Merge pull request #1829 from milaboratory/fixes

Fixes
milaboratory · Oct 24, 2024 · cc74062 · cc74062
2 parents d97d7f9 + 0cbd8c2
commit cc74062
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Showing 17 changed files with 133 additions and 96 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 = "4.7.0-26-align-retry"
+val mixcrAlgoVersion = "4.7.0-31-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/v4.7.1.md b/changelogs/v4.7.1.md
@@ -2,10 +2,12 @@
 
 - Tracking the progres of fasta[.gz] inputs on `align`.
 - Improved alignment rate of short parts of genes in reads with height rate of mutations
+- Fixed combination of `-Massemble.sortBySequence=true` and `--assemble-clonotypes-by` with composite feature
+- For `findShmTree` command `--alleles-search-could-be-skipped` option is added for special cases
 
 ## 📚 New Presets
 
 - Added preset `bruker-human-sc-xcr-vdj-beacon` for TCR/BCR analyses of Bruker Beacon data  
 - Added presets for new Qiagen kits: `qiagen-human-rna-tcr-umi-targeted-qiaseq` and `qiagen-mouse-rna-tcr-umi-targeted-qiaseq`
 - Added preset `illumina-human-dna-trb-ampliseq-sr`
-- Removed layout for Illumina kits, iRepertoire and Thermofisher kits.
+- Removed layout for Illumina kits, iRepertoire and Thermofisher kits.
diff --git a/regression/cli-help/findShmTrees.txt b/regression/cli-help/findShmTrees.txt
@@ -1,9 +1,9 @@
 Usage: mixcr findShmTrees [--v-gene-names <gene_name>]... [--j-gene-names <gene_name>]...
                           [--cdr3-lengths <n>]... [--min-count <n>] [--productive-only]
-                          [--dont-combine-tree-by-cells] [-O <key=value>]... [--report <path>]
-                          [--json-report <path>] [--use-local-temp] [--threads <n>]
-                          [--force-overwrite] [--no-warnings] [--verbose] [--help] (input_file.
-                          clns|directory)... output_file.shmt
+                          [--dont-combine-tree-by-cells] [--alleles-search-could-be-skipped] [-O
+                          <key=value>]... [--report <path>] [--json-report <path>]
+                          [--use-local-temp] [--threads <n>] [--force-overwrite] [--no-warnings]
+                          [--verbose] [--help] (input_file.clns|directory)... output_file.shmt
 Builds SHM trees.
 All inputs must be fully covered by the same feature, have the same library produced by
 `findAlleles`, the same scoring of V and J genes and the same features to align.
@@ -22,6 +22,16 @@ All inputs must be fully covered by the same feature, have the same library prod
                                and no out of frame in CDR3)
       --dont-combine-tree-by-cells
                              In case of data with cell groups, will not combine trees by cells.
+      --alleles-search-could-be-skipped
+                             In specific cases preliminary search for alleles could be skipped. For
+                               example:
+                              - reads were aligned on gene library for the donor, that wes found
+                               beforehand
+                              - data is synthetic (in biological or computational way) and don't
+                               have natural patterns of homo-hetero zygotes
+                              - you have homogeneous specie and have a library with all presented
+                               genes beforehand (but better to run `findAlleles` to check that
+                               there is no diversity)
   -O  <key=value>            Overrides default build SHM parameter values
   -r, --report <path>        Report file (human readable version, see `-j / --json-report` for
                                machine readable report).

diff --git a/regression/presets/analyze/10x-sc-xcr-vdj.yaml b/regression/presets/analyze/10x-sc-xcr-vdj.yaml
@@ -71,8 +71,8 @@ mitool:
         - Molecule
       payloadTagTypes:
         - Targets
-      safeUnusedReads: true
-      safeDiscardedReads: true
+      saveUnusedReads: true
+      saveDiscardedReads: true
       inferMinRecordsPerConsensus: true
     - parameters:
         aAssemblerParameters:
@@ -108,8 +108,8 @@ mitool:
         - Molecule
       payloadTagTypes:
         - Targets
-      safeUnusedReads: true
-      safeDiscardedReads: true
+      saveUnusedReads: true
+      saveDiscardedReads: true
       inferMinRecordsPerConsensus: true
     - parameters:
         aAssemblerParameters:
@@ -144,8 +144,8 @@ mitool:
         - Cell
       payloadTagTypes:
         - Targets
-      safeUnusedReads: true
-      safeDiscardedReads: true
+      saveUnusedReads: true
+      saveDiscardedReads: true
       inferMinRecordsPerConsensus: true
     - parameters:
         aAssemblerParameters:
@@ -180,8 +180,8 @@ mitool:
         - Cell
       payloadTagTypes:
         - Targets
-      safeUnusedReads: true
-      safeDiscardedReads: true
+      saveUnusedReads: true
+      saveDiscardedReads: true
       inferMinRecordsPerConsensus: true
 align:
   species: ""

