Merge pull request #1534 from milaboratory/reduceToCommonAssembleFeature

Reduce to common assemble feature

build.gradle.kts

@@ -134,7 +134,7 @@ val toObfuscate: Configuration by configurations.creating {
 val obfuscationLibs: Configuration by configurations.creating
 
 
-val mixcrAlgoVersion = "4.6.0-43-fixes"
+val mixcrAlgoVersion = "4.6.0-46-reduceToCommonAssembleFeature"
 // may be blank (will be inherited from mixcr-algo)
 val milibVersion = ""
 // may be blank (will be inherited from mixcr-algo or milib)

regression/cli-help/findAlleles.txt

@@ -12,14 +12,13 @@ of V and J genes and the same features to align.
                              In case of directory no filter by file type will be applied.
       --output-template <template.clns>
                              Output template may contain {file_name} and {file_dir_path},
-                             outputs for '-o /output/folder/{file_name}_with_alleles.clns
-                               input_file.clns input_file2.clns' will be
-                               /output/folder/input_file_with_alleles.clns and
-                               /output/folder/input_file2_with_alleles.clns,
-                             outputs for '-o {file_dir_path}/{file_name}_with_alleles.clns
+                             outputs for '-o /output/folder/{file_name}_suffix.clns input_file.clns
+                               input_file2.clns' will be /output/folder/input_file_suffix.clns and
+                               /output/folder/input_file2_suffix.clns,
+                             outputs for '-o {file_dir_path}/{file_name}_suffix.clns
                                /some/folder1/input_file.clns /some/folder2/input_file2.clns' will
-                               be /seme/folder1/input_file_with_alleles.clns and
-                               /some/folder2/input_file2_with_alleles.clns
+                               be /seme/folder1/input_file_suffix.clns and
+                               /some/folder2/input_file2_suffix.clns
                              Resulted outputs must be uniq
       --no-clns-output       Command will not realign input clns files. Must be specified if
                                `--output-template` is omitted.
@@ -81,7 +80,7 @@ of V and J genes and the same features to align.
                                allele.
       --dont-remove-unused-genes
                              Don't remove genes that weren't used in clones in the result library
-  -O  <key=value>            Overrides default build SHM parameter values
+  -O  <key=value>            Overrides default find alleles parameter values
   -r, --report <path>        Report file (human readable version, see `-j / --json-report` for
                                machine readable report).
   -j, --json-report <path>   JSON formatted report file.

src/main/kotlin/com/milaboratory/mixcr/cli/CommandAlign.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:
@@ -73,9 +73,9 @@ import com.milaboratory.mixcr.cli.CommonDescriptions.Labels
 import com.milaboratory.mixcr.cli.MiXCRCommand.OptionsOrder
 import com.milaboratory.mixcr.presets.AlignMixins
 import com.milaboratory.mixcr.presets.AlignMixins.LimitInput
+import com.milaboratory.mixcr.presets.AnalyzeCommandDescriptor
+import com.milaboratory.mixcr.presets.AnalyzeCommandDescriptor.Companion.dotAfterIfNotBlank
 import com.milaboratory.mixcr.presets.FullSampleSheetParsed
-import com.milaboratory.mixcr.presets.MiXCRCommandDescriptor
-import com.milaboratory.mixcr.presets.MiXCRCommandDescriptor.Companion.dotAfterIfNotBlank
 import com.milaboratory.mixcr.presets.MiXCRParamsBundle
 import com.milaboratory.mixcr.presets.MiXCRParamsSpec
 import com.milaboratory.mixcr.presets.MiXCRStepParams
@@ -127,7 +127,7 @@ import kotlin.io.path.readText
 import kotlin.math.max
 
 object CommandAlign {
-    const val COMMAND_NAME = MiXCRCommandDescriptor.align.name
+    const val COMMAND_NAME = AnalyzeCommandDescriptor.align.name
 
