changelog and better error message

milaboratory · Apr 26, 2024 · b518de7 · b518de7
1 parent 2e80112
commit b518de7
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diff --git a/changelogs/v4.6.1.md b/changelogs/v4.6.1.md
@@ -4,6 +4,9 @@
   different expression levels on the consensus assembly algorithm. This change is specifically important for single-cell
   presets with cell-level assembly (most of the MiXCR presets for single-cell data).
 - Export of trees and tree nodes now support imputed features
+- Options `--dont-correct-tag-with-name <tag_name>` or `--dont-correct-tag-type (Molecule|Cell|Sample)` could be
+  specified to skip tag correction. It will degrade the overall quality of analysis, but will decrease memory
+  consumption
 
 ## 🛠️ Minor improvements & fixes
 

diff --git a/src/main/kotlin/com/milaboratory/mixcr/cli/CommandRefineTagsAndSort.kt b/src/main/kotlin/com/milaboratory/mixcr/cli/CommandRefineTagsAndSort.kt
@@ -366,7 +366,13 @@ object CommandRefineTagsAndSort {
 
                         // Running correction, results are temporarily persisted in temp file, so the object can be used
                         // multiple time to perform the correction and stream corrected and filtered results
-                        corrector.calculate()
+                        try {
+                            corrector.calculate()
+                        } catch (e: Throwable) {
+                            throw TagCorrectionError(
+                                correctionEnabled.mapIndexedNotNull { i, b -> tagNames[i].takeIf { b } }, e
+                            )
+                        }
 
                         // Available after calculation finishes
                         mitoolReport = corrector.report
@@ -464,3 +470,6 @@ object CommandRefineTagsAndSort {
         }
     }
 }
+
+class TagCorrectionError(val tags: List<String>, cause: Throwable) :
+    RuntimeException("Error on tag correction of $tags", cause)
diff --git a/src/main/kotlin/com/milaboratory/mixcr/cli/Main.kt b/src/main/kotlin/com/milaboratory/mixcr/cli/Main.kt
@@ -39,6 +39,7 @@ import com.milaboratory.mixcr.cli.qc.CommandExportQcCoverage
 import com.milaboratory.mixcr.cli.qc.CommandExportQcTags
 import com.milaboratory.mixcr.clonegrouping.CellType
 import com.milaboratory.mixcr.presets.Presets
+import com.milaboratory.mixcr.presets.RefineTagsAndSortMixins
 import com.milaboratory.mixcr.util.MiXCRVersionInfo
 import com.milaboratory.util.NoSpaceOnDiskException
 import com.milaboratory.util.TempFileManager
@@ -100,24 +101,33 @@ object Main {
         exitProcess(execute(*args))
     }
 
-    fun execute(vararg args: String): Int {
-        val commandLine = mkCmd(args)
-        try {
-            return commandLine.execute(*args)
-        } catch (e: OutOfMemoryError) {
-            if (logger.verbose) {
-                e.printStackTrace()
+    fun execute(vararg args: String): Int = try {
+        mkCmd(args).execute(*args)
+    } catch (e: OutOfMemoryError) {
+        if (logger.verbose) {
+            e.printStackTrace()
+        }
+        val memoryInOSMessage = memoryInOS()?.let { "${it / FileUtils.ONE_MB} Mb" }
+        val mb = Runtime.getRuntime().maxMemory() / FileUtils.ONE_MB
+        System.err.println("Not enough memory for run command. This run used approximately ${mb}m of memory, this machine has ${memoryInOSMessage ?: "unknown"} in total")
+        System.err.println()
+        System.err.println("Try to increase -Xmx. For example:")
+        System.err.println("mixcr -Xmx40g ${args.joinToString(" ")}")
+        val tagCorrectionError = e.suppressed.filterIsInstance<TagCorrectionError>().firstOrNull()
+        if (tagCorrectionError != null && tagCorrectionError.tags.isNotEmpty()) {
+            System.err.println()
+            System.err.println("Or try to disable correction for some tags. It will degrade the overall quality of analysis, but also will lover memory consumption. For example:")
+            (1..tagCorrectionError.tags.size).forEach { size ->
+                val tagOptions = tagCorrectionError.tags.take(size)
+                    .flatMap { tag -> listOf(RefineTagsAndSortMixins.DontCorrectTagName.CMD_OPTION, tag) }
+                val optionsLeft = args.drop(1)
+                System.err.println("mixcr ${args.first()} ${(tagOptions + optionsLeft).joinToString(" ")}")
             }
-            val memoryInOSMessage = memoryInOS()?.let { "${it / FileUtils.ONE_MB} Mb" }
-            System.err.println("Not enough memory for run command, try to increase -Xmx. Available memory: ${memoryInOSMessage ?: "unknown"}")
-            System.err.println("Example: `mixcr -Xmx40g ${args.joinToString(" ")}`")
-            val mb = Runtime.getRuntime().maxMemory() / FileUtils.ONE_MB
-            System.err.println("This run used approximately ${mb}m of memory")
-            return 2
-        } catch (e: Error) {
-            System.err.println("App version: " + MiXCRVersionInfo.get().shortestVersionString)
-            throw e
         }
+        2
+    } catch (e: Error) {
+        System.err.println("App version: " + MiXCRVersionInfo.get().shortestVersionString)
+        throw e
     }
 
     private fun assertionsDisabled(): Boolean = System.getProperty("noAssertions") != null