Scala error when trying to build latest version of pilon
Hi Pierre (and others)
when trying to build the latest version of pilon[1] I get:
...
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
make[1]: *** [debian/rules:10: override_dh_auto_build] Fehler 1
Any hint how to fix this?
Kind regards
Andreas.
[1] https://salsa.debian.org/med-team/pilon
--
http://fam-tille.de
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