     const val SAVE_OUTPUT_FILE_NAMES_OPTION = "--save-output-file-names"
     const val STRICT_SAMPLE_NAME_MATCHING_OPTION = "--strict-sample-sheet-matching"
@@ -1165,7 +1165,7 @@ object CommandAlign {
                     MiXCRHeader(
                         inputHash,
                         dontSavePresetOption.presetToSave(paramsSpecPacked),
-                        MiXCRStepParams().add(MiXCRCommandDescriptor.align, cmdParams),
+                        MiXCRStepParams().add(AnalyzeCommandDescriptor.align, cmdParams),
                         tagsExtractor.tagsInfo,
                         aligner.parameters,
                         aligner.parameters.featuresToAlignMap,
@@ -1306,7 +1306,7 @@ object CommandAlign {
                 reportBuilder.setTransformerReports(tagsExtractor.transformerReports)
 
                 val report = reportBuilder.buildReport()
-                writers?.setFooter(MiXCRFooter().addStepReport(MiXCRCommandDescriptor.align, report))
+                writers?.setFooter(MiXCRFooter().addStepReport(AnalyzeCommandDescriptor.align, report))
 
                 // Writing report to stout
                 ReportUtil.writeReportToStdout(report)

src/main/kotlin/com/milaboratory/mixcr/cli/CommandAnalyze.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:
@@ -22,10 +22,9 @@ import com.milaboratory.mixcr.cli.CommandAlign.inputFileGroups
 import com.milaboratory.mixcr.cli.CommandAlign.listSamplesForSeedFileName
 import com.milaboratory.mixcr.cli.CommonDescriptions.Labels
 import com.milaboratory.mixcr.presets.AlignMixins
-import com.milaboratory.mixcr.presets.AnyMiXCRCommand
+import com.milaboratory.mixcr.presets.AnalyzeCommandDescriptor
+import com.milaboratory.mixcr.presets.AnalyzeCommandDescriptor.Companion.dotAfterIfNotBlank
 import com.milaboratory.mixcr.presets.FullSampleSheetParsed
-import com.milaboratory.mixcr.presets.MiXCRCommandDescriptor
-import com.milaboratory.mixcr.presets.MiXCRCommandDescriptor.Companion.dotAfterIfNotBlank
 import com.milaboratory.mixcr.presets.MiXCRParamsBundle
 import com.milaboratory.mixcr.presets.MiXCRParamsSpec
 import com.milaboratory.mixcr.presets.MiXCRPipeline
@@ -338,7 +337,7 @@ object CommandAnalyze {
                 .let { (first, second) -> first to second.steps.sortedBy { it.order } }
 
             // Creating execution plan
-            if (pipeline[0] != MiXCRCommandDescriptor.align)
+            if (pipeline[0] != AnalyzeCommandDescriptor.align)
                 throw ValidationException("Pipeline must stat from the align action.")
 
             val planBuilder = PlanBuilder(
@@ -365,7 +364,7 @@ object CommandAnalyze {
             // Adding "align" step
             if (outputNoUsedReads)
                 pathsForNotAligned.fillWithDefaults(inputFileGroups.inputType, outputFolder, outputNamePrefix)
-            planBuilder.addStep(MiXCRCommandDescriptor.align) { _, _, _ ->
+            planBuilder.addStep(AnalyzeCommandDescriptor.align) { _, _, _ ->
                 listOf("--preset", presetName) + extraAlignArgs +
                         mixins.flatMap { it.cmdArgs } + pathsForNotAligned.argsForAlign()
             }
@@ -381,24 +380,24 @@ object CommandAnalyze {
             // Adding all steps with calculations
             pipeline
                 .drop(1)
-                .filter { cmd -> cmd !is MiXCRCommandDescriptor.ExportCommandDescriptor }
+                .filter { cmd -> cmd !is AnalyzeCommandDescriptor.ExportCommandDescriptor }
                 .forEach { cmd ->
                     planBuilder.addStep(cmd) { outputFolder, prefix, sampleName ->
                         when (cmd) {
-                            MiXCRCommandDescriptor.assemble -> {
+                            AnalyzeCommandDescriptor.assemble -> {
                                 val additionalArgs = mutableListOf<String>()
                                 if (consensusAlignments)
                                     additionalArgs += listOf(
                                         "--consensus-alignments",
                                         outputFolder.resolve(
-                                            MiXCRCommandDescriptor.assemble.consensusAlignments(prefix, sampleName)
+                                            AnalyzeCommandDescriptor.assemble.consensusAlignments(prefix, sampleName)
                                         ).toString()
                                     )
                                 if (consensusStateStats)
                                     additionalArgs += listOf(
                                         "--consensus-state-stat",
                                         outputFolder.resolve(
-                                            MiXCRCommandDescriptor.assemble.consensusStateStats(prefix, sampleName)
+                                            AnalyzeCommandDescriptor.assemble.consensusStateStats(prefix, sampleName)
                                         ).toString()
                                     )
                                 consensusStateStatsDownsampling?.let {
@@ -417,7 +416,7 @@ object CommandAnalyze {
             }
 
