Pilon might need newer scala

[Andreas Tille <andreas@an3as.eu>]

Hi,

I intended to update pilon to its latest upstream version but
got:

scalac -classpath /usr/share/java/htsjdk.jar -d pilon.jar src/main/scala/org/broadinstitute/pilon/*
src/main/scala/org/broadinstitute/pilon/BamFile.scala:24: error: object jdk is not a member of package scala
import scala.jdk.CollectionConverters._
             ^
src/main/scala/org/broadinstitute/pilon/BamFile.scala:65: error: value asScala is not a member of java.util.List[htsjdk.samtools.SAMSequenceRecord]
    val seqs = r.getFileHeader.getSequenceDictionary.getSequences.asScala
                                                                  ^
src/main/scala/org/broadinstitute/pilon/BamFile.scala:96: error: value asScala is not a member of htsjdk.samtools.SAMRecordIterator
    val reads = r.queryUnmapped.asScala.filter(validateRead(_)).toList
                                ^
src/main/scala/org/broadinstitute/pilon/BamFile.scala:119: error: value asScala is not a member of htsjdk.samtools.SAMRecordIterator
possible cause: maybe a semicolon is missing before `value asScala'?
      (region.start-10000) max 0, (region.stop+10000) min region.contig.length).asScala
                                                                                ^
src/main/scala/org/broadinstitute/pilon/PileUpRegion.scala:22: error: object jdk is not a member of package scala
import scala.jdk.CollectionConverters._
             ^
src/main/scala/org/broadinstitute/pilon/BamFile.scala:297: error: value asScala is not a member of htsjdk.samtools.SAMRecordIterator
    for (read <- r.iterator.asScala) {
                            ^
src/main/scala/org/broadinstitute/pilon/BamFile.scala:341: error: value asScala is not a member of htsjdk.samtools.SAMRecordIterator
    val reads = r.queryOverlapping(region.name, region.start, region.stop).asScala.filter(validateRead(_)).toList
                                                                           ^
src/main/scala/org/broadinstitute/pilon/Scaffold.scala:31: error: object jdk is not a member of package scala
import scala.jdk.CollectionConverters._
             ^
src/main/scala/org/broadinstitute/pilon/PileUpRegion.scala:136: error: value asScala is not a member of java.util.List[htsjdk.samtools.CigarElement]
    val cigarElements = cigar.getCigarElements.asScala
                                               ^
src/main/scala/org/broadinstitute/pilon/Scaffold.scala:351: error: value asScala is not a member of htsjdk.samtools.SAMRecordIterator
    for (read <- reader.iterator.asScala if (!read.getReadUnmappedFlag)) {
                                 ^
10 errors found


Just verifying with Pierre whether my assumption that this requires
newer Scala is correct or whether there might be possibly a simple fix.

Kind regards

     Andreas.

-- 
http://fam-tille.de