diff --git a/regression/presets/analyze/10x-vdj-bcr-full-length.yaml b/regression/presets/analyze/10x-vdj-bcr-full-length.yaml
@@ -71,8 +71,8 @@ mitool:
         - Molecule
       payloadTagTypes:
         - Targets
-      safeUnusedReads: true
-      safeDiscardedReads: true
+      saveUnusedReads: true
+      saveDiscardedReads: true
       inferMinRecordsPerConsensus: true
     - parameters:
         aAssemblerParameters:
@@ -108,8 +108,8 @@ mitool:
         - Molecule
       payloadTagTypes:
         - Targets
-      safeUnusedReads: true
-      safeDiscardedReads: true
+      saveUnusedReads: true
+      saveDiscardedReads: true
       inferMinRecordsPerConsensus: true
     - parameters:
         aAssemblerParameters:
@@ -144,8 +144,8 @@ mitool:
         - Cell
       payloadTagTypes:
         - Targets
-      safeUnusedReads: true
-      safeDiscardedReads: true
+      saveUnusedReads: true
+      saveDiscardedReads: true
       inferMinRecordsPerConsensus: true
     - parameters:
         aAssemblerParameters:
@@ -180,8 +180,8 @@ mitool:
         - Cell
       payloadTagTypes:
         - Targets
-      safeUnusedReads: true
-      safeDiscardedReads: true
+      saveUnusedReads: true
+      saveDiscardedReads: true
       inferMinRecordsPerConsensus: true
 align:
   species: ""

diff --git a/regression/presets/analyze/10x-vdj-bcr.yaml b/regression/presets/analyze/10x-vdj-bcr.yaml
@@ -71,8 +71,8 @@ mitool:
         - Molecule
       payloadTagTypes:
         - Targets
-      safeUnusedReads: true
-      safeDiscardedReads: true
+      saveUnusedReads: true
+      saveDiscardedReads: true
       inferMinRecordsPerConsensus: true
     - parameters:
         aAssemblerParameters:
@@ -108,8 +108,8 @@ mitool:
         - Molecule
       payloadTagTypes:
         - Targets
-      safeUnusedReads: true
-      safeDiscardedReads: true
+      saveUnusedReads: true
+      saveDiscardedReads: true
       inferMinRecordsPerConsensus: true
     - parameters:
         aAssemblerParameters:
@@ -144,8 +144,8 @@ mitool:
         - Cell
       payloadTagTypes:
         - Targets
-      safeUnusedReads: true
-      safeDiscardedReads: true
+      saveUnusedReads: true
+      saveDiscardedReads: true
       inferMinRecordsPerConsensus: true
     - parameters:
         aAssemblerParameters:
@@ -180,8 +180,8 @@ mitool:
         - Cell
       payloadTagTypes:
         - Targets
-      safeUnusedReads: true
-      safeDiscardedReads: true
+      saveUnusedReads: true
+      saveDiscardedReads: true
       inferMinRecordsPerConsensus: true
 align:
   species: ""

diff --git a/regression/presets/analyze/10x-vdj-tcr-alias-multi-barcode-test.yaml b/regression/presets/analyze/10x-vdj-tcr-alias-multi-barcode-test.yaml
@@ -71,8 +71,8 @@ mitool:
         - Molecule
       payloadTagTypes:
         - Targets
-      safeUnusedReads: true
-      safeDiscardedReads: true
+      saveUnusedReads: true
+      saveDiscardedReads: true
       inferMinRecordsPerConsensus: true
     - parameters:
         aAssemblerParameters:
@@ -108,8 +108,8 @@ mitool:
         - Molecule
       payloadTagTypes:
         - Targets
-      safeUnusedReads: true
-      safeDiscardedReads: true
+      saveUnusedReads: true
+      saveDiscardedReads: true
       inferMinRecordsPerConsensus: true
     - parameters:
         aAssemblerParameters:
@@ -144,8 +144,8 @@ mitool:
         - Cell
       payloadTagTypes:
         - Targets
-      safeUnusedReads: true
-      safeDiscardedReads: true
+      saveUnusedReads: true
+      saveDiscardedReads: true
       inferMinRecordsPerConsensus: true
     - parameters:
         aAssemblerParameters:
@@ -180,8 +180,8 @@ mitool:
         - Cell
       payloadTagTypes:
         - Targets
-      safeUnusedReads: true
-      safeDiscardedReads: true
+      saveUnusedReads: true
+      saveDiscardedReads: true
       inferMinRecordsPerConsensus: true
 align:
   species: ""