             pipeline
-                .filterIsInstance<MiXCRCommandDescriptor.ExportCommandDescriptor<*>>()
+                .filterIsInstance<AnalyzeCommandDescriptor.ExportCommandDescriptor<*>>()
                 .forEach { cmd ->
                     planBuilder.addExportStep(cmd)
                 }
@@ -442,9 +441,9 @@ object CommandAnalyze {
             private val forceOverride: Boolean
         ) {
             private val executionPlan = mutableListOf<ExecutionStep>()
-            private val rounds = mutableMapOf<AnyMiXCRCommand, Int>()
+            private val rounds = mutableMapOf<AnalyzeCommandDescriptor<*, *>, Int>()
             private var nextInputs: List<InputFileSet> = listOf(InputFileSet("", initialInputs.map { it.toString() }))
-            private val outputsForCommands = mutableListOf<Pair<AnyMiXCRCommand, List<InputFileSet>>>()
+            private val outputsForCommands = mutableListOf<Pair<AnalyzeCommandDescriptor<*, *>, List<InputFileSet>>>()
 
             fun setActualAlignOutputs(fileNames: List<String>) {
                 val outputSeed = Path(nextInputs.requireSingleton().fileNames.requireSingleton()).name
@@ -483,7 +482,7 @@ object CommandAnalyze {
                 for (input in inputsForQc) {
                     check(input.fileNames.size == 1)
                     val round = 0
-                    val cmd = MiXCRCommandDescriptor.qc
+                    val cmd = AnalyzeCommandDescriptor.qc
                     val outputName = cmd.outputName(outputNamePrefix, input.sampleName, paramsBundle, round)
                     val arguments = mutableListOf("--print-to-stdout")
                     if (forceOverride)
@@ -503,7 +502,7 @@ object CommandAnalyze {
                 }
             }
 
-            fun addExportStep(cmd: MiXCRCommandDescriptor.ExportCommandDescriptor<*>) {
+            fun addExportStep(cmd: AnalyzeCommandDescriptor.ExportCommandDescriptor<*>) {
                 val runAfter = cmd.runAfterLastOf()
                 val inputsForExport = outputsForCommands.findLast { (cmd) -> cmd in runAfter }!!.second
                 for (input in inputsForExport) {
@@ -527,7 +526,7 @@ object CommandAnalyze {
             }
 
             fun addStep(
-                cmd: AnyMiXCRCommand,
+                cmd: AnalyzeCommandDescriptor<*, *>,
                 extraArgs: (outputFolder: Path, prefix: String, sampleName: String) -> List<String> = { _, _, _ -> emptyList() }
             ) {
                 val round = rounds.compute(cmd) { c, p ->

