Merge pull request #1749 from milaboratory/track-fasta-progress

align could track the progress of gz input
milaboratory · Aug 14, 2024 · 80774d1 · 80774d1
2 parents b7ea937 + 507979b
commit 80774d1
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Showing 4 changed files with 5 additions and 3 deletions.
diff --git a/build.gradle.kts b/build.gradle.kts
@@ -136,7 +136,7 @@ val obfuscationLibs: Configuration by configurations.creating
 
 val mixcrAlgoVersion = "4.7.0"
 // may be blank (will be inherited from mixcr-algo)
-val milibVersion = ""
+val milibVersion = "3.5.0-1-add-progress-to-fasta"
 // may be blank (will be inherited from mixcr-algo or milib)
 val miuVersion = ""
 // may be blank (will be inherited from mixcr-algo)

diff --git a/changelogs/v4.7.1.md b/changelogs/v4.7.1.md
@@ -0,0 +1,3 @@
+## 🛠️ Other improvements & fixes
+
+- Tracking the progres of fasta[.gz] inputs on `align`.
diff --git a/changelogs/v4.8.0.md b/changelogs/v4.8.0.md
diff --git a/src/main/kotlin/com/milaboratory/mixcr/cli/CommandAlign.kt b/src/main/kotlin/com/milaboratory/mixcr/cli/CommandAlign.kt
@@ -113,7 +113,6 @@ import com.milaboratory.util.SmartProgressReporter
 import com.milaboratory.util.TempFileManager
 import com.milaboratory.util.limit
 import com.milaboratory.util.parseAndRunAndCorrelateFSPattern
-import com.milaboratory.util.unzippedInputStream
 import com.milaboratory.util.use
 import com.milaboratory.util.withExpectedSize
 import io.repseq.core.Chains
@@ -1061,7 +1060,7 @@ object CommandAlign {
                         throw ValidationException("File concatenation not supported for fasta files.")
                     val inputFile = inputFileGroups.fileGroups.first().files.first()
                     FastaSequenceReaderWrapper(
-                        FastaReader(inputFile.unzippedInputStream(), NucleotideSequence.ALPHABET),
+                        FastaReader(inputFile.toFile(), NucleotideSequence.ALPHABET),
                         cmdParams.replaceWildcards
                     ).map { ProcessingBundle.fromRead(it, it.weight()) }
                 }