trees exports

build.gradle.kts

@@ -134,7 +134,7 @@ val toObfuscate: Configuration by configurations.creating {
 val obfuscationLibs: Configuration by configurations.creating
 
 
-val mixcrAlgoVersion = "4.7.0-31-fixes"
+val mixcrAlgoVersion = "4.7.0-35-exports-for-trees"
 // may be blank (will be inherited from mixcr-algo)
 val milibVersion = ""
 // may be blank (will be inherited from mixcr-algo or milib)

changelogs/v4.7.1.md

@@ -1,9 +1,19 @@
+## ❗ Breaking changes
+
+- Shortcut options `-p` and `-pf` are removed from export commands. They are conflicting with new added export fields
+  `-pN`, `-pS` and `-pNpS`
+
 ## 🛠️ Other improvements & fixes
 
 - 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
+- Added `[withAlignmentGaps]` option to features exports in `exportShmTreesWithNodes` command. That will add gaps, so
+  results could be interpreted as alignments of all nodes to root sequence
+- Added `-pN`, `-pS`, `-pNpS` options for `exportShmTreesWithNodes` command
+- Fixed `findShmTrees` command. Now it outputs root node with the reconstructed NDN region (before it was filled with N
+  letters)
 
 ## 📚 New Presets
 

src/main/kotlin/com/milaboratory/mixcr/cli/ExportUtil.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:
@@ -65,7 +65,7 @@ fun <T : Any> FieldExtractorsFactory<T>.addOptionsToSpec(
     if (this is FieldExtractorsFactoryWithPresets) {
         spec.addOption(
             OptionSpec
-                .builder("-p", "--preset")
+                .builder("--preset")
                 .description("Specify preset of export fields. Possible values: \${COMPLETION-CANDIDATES}.")
                 .order(50_000 - 300)
                 .required(false)
@@ -82,7 +82,7 @@ fun <T : Any> FieldExtractorsFactory<T>.addOptionsToSpec(
         )
         spec.addOption(
             OptionSpec
-                .builder("-pf", "--preset-file")
+                .builder("--preset-file")
                 .description("Specify preset file of export fields")
                 .order(50_000 - 200)
                 .required(false)