src/main/kotlin/com/milaboratory/mixcr/cli/CommandAssemble.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:
@@ -42,7 +42,7 @@ import com.milaboratory.mixcr.basictypes.tag.TagType
 import com.milaboratory.mixcr.basictypes.validateCompositeFeatures
 import com.milaboratory.mixcr.cli.CommonDescriptions.DEFAULT_VALUE_FROM_PRESET
 import com.milaboratory.mixcr.cli.CommonDescriptions.Labels
-import com.milaboratory.mixcr.presets.MiXCRCommandDescriptor
+import com.milaboratory.mixcr.presets.AnalyzeCommandDescriptor
 import com.milaboratory.mixcr.presets.MiXCRParamsBundle
 import com.milaboratory.util.ArraysUtils
 import com.milaboratory.util.HashFunctions
@@ -66,7 +66,7 @@ import kotlin.io.path.bufferedWriter
 import kotlin.io.path.extension
 
 object CommandAssemble {
-    const val COMMAND_NAME = MiXCRCommandDescriptor.assemble.name
+    const val COMMAND_NAME = AnalyzeCommandDescriptor.assemble.name
 
     abstract class CmdBase : MiXCRCommandWithOutputs(), MiXCRPresetAwareCommand<CommandAssembleParams> {
         @Option(
@@ -388,7 +388,7 @@ object CommandAssemble {
                     val resultHeader = inputHeader
                         .withAssemblerParameters(cloneAssemblerParameters)
                         .addStepParams(
-                            MiXCRCommandDescriptor.assemble,
+                            AnalyzeCommandDescriptor.assemble,
                             paramsResolver.resolve(paramSpec).second
                         )
                         .copy(paramsSpec = dontSavePresetOption.presetToSave(paramSpec))
@@ -440,7 +440,7 @@ object CommandAssemble {
                             report = reportBuilder.buildReport()
                             writer.setFooter(
                                 alignmentsReader.footer.addStepReport(
-                                    MiXCRCommandDescriptor.assemble,
+                                    AnalyzeCommandDescriptor.assemble,
                                     report
                                 )
                             )
@@ -453,7 +453,7 @@ object CommandAssemble {
                             report = reportBuilder.buildReport()
                             writer.setFooter(
                                 alignmentsReader.footer.addStepReport(
-                                    MiXCRCommandDescriptor.assemble,
+                                    AnalyzeCommandDescriptor.assemble,
                                     report
                                 )
                             )

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

@@ -36,7 +36,7 @@ import com.milaboratory.mixcr.basictypes.VDJCSProperties.CloneOrdering
 import com.milaboratory.mixcr.basictypes.validateCompositeFeatures
 import com.milaboratory.mixcr.cli.CommonDescriptions.DEFAULT_VALUE_FROM_PRESET
 import com.milaboratory.mixcr.cli.CommonDescriptions.Labels
-import com.milaboratory.mixcr.presets.MiXCRCommandDescriptor
+import com.milaboratory.mixcr.presets.AnalyzeCommandDescriptor
 import com.milaboratory.mixcr.presets.MiXCRParamsBundle
 import com.milaboratory.mixcr.presets.MiXCRParamsSpec
 import com.milaboratory.mixcr.util.Concurrency
@@ -66,7 +66,7 @@ import java.nio.file.Path
 import java.util.*
 
 object CommandAssembleContigs {
-    const val COMMAND_NAME = MiXCRCommandDescriptor.assembleContigs.name
+    const val COMMAND_NAME = AnalyzeCommandDescriptor.assembleContigs.name
 
     abstract class CmdBase : MiXCRCommandWithOutputs(), MiXCRPresetAwareCommand<CommandAssembleContigsParams> {
         @Option(
@@ -172,19 +172,19 @@ object CommandAssembleContigs {
 
                 validateParams(cmdParams, reader.header)
 