diff --git a/regression/presets/analyze/10x-vdj-tcr-full-length.yaml b/regression/presets/analyze/10x-vdj-tcr-full-length.yaml
@@ -71,8 +71,8 @@ mitool:
         - Molecule
       payloadTagTypes:
         - Targets
-      safeUnusedReads: true
-      safeDiscardedReads: true
+      saveUnusedReads: true
+      saveDiscardedReads: true
       inferMinRecordsPerConsensus: true
     - parameters:
         aAssemblerParameters:
@@ -108,8 +108,8 @@ mitool:
         - Molecule
       payloadTagTypes:
         - Targets
-      safeUnusedReads: true
-      safeDiscardedReads: true
+      saveUnusedReads: true
+      saveDiscardedReads: true
       inferMinRecordsPerConsensus: true
     - parameters:
         aAssemblerParameters:
@@ -144,8 +144,8 @@ mitool:
         - Cell
       payloadTagTypes:
         - Targets
-      safeUnusedReads: true
-      safeDiscardedReads: true
+      saveUnusedReads: true
+      saveDiscardedReads: true
       inferMinRecordsPerConsensus: true
     - parameters:
         aAssemblerParameters:
@@ -180,8 +180,8 @@ mitool:
         - Cell
       payloadTagTypes:
         - Targets
-      safeUnusedReads: true
-      safeDiscardedReads: true
+      saveUnusedReads: true
+      saveDiscardedReads: true
       inferMinRecordsPerConsensus: true
 align:
   species: ""

diff --git a/regression/presets/analyze/10x-vdj-tcr-qc-test.yaml b/regression/presets/analyze/10x-vdj-tcr-qc-test.yaml
@@ -71,8 +71,8 @@ mitool:
         - Molecule
       payloadTagTypes:
         - Targets
-      safeUnusedReads: true
-      safeDiscardedReads: true
+      saveUnusedReads: true
+      saveDiscardedReads: true
       inferMinRecordsPerConsensus: true
     - parameters:
         aAssemblerParameters:
@@ -108,8 +108,8 @@ mitool:
         - Molecule
       payloadTagTypes:
         - Targets
-      safeUnusedReads: true
-      safeDiscardedReads: true
+      saveUnusedReads: true
+      saveDiscardedReads: true
       inferMinRecordsPerConsensus: true
     - parameters:
         aAssemblerParameters:
@@ -144,8 +144,8 @@ mitool:
         - Cell
       payloadTagTypes:
         - Targets
-      safeUnusedReads: true
-      safeDiscardedReads: true
+      saveUnusedReads: true
+      saveDiscardedReads: true
       inferMinRecordsPerConsensus: true
     - parameters:
         aAssemblerParameters:
@@ -180,8 +180,8 @@ mitool:
         - Cell
       payloadTagTypes:
         - Targets
-      safeUnusedReads: true
-      safeDiscardedReads: true
+      saveUnusedReads: true
+      saveDiscardedReads: true
       inferMinRecordsPerConsensus: true
 align:
   species: ""

diff --git a/regression/presets/analyze/10x-vdj-tcr.yaml b/regression/presets/analyze/10x-vdj-tcr.yaml
@@ -71,8 +71,8 @@ mitool:
         - Molecule
       payloadTagTypes:
         - Targets
-      safeUnusedReads: true
-      safeDiscardedReads: true
+      saveUnusedReads: true
+      saveDiscardedReads: true
       inferMinRecordsPerConsensus: true
     - parameters:
         aAssemblerParameters:
@@ -108,8 +108,8 @@ mitool:
         - Molecule
       payloadTagTypes:
         - Targets
-      safeUnusedReads: true
-      safeDiscardedReads: true
+      saveUnusedReads: true
+      saveDiscardedReads: true
       inferMinRecordsPerConsensus: true
     - parameters:
         aAssemblerParameters:
@@ -144,8 +144,8 @@ mitool:
         - Cell
       payloadTagTypes:
         - Targets
-      safeUnusedReads: true
-      safeDiscardedReads: true
+      saveUnusedReads: true
+      saveDiscardedReads: true
       inferMinRecordsPerConsensus: true
     - parameters:
         aAssemblerParameters:
@@ -180,8 +180,8 @@ mitool:
         - Cell
       payloadTagTypes:
         - Targets
-      safeUnusedReads: true
-      safeDiscardedReads: true
+      saveUnusedReads: true
+      saveDiscardedReads: true
       inferMinRecordsPerConsensus: true
 align:
   species: ""

diff --git a/regression/presets/analyze/bruker-sc-xcr-vdj-beacon.yaml b/regression/presets/analyze/bruker-sc-xcr-vdj-beacon.yaml
@@ -79,8 +79,8 @@ mitool:
         - Cell
       payloadTagTypes:
         - Targets
-      safeUnusedReads: true
-      safeDiscardedReads: true
+      saveUnusedReads: true
+      saveDiscardedReads: true
       inferMinRecordsPerConsensus: true
     - parameters:
         aAssemblerParameters:
@@ -115,8 +115,8 @@ mitool:
         - Cell
       payloadTagTypes:
         - Targets
-      safeUnusedReads: true
-      safeDiscardedReads: true
+      saveUnusedReads: true
+      saveDiscardedReads: true
       inferMinRecordsPerConsensus: true
 align:
   species: ""

diff --git a/regression/schemas/analyzeBundle/parameters/consensus.schema.yaml b/regression/schemas/analyzeBundle/parameters/consensus.schema.yaml
@@ -103,7 +103,7 @@ properties:
         type: array
         items:
           type: string
-      safeDiscardedReads:
+      saveDiscardedReads:
         type: boolean
-      safeUnusedReads:
+      saveUnusedReads:
         type: boolean