Hi Bruce and Andreas,
Le 05/02/2021 à 05:12, Bruce Walker a écrit :
Hi Andreas,
I am the upstream author of Pilon, and I built the new 1.24 release using a
modern 2.13.x Scala compiler and library (along with a java 11 JRE, previously
was java 8). I’m sure the issue is in those changes. I will take a look when I
get a chance (probably over the weekend).
This is likely an issue linked to Scala, as Scala is unfortunately stuck
to version 2.11 in Debian. Updating Scala in Debian would imply updating
Scala Build Tool, which in turn should be compiled with Scala... Well,
quite a lot of work (which will need to be done one day, still).
Bruce, besides, could you please tell us what version of htsjdk you are
relying on? I am noticing the error
error: value asScala is not a member of htsjdk.samtools.SAMRecordIterator
—bruce
Best regards,
Pierre
On Feb 4, 2021, at 5:03 PM, Andreas Tille <[email protected]> wrote:
Hi,
I've commited the latest upstream version of pilon to Git[1] but
there are build issues:
...
debian/rules override_dh_auto_build
make[1]: Entering directory '/build/pilon-1.24'
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] Error 1
Any idea how this can be fixed?
Kind regards
Andreas.
[1] https://salsa.debian.org/med-team/pilon
--
http://fam-tille.de
