Rename OutputFormats to Output

jtnystrom · Jan 16, 2023 · 9a46e62 · 9a46e62
1 parent 56969c5
commit 9a46e62
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Showing 4 changed files with 8 additions and 8 deletions.
diff --git a/src/main/scala/com/jnpersson/discount/spark/CountedKmers.scala b/src/main/scala/com/jnpersson/discount/spark/CountedKmers.scala
@@ -60,7 +60,7 @@ class CountedKmers(val counts: Dataset[(Array[Long], Abundance)], splitter: Broa
    * @param output Directory to write to (prefix name)
    */
   def writeFasta(output: String): Unit = {
-    OutputFormats.writeFastaCounts(withSequences, output)
+    Output.writeFastaCounts(withSequences, output)
   }
 
   /**
@@ -71,9 +71,9 @@ class CountedKmers(val counts: Dataset[(Array[Long], Abundance)], splitter: Broa
    */
   def writeTSV(withKmers: Boolean, output: String): Unit = {
     if (withKmers) {
-      OutputFormats.writeTSV(withSequences, output)
+      Output.writeTSV(withSequences, output)
     } else {
-      OutputFormats.writeTSV(counts.map(_._2), output)
+      Output.writeTSV(counts.map(_._2), output)
     }
   }
 }
diff --git a/src/main/scala/com/jnpersson/discount/spark/Index.scala b/src/main/scala/com/jnpersson/discount/spark/Index.scala
@@ -212,7 +212,7 @@ class Index(val params: IndexParams, val buckets: Dataset[ReducibleBucket])
    * @param output Directory to write to (prefix name)
    */
   def writeHistogram(output: String): Unit =
-    OutputFormats.writeTSV(histogram, output)
+    Output.writeTSV(histogram, output)
 
   /** Write per-bucket statistics to HDFS.
    * This action triggers a computation.
@@ -222,15 +222,15 @@ class Index(val params: IndexParams, val buckets: Dataset[ReducibleBucket])
     val bkts = stats()
     bkts.cache()
     bkts.write.mode(SaveMode.Overwrite).option("sep", "\t").csv(s"${location}_bucketStats")
-    OutputFormats.showStats(bkts, Some(location))
+    Output.showStats(bkts, Some(location))
     bkts.unpersist()
   }
 
   /** Show summary stats for this index.
    * This action triggers a computation.
    */
   def showStats(outputLocation: Option[String] = None): Unit = {
-    OutputFormats.showStats(stats(), outputLocation)
+    Output.showStats(stats(), outputLocation)
   }
 
   /** Write this index to a location.

diff --git a/...ersson/discount/spark/OutputFormats.scala → ...com/jnpersson/discount/spark/Output.scala b/...ersson/discount/spark/OutputFormats.scala → ...com/jnpersson/discount/spark/Output.scala
@@ -26,7 +26,7 @@ import org.apache.spark.sql.{Dataset, SaveMode, SparkSession}
 /**
  * Output format helper methods
  */
-object OutputFormats {
+object Output {
   /**
    * Write a data table as TSV to the filesystem.
    * @param allKmers data to write

diff --git a/src/main/scala/com/jnpersson/discount/spark/SparkTool.scala b/src/main/scala/com/jnpersson/discount/spark/SparkTool.scala
@@ -151,7 +151,7 @@ private[jnpersson] class DiscountConf(args: Array[String]) extends SparkToolConf
     requireOne(inputFiles, indexLocation)
 
     def run(implicit spark: SparkSession) : Unit =
-      OutputFormats.showStats(inputIndex().stats(min.toOption, max.toOption), output.toOption)
+      Output.showStats(inputIndex().stats(min.toOption, max.toOption), output.toOption)
   }
   addSubcommand(stats)