fix: fixes inferMinRecordsPerConsensus to always use molecular thresh…

…olds

chore: dep upgrade & changelog corrections

build.gradle.kts

@@ -134,14 +134,14 @@ val toObfuscate: Configuration by configurations.creating {
 
 val obfuscationLibs: Configuration by configurations.creating
 
-val mixcrAlgoVersion = "4.3.0-24-fix_alleles"
+val mixcrAlgoVersion = "4.3.0-27-develop"
 val milibVersion = "2.4.0-4-master"
-val mitoolVersion = "1.7.0"
-val repseqioVersion = "1.8.0-10-fix_mark_alleles"
+val mitoolVersion = "1.7.0-1-main"
+val repseqioVersion = "1.8.0-11-master"
 
 val picocliVersion = "4.6.3"
 val jacksonBomVersion = "2.14.2"
-val milmVersion = "3.3.0"
+val milmVersion = "3.4.0"
 
 val cliktVersion = "3.5.0"
 val jcommanderVersion = "1.72"

changelogs/v4.3.1.md

@@ -5,8 +5,10 @@
 - added `-isProductive <gene_feature>` column to export
 - improvements of report and alleles description table for `findAlleles` command
 - removing of unused genes from result library in `findAlleles` command
-- 'findAlleles' now more resilient to case when most allele variants of donor differ from *00 alleles in a library
+- `findAlleles` now more resilient to case when most allele variants of donor differ from `*00` alleles in a library
 
-# Bug fixes
+## Bug fixes
 
 - fixed AssertionError in `findAlleles` command with `--output-template` argument
+- fixed wrong behaviour with `inferMinRecordsPerConsensus == true` and cell level assembly
+- fixed `minRecordsPerConsensus` inference mechanism for new filtering features introduced in previous version (4.3.0)

src/main/kotlin/com/milaboratory/mixcr/cli/CommandAssemble.kt

@@ -214,6 +214,8 @@ object CommandAssemble {
                     if (!cp.inferMinRecordsPerConsensus || cp.consensusAssemblerParameters == null)
                         return@resolve cp
 
+                    // All the code below executed only if inferMinRecordsPerConsensus == true
+
                     if (cp.consensusAssemblerParameters!!.assembler.minRecordsPerConsensus != 0) {
                         println(
                             "WARNING: minRecordsPerConsensus has non default value (not equal to 0), the automatic " +
@@ -222,10 +224,10 @@ object CommandAssemble {
                         return@resolve cp
                     }
 
-                    val groupingLevel = if (cp.cellLevel) TagType.Cell else TagType.Molecule
-                    val groupingTags = (0 until inputHeader.tagsInfo.getDepthFor(groupingLevel))
+                    // Here we search specifically for "reads per UMI" threshold, even if we do cell-level assembly,
+                    // as the most meaningful estimation for the minRecordsPerConsensus parameter
+                    val groupingTags = (0 until inputHeader.tagsInfo.getDepthFor(TagType.Molecule))
                         .map { i -> inputHeader.tagsInfo[i].name }
-
                     val threshold = inputFooter.thresholds[MinGroupsPerGroup(groupingTags, null)]
                     if (threshold == null) {
                         println(