Hi,
On Sat, Mar 17, 2018 at 10:27:38AM +0200, Adrian Bunk wrote:
> Source: artemis
> Version: 16.0.17+dfsg-3
> Severity: serious
I injected Artemis 17.0.1 into Git which seems to fix this issue.
Unfortunately there are other Build problems:
...
/build/artemis-17.0.1+dfsg/uk/ac/sanger/artemis/j2ssh/SshFileManager.java:437:
warning: [removal] destroy() in Thread has been deprecated and marked for
removal
public void destroy()
^
/build/artemis-17.0.1+dfsg/uk/ac/sanger/artemis/components/alignment/BamView.java:565:
error: cannot find symbol
FTPSeekableStream fss = new FTPSeekableStream(new URL(alignmentFile),
ftpSocketTimeout);
^
symbol: class FTPSeekableStream
location: class BamView
/build/artemis-17.0.1+dfsg/uk/ac/sanger/artemis/components/alignment/BamView.java:565:
error: cannot find symbol
FTPSeekableStream fss = new FTPSeekableStream(new URL(alignmentFile),
ftpSocketTimeout);
^
symbol: class FTPSeekableStream
location: class BamView
/build/artemis-17.0.1+dfsg/uk/ac/sanger/artemis/components/alignment/BamView.java:4204:
error: cannot find symbol
(sam.isSecondaryAlignment() ? "yes" : "no"), Level.DEBUG);
^
symbol: method isSecondaryAlignment()
location: variable sam of type SAMRecord
...
I suspect these are compatibility issues with latest samtools.
Could somebody more familiar with this like me please have a look.
Kind regards
Andreas.
--
http://fam-tille.de
