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Description: using again a scala 2.11 idiom to iterate over Java lists
This is necessary until scala 2.13 gets packaged in Debian.
Author: Pierre Gruet <pgt@debian.org>
Forwarded: not-needed
Last-Update: 2021-12-17
--- a/build.sbt
+++ b/build.sbt
@@ -2,7 +2,7 @@
version := "1.24"
-scalaVersion := "2.13.4"
+scalaVersion := "2.11.12"
scalacOptions += "-deprecation"
--- a/build.sh
+++ b/build.sh
@@ -12,5 +12,5 @@
<$tmp >$f
#sbt $* package
sbt $* assembly
-ln -sf `pwd`/target/scala-2.13/pilon-assembly-$version.jar ~/lib/pilon/pilon-dev.jar
+ln -sf `pwd`/target/scala-2.11/pilon-assembly-$version.jar ~/lib/pilon/pilon-dev.jar
mv $tmp $f
--- a/src/main/scala/org/broadinstitute/pilon/BamFile.scala
+++ b/src/main/scala/org/broadinstitute/pilon/BamFile.scala
@@ -21,7 +21,7 @@
import collection.mutable.{HashMap,Map}
import java.io.File
-import scala.jdk.CollectionConverters._
+import scala.collection.JavaConverters._
import htsjdk.samtools._
object BamFile {
--- a/src/main/scala/org/broadinstitute/pilon/PileUpRegion.scala
+++ b/src/main/scala/org/broadinstitute/pilon/PileUpRegion.scala
@@ -19,7 +19,7 @@
package org.broadinstitute.pilon
-import scala.jdk.CollectionConverters._
+import scala.collection.JavaConverters._
import htsjdk.samtools._
import Utils._
--- a/src/main/scala/org/broadinstitute/pilon/Scaffold.scala
+++ b/src/main/scala/org/broadinstitute/pilon/Scaffold.scala
@@ -28,7 +28,7 @@
*/
-import scala.jdk.CollectionConverters._
+import scala.collection.JavaConverters._
import collection.mutable.{ Map, HashMap }
import htsjdk.samtools._
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