Merge pull request #1258 from milaboratory/small-fixes

fix file name in downsample
milaboratory · Jul 24, 2023 · 439e61d · 439e61d
2 parents f053570 + b34b7c1
commit 439e61d
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Showing 4 changed files with 10 additions and 5 deletions.
diff --git a/build.gradle.kts b/build.gradle.kts
@@ -133,8 +133,8 @@ val toObfuscate: Configuration by configurations.creating {
 val obfuscationLibs: Configuration by configurations.creating
 
 
-val mixcrAlgoVersion = "4.4.0-12-tag-sequence-quality-fix"
-val milibVersion = "3.1.0-2-master"
+val mixcrAlgoVersion = "4.4.0-15-small-fixes"
+val milibVersion = ""
 val mitoolVersion = ""
 val repseqioVersion = ""
 

diff --git a/src/main/kotlin/com/milaboratory/mixcr/cli/CommandExportOverlap.kt b/src/main/kotlin/com/milaboratory/mixcr/cli/CommandExportOverlap.kt
@@ -170,7 +170,7 @@ class CommandExportOverlap : MiXCRCommandWithOutputs() {
 
     override fun run1() {
         val samples = inputFiles
-        val chains = this.chains?.let { ChainsFilter.parseChainsList(this.chains) }
+        val chains = this.chains?.let { ChainsFilter.parseChainsList(it) }
         val criteria = OverlapUtil.parseCriteria(overlapCriteria)
         val extractors = mutableListOf<OverlapFieldExtractor>()
         extractors += ExtractorUnique(

diff --git a/src/main/kotlin/com/milaboratory/mixcr/cli/CommandExportShmTreesTableWithNodes.kt b/src/main/kotlin/com/milaboratory/mixcr/cli/CommandExportShmTreesTableWithNodes.kt
@@ -113,7 +113,7 @@ class CommandExportShmTreesTableWithNodes : CommandExportShmTreesAbstract() {
         ValidationException.requireNotNull(out) {
             "With --use-local-temp explicit output path is required"
         }
-        TempFileManager.smartTempDestination(out, ".build_trees", !useLocalTemp.value)
+        TempFileManager.smartTempDestination(out!!, ".build_trees", !useLocalTemp.value)
     }
 
     override val outputFiles

diff --git a/src/main/kotlin/com/milaboratory/mixcr/cli/postanalysis/CommandDownsample.kt b/src/main/kotlin/com/milaboratory/mixcr/cli/postanalysis/CommandDownsample.kt
@@ -103,7 +103,12 @@ class CommandDownsample : MiXCRCommandWithOutputs() {
         val fileNameWithoutExtension = input.fileName.toString()
             .replace(".clna", "")
             .replace(".clns", "")
-        val outName = "$fileNameWithoutExtension.$chains.$suffix.clns"
+        val suffix = when {
+            chains == null || chains!!.isEmpty() -> ""
+            chains!!.size == 1 -> "${chains!!.first()}."
+            else -> "$chains."
+        }
+        val outName = "$fileNameWithoutExtension.$suffix$suffix.clns"
         return (outPath?.resolve(outName) ?: Paths.get(outName)).toAbsolutePath()
     }