Merge pull request #1512 from milaboratory/bug-fixes

update version

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)

changelogs/v4.6.1.md

@@ -4,12 +4,16 @@
 
 ## 🛠️ 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
 - Fixed usage `--remove-step qc`
 - 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` 

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}" }