Merge pull request #879 from milaboratory/release-411

Last things for release 4.1.1
milaboratory · Nov 11, 2022 · 3418ff5 · 3418ff5
2 parents b1f6ec6 + 1500d5a
commit 3418ff5
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diff --git a/build.gradle.kts b/build.gradle.kts
@@ -101,7 +101,7 @@ repositories {
 val milibVersion = "2.1.0"
 val repseqioVersion = "1.5.0"
 val miplotsVersion = "1.1.0"
-val mitoolVersion = "1.2.0-15-main"
+val mitoolVersion = "1.3.0"
 val jacksonBomVersion = "2.14.0"
 val redberryPipeVersion = "1.3.0"
 

diff --git a/changelogs/v4.1.1.md b/changelogs/v4.1.1.md
@@ -0,0 +1,24 @@
+With this release we continue extending the set of supported single-cell protocols by adding new ready-to-use presets to our collection.
+Additionally to newly supported protocols and features required for their reliable analysis this release comes with many usability optimizations and stability improvements. See details below:
+
+# Major changes
+
+- presets for analysis of all types of BD Rhapsody data (see [docs](https://docs.milaboratories.com/mixcr/reference/overview-built-in-presets/#bd-rhapsody) for the list of supported kits)
+- analysis of data produced by protocol described in [Han et al. (2014)](https://doi.org/10.1038/nbt.2938) (see [docs](https://docs.milaboratories.com/mixcr/reference/overview-built-in-presets/#han-et-al-2014))
+- special presets for exom data analysis `exom-cdr3` and `exom-full-length`
+- initial support for overlap-extension-based chain pairing protocols
+- possibility to export groups of similar columns specifying single option (like `-allAAFeatures <from_reference_point> <to_reference_point>`)
+- more user-friendly alternative for `-uniqueTagsCount` - `-allUniqueTagsCount`; allows to export counts of unique tag combinations (useful for protocols with multiple `CELL` and `UMI` barcodes)
+- new "by sequence" filters for all somatic hypermutation trees (SHMT) exports
+- new weighted auto-threshold selection and complementary metric histogram aggregation modes (i.e. y-axis on reads-pre-UMI plots now can show number of reads instead of number of UMIs)
+- detected allelic variants are now can also be exported in fasta format right from the `findAlleles` command
+- better algorithm for seed sequence selection in consensus assembly routine in `assemble`; increases productive consensus count for cases with multi-variant tag groups (i.e. birthday paradoxes in UMI data or single-cell data analysis without UMIs)
+
+# Minor changes:
+
+- minor adjustments for existing presets
+- many CLI and parameter validation fixes, more human-readable error messages, better protection from common input errors
+- support for preset-embedded tag whitelists for protocols with small number of barcode variants
+- options `--use-local-temp`, `--threads`, `--not-aligned-R1`(`R2`) and `--not-parsed-R1`(`R2`)  are now available in `analyze`, additionally to individual step commands
+- bugfix for imputation in export for compound gene features
+- other minor fixes and enhancements
diff --git a/src/main/kotlin/com/milaboratory/mixcr/Mixins.kt b/src/main/kotlin/com/milaboratory/mixcr/Mixins.kt
@@ -578,7 +578,7 @@ object ExportMixins {
             "-aaFeature" -> "-aaFeatureImputed"
             "-allNFeatures" -> "-allNFeaturesImputed"
             "-allNFeaturesWithMinQuality" -> "-allNFeaturesImputedWithMinQuality"
-            "-allAaFeatures" -> "-allAaFeaturesImputed"
+            "-allAAFeatures" -> "-allAAFeaturesImputed"
             else -> field
         }
 
