234c4df8 100644 --- a/build.gradle.kts +++ b/build.gradle.kts @@ -134,7 +134,7 @@ val toObfuscate: Configuration by configurations.creating { val obfuscationLibs: Configuration by configurations.creating -val mixcrAlgoVersion = "4.6.0-20-add-clones-to-shmt" +val mixcrAlgoVersion = "4.6.0-22-bug-fixes" // may be blank (will be inherited from mixcr-algo) val milibVersion = "" // may be blank (will be inherited from mixcr-algo or milib) diff --git a/changelogs/v4.6.1.md b/changelogs/v4.6.1.md index 45d2c54ec..504700dbe 100644 --- a/changelogs/v4.6.1.md +++ b/changelogs/v4.6.1.md @@ -4,8 +4,10 @@ ## 🛠️ Minor improvements & fixes -- Fixed parsing of optional arguments for `exportShmTreesWithNodes`: `-nMutationsRelative`, `-aaMutations`, `-nMutations`, `-aaMutationsRelative`, `-allNMutations`, `-allAAMutations`, `-allNMutationsCount`, `-allAAMutationsCount`. -- Fixed parsing of optional arguments for `exportClones` and `exportAlignments`: `-allNMutations`, `-allAAMutations`, `-allNMutationsCount`, `-allAAMutationsCount`. +- Fixed parsing of optional arguments + for `exportShmTreesWithNodes`: `-nMutationsRelative`, `-aaMutations`, `-nMutations`, `-aaMutationsRelative`, `-allNMutations`, `-allAAMutations`, `-allNMutationsCount`, `-allAAMutationsCount`. +- Fixed parsing of optional arguments for `exportClones` + and `exportAlignments`: `-allNMutations`, `-allAAMutations`, `-allNMutationsCount`, `-allAAMutationsCount`. - Fixed possible errors on exporting amino acid mutations in `exportShmTreesWithNodes` - Fixed list of required options in `listPresets` command - Fixed error on building trees in case of JBeginTrimmed started before CDR3Begin @@ -13,3 +15,5 @@ - Added `--remove-qc-check` option - Remove `-topChains` field from `exportShmTreesWithNodes` command. Use `-chains` instead - Removed default splitting clones by V and J for presets where clones are assembled by full-length. +- Fixed NullPointerException in some cases of building trees by SC+bulk data +- Fixed `java.lang.IllegalArgumentException: While adding VEndTrimmed` in `exportClones` diff --git a/src/main/kotlin/com/milaboratory/mixcr/cli/CommandFindAlleles.kt b/src/main/kotlin/com/milaboratory/mixcr/cli/CommandFindAlleles.kt index 3f76ef363..07d8fd0db 100644 --- a/src/main/kotlin/com/milaboratory/mixcr/cli/CommandFindAlleles.kt +++ b/src/main/kotlin/com/milaboratory/mixcr/cli/CommandFindAlleles.kt @@ -1,5 +1,5 @@ /* - * Copyright (c) 2014-2023, MiLaboratories Inc. All Rights Reserved + * Copyright (c) 2014-2024, MiLaboratories Inc. All Rights Reserved * * Before downloading or accessing the software, please read carefully the * License Agreement available at: @@ -308,7 +308,7 @@ class CommandFindAlleles : MiXCRCommandWithOutputs() { } ValidationException.requireTheSame(datasets.flatMap { it.usedGenes }.map { it.id.libraryId }) { - "input files must be aligned on the same library" + "Input files must be aligned on the same library" } val originalLibrary = datasets.first().usedGenes.first().parentLibrary logger.debug { "Name of the original library: ${originalLibrary.libraryId.libraryName}" }