-                require(reader.assemblingFeatures.size == 1) {
+                ValidationException.require(reader.assemblingFeatures.size == 1) {
                     "Supports only singular assemblingFeature."
                 }
                 val assemblingFeature = reader.assemblingFeatures.first()
-                require(!assemblingFeature.isComposite) {
+                ValidationException.require(!assemblingFeature.isComposite) {
                     "Supports only non-composite gene features as an assemblingFeature."
                 }
 
                 if (assemblingRegions != null) {
                     val fullyIncluded = assemblingRegions.features.any { assemblingRegion ->
                         GeneFeature.intersection(assemblingRegion, assemblingFeature) == assemblingFeature
                     }
-                    require(fullyIncluded) {
+                    ValidationException.require(fullyIncluded) {
                         "AssemblingFeature of input must be included fully in assemblingRegions"
                     }
                 }
@@ -305,10 +305,10 @@ object CommandAssembleContigs {
                     clones += clone.withId(cloneId++)
                 }
             }
-            val allFullyCoveredBy = cmdParams.allClonesWillBeCoveredByFeature()
+            val allFullyCoveredBy = cmdParams.parameters.allClonesWillBeCoveredByFeature()
             val resultHeader = header
                 .copy(allFullyCoveredBy = if (allFullyCoveredBy) assemblingRegions else null)
-                .addStepParams(MiXCRCommandDescriptor.assembleContigs, cmdParams)
+                .addStepParams(AnalyzeCommandDescriptor.assembleContigs, cmdParams)
                 .copy(paramsSpec = dontSavePresetOption.presetToSave(paramsSpec))
 
             val cloneSet = CloneSet.Builder(clones, genes, resultHeader)
@@ -327,7 +327,7 @@ object CommandAssembleContigs {
                 // Writing report to stout
                 ReportUtil.writeReportToStdout(report)
                 reportOptions.appendToFiles(report)
-                writer.setFooter(footer.addStepReport(MiXCRCommandDescriptor.assembleContigs, report))
+                writer.setFooter(footer.addStepReport(AnalyzeCommandDescriptor.assembleContigs, report))
             }
         }
     }

src/main/kotlin/com/milaboratory/mixcr/cli/CommandAssemblePartial.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:
@@ -25,7 +25,7 @@ import com.milaboratory.mixcr.basictypes.tag.TagType
 import com.milaboratory.mixcr.cli.CommonDescriptions.DEFAULT_VALUE_FROM_PRESET
 import com.milaboratory.mixcr.cli.CommonDescriptions.Labels
 import com.milaboratory.mixcr.partialassembler.PartialAlignmentsAssembler
-import com.milaboratory.mixcr.presets.MiXCRCommandDescriptor
+import com.milaboratory.mixcr.presets.AnalyzeCommandDescriptor
 import com.milaboratory.mixcr.presets.MiXCRParamsBundle
 import com.milaboratory.util.ReportUtil
 import com.milaboratory.util.SmartProgressReporter
@@ -38,7 +38,7 @@ import picocli.CommandLine.Parameters
 import java.nio.file.Path
 
 object CommandAssemblePartial {
-    const val COMMAND_NAME = MiXCRCommandDescriptor.assemblePartial.name
+    const val COMMAND_NAME = AnalyzeCommandDescriptor.assemblePartial.name
 
     abstract class CmdBase : MiXCRCommandWithOutputs(), MiXCRPresetAwareCommand<CommandAssemblePartialParams> {
         @Option(
@@ -144,7 +144,7 @@ object CommandAssemblePartial {
                 writer.writeHeader(
                     header
                         .updateTagInfo { ti -> ti.setSorted(groupingDepth) } // output data will be grouped only up to a groupingDepth
-                        .addStepParams(MiXCRCommandDescriptor.assemblePartial, cmdParams)
+                        .addStepParams(AnalyzeCommandDescriptor.assemblePartial, cmdParams)
                         .copy(paramsSpec = dontSavePresetOption.presetToSave(paramsSpec)),
                     reader.usedGenes
                 )
@@ -203,7 +203,7 @@ object CommandAssemblePartial {
                 }
                 reportOptions.appendToFiles(report)
                 writer.setNumberOfProcessedReads(reader.numberOfReads - assembler.overlapped.get())
-                writer.setFooter(reader.footer.addStepReport(MiXCRCommandDescriptor.assemblePartial, report))
+                writer.setFooter(reader.footer.addStepReport(AnalyzeCommandDescriptor.assemblePartial, report))
             }
         }
     }