@@ -588,7 +588,7 @@ object ExportMixins {
             "-aaFeatureImputed" -> "-aaFeature"
             "-allNFeaturesImputed" -> "-allNFeatures"
             "-allNFeaturesImputedWithMinQuality" -> "-allNFeaturesWithMinQuality"
-            "-allAaFeaturesImputed" -> "-allAaFeatures"
+            "-allAAFeaturesImputed" -> "-allAAFeatures"
             else -> field
         }
 

diff --git a/src/main/kotlin/com/milaboratory/mixcr/export/SHMTreeFieldsExtractorsFactory.kt b/src/main/kotlin/com/milaboratory/mixcr/export/SHMTreeFieldsExtractorsFactory.kt
@@ -138,7 +138,7 @@ object SHMTreeFieldsExtractorsFactory : FieldExtractorsFactoryWithPresets<SHMTre
             this += aaFeatureField
             this += FieldsCollection(
                 Order.`-aaFeature` + 1,
-                "-allAaFeatures",
+                "-allAAFeatures",
                 "Export nucleotide sequences for all covered gene features.",
                 aaFeatureField,
                 nodeTypeParam("Of", withParent = false)

diff --git a/src/main/kotlin/com/milaboratory/mixcr/export/SHMTreeNodeFieldsExtractor.kt b/src/main/kotlin/com/milaboratory/mixcr/export/SHMTreeNodeFieldsExtractor.kt
@@ -123,7 +123,7 @@ object SHMTreeNodeFieldsExtractor {
         this += aaFeatureField
         this += FieldsCollection(
             Order.`-aaFeature` + 1,
-            "-allAaFeatures",
+            "-allAAFeatures",
             "Export amino acid sequences for all covered gene features.%n${nodeParamDescription("feature")}",
             aaFeatureField,
             nodeTypeParamOptional("Of")

diff --git a/src/main/kotlin/com/milaboratory/mixcr/export/SplittedTreeNodeFieldsExtractorsFactory.kt b/src/main/kotlin/com/milaboratory/mixcr/export/SplittedTreeNodeFieldsExtractorsFactory.kt
@@ -53,7 +53,7 @@ object SplittedTreeNodeFieldsExtractorsFactory : FieldExtractorsFactoryWithPrese
             ExportFieldDescription("-jAlignments"),
             ExportFieldDescription("-cAlignments"),
             ExportFieldDescription("-allNFeatures"),
-            ExportFieldDescription("-allAaFeatures"),
+            ExportFieldDescription("-allAAFeatures"),
             ExportFieldDescription("-defaultAnchorPoints")
         )
     }

diff --git a/src/main/kotlin/com/milaboratory/mixcr/export/VDJCObjectFieldExtractors.kt b/src/main/kotlin/com/milaboratory/mixcr/export/VDJCObjectFieldExtractors.kt
@@ -336,8 +336,8 @@ object VDJCObjectFieldExtractors {
 
             this += FieldsCollection(
                 Order.`-aaFeature` + 1,
-                "-allAaFeatures",
-                "Export amino acid sequence ${commonDescriptionForFeatures("-allAaFeatures", aaFeatureField)}",
+                "-allAAFeatures",
+                "Export amino acid sequence ${commonDescriptionForFeatures("-allAAFeatures", aaFeatureField)}",
                 aaFeatureField,
                 referencePointParamOptional("<from_reference_point>"),
                 referencePointParamOptional("<to_reference_point>"),
@@ -401,9 +401,9 @@ object VDJCObjectFieldExtractors {
         if (!forTreesExport) {
             this += FieldsCollection(
                 Order.features + 501,
-                "-allAaFeaturesImputed",
+                "-allAAFeaturesImputed",
                 "Export amino acid sequence using letters from germline (marked lowercase) for uncovered regions " +
-                        commonDescriptionForFeatures("-allAaFeaturesImputed", aaFeatureImputedField),
+                        commonDescriptionForFeatures("-allAAFeaturesImputed", aaFeatureImputedField),
                 aaFeatureImputedField,
                 referencePointParamOptional("<from_reference_point>"),
                 referencePointParamOptional("<to_reference_point>"),
@@ -416,7 +416,7 @@ object VDJCObjectFieldExtractors {
         } else {
             this += FieldsCollection(
                 Order.features + 501,
-                "-allAaFeaturesImputed",
+                "-allAAFeaturesImputed",
                 "Export amino acid sequence using letters from germline (marked lowercase) for uncovered regions for all covered features",
                 aaFeatureImputedField
             ) {

