Ignore non-productive alignemnts in consensus assembly in assemble ac…

…tion (#1043) * chore: algo upgrade * chore: changelog
milaboratory · Mar 17, 2023 · fe32883 · fe32883
1 parent f92242a
commit fe32883
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Showing 3 changed files with 2 additions and 2 deletions.
diff --git 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 = "4.2.0-76-intersection-debug"
+val mixcrAlgoVersion = "4.2.0-78-ignore-non-productive-in-consensus"
 val milibVersion = "2.3.0-24-fix_obfuscation"
 val mitoolVersion = "1.6.0-57-main"
 val repseqioVersion = "1.7.0-36-intersect-debug"

diff --git a/changelogs/v4.3.0.md b/changelogs/v4.3.0.md
@@ -38,3 +38,4 @@
   to `:`), allowing multi-sample analysis on Windows
 - Fixed usage of composite features for `--assemble-contigs-by`
 - Removed some restrictions for possible combinations of gene features used in analysis and export  
+- Fixed behaviour of empirical alignment assignment in `assemble` if `--write-all` was used in `align`
diff --git a/src/main/kotlin/com/milaboratory/mixcr/cli/CommandRefineTagsAndSort.kt b/src/main/kotlin/com/milaboratory/mixcr/cli/CommandRefineTagsAndSort.kt
@@ -246,7 +246,6 @@ object CommandRefineTagsAndSort {
         override fun run1() {
             val startTimeMillis = System.currentTimeMillis()
 
-
             val refineTagsAndSortReport: RefineTagsAndSortReport
             val mitoolReport: TagCorrectionReport?
             var thresholds: Map<CriticalThresholdKey, Double> = emptyMap()