diff --git a/src/main/resources/mixcr_presets/blocks/03-exportAlignments.yaml b/src/main/resources/mixcr_presets/blocks/03-exportAlignments.yaml
@@ -14,5 +14,5 @@
       - field: "-jAlignments"
       - field: "-cAlignments"
       - field: "-allNFeaturesWithMinQuality"
-      - field: "-allAaFeatures"
+      - field: "-allAAFeatures"
       - field: "-defaultAnchorPoints"
diff --git a/src/main/resources/mixcr_presets/blocks/08-exportClones.yaml b/src/main/resources/mixcr_presets/blocks/08-exportClones.yaml
@@ -18,7 +18,7 @@
       - field: "-jAlignments"
       - field: "-cAlignments"
       - field: "-allNFeaturesWithMinQuality"
-      - field: "-allAaFeatures"
+      - field: "-allAAFeatures"
       - field: "-defaultAnchorPoints"
 
 "exportClones-umi-full":
@@ -45,7 +45,7 @@
       - field: "-jAlignments"
       - field: "-cAlignments"
       - field: "-allNFeaturesWithMinQuality"
-      - field: "-allAaFeatures"
+      - field: "-allAAFeatures"
       - field: "-defaultAnchorPoints"
 
 "exportClones-single-cell-full":
@@ -71,5 +71,5 @@
       - field: "-jAlignments"
       - field: "-cAlignments"
       - field: "-allNFeaturesWithMinQuality"
-      - field: "-allAaFeatures"
+      - field: "-allAAFeatures"
       - field: "-defaultAnchorPoints"
diff --git a/src/main/resources/mixcr_presets/test.yaml b/src/main/resources/mixcr_presets/test.yaml
@@ -273,7 +273,7 @@
       - field: "-jAlignments"
       - field: "-cAlignments"
       - field: "-allNFeaturesWithMinQuality"
-      - field: "-allAaFeatures"
+      - field: "-allAAFeatures"
       - field: "-defaultAnchorPoints"
 
 "pereshlop-test":
@@ -314,7 +314,7 @@
       - field: "-jAlignments"
       - field: "-cAlignments"
       - field: "-allNFeaturesWithMinQuality"
-      - field: "-allAaFeatures"
+      - field: "-allAAFeatures"
       - field: "-defaultAnchorPoints"
 
 "umi-guided-consensus-test":
@@ -408,5 +408,5 @@
       - field: "-jAlignments"
       - field: "-cAlignments"
       - field: "-allNFeaturesWithMinQuality"
-      - field: "-allAaFeatures"
+      - field: "-allAAFeatures"
       - field: "-defaultAnchorPoints"
diff --git a/src/test/kotlin/com/milaboratory/mixcr/cli/CommandExportPresetTest.kt b/src/test/kotlin/com/milaboratory/mixcr/cli/CommandExportPresetTest.kt
@@ -38,11 +38,11 @@ class CommandExportPresetTest {
         output.delete()
         TestMain.execute(
             "exportPreset --species hs --dna " +
-                    "--append-export-clones-field -allAaFeatures " +
+                    "--append-export-clones-field -allAAFeatures " +
                     "--preset-name test-tcr-shotgun ${output.path}"
         )
         val result = K_YAML_OM.readValue<MiXCRParamsBundle>(output)
-        result.exportClones!!.fields shouldContain ExportFieldDescription("-allAaFeatures")
+        result.exportClones!!.fields shouldContain ExportFieldDescription("-allAAFeatures")
     }
 
     @Test