Re: Help needed with Java htsjdk for package surankco

Le ven. 25 mars 2016 à 07:00, olivier sallou <olivier.sallou@gmail.com> a écrit :

I will have a look today

Le jeu. 24 mars 2016 18:44, olivier sallou <olivier.sallou@gmail.com> a écrit :
Indeed, looks like incompatible classes between versions

Olivier

Le jeu. 24 mars 2016 17:28, Andreas Tille <andreas@an3as.eu> a écrit :
Hi,

I've just injected surankco[1] which failed to build with:

jh_build --javacopts='-target 1.7' --javacopts='-source 1.7' surankco.jar src
find src -name *.java -and -type f -print0 | xargs -s 512000 -0 /usr/lib/jvm/default-java/bin/javac -g -cp /usr/share/java/htsjdk.jar:debian/_jh_build.surankco -d debian/_jh_build.surankco -target 1.7 -source 1.7
warning: [options] bootstrap class path not set in conjunction with -source 1.7
src/de/rki/ng4/surankco/data/Reads.java:30: error: incompatible types: Reads cannot be converted to FastqReads
new Qual(filename, this);
^
src/de/rki/ng4/surankco/data/Reads.java:33: error: incompatible types: Reads cannot be converted to FastqReads
new Fastq(filename, this, parameter);

This does not look at issue of htsjdk version.

Qual (which is part of surankco, not htsjdklib) accepts only FastqReads as input, not Reads (which does not extend FastqReads).

Same for Fastq.

I see no call to Reads in the code, could it be an old code not used anymore? (to be removed)

If I remove this file (Reads.java), it compiles. Build ends in error due to missing jar because it is a build root and not in debian dir

Olivier

^
Note: Some messages have been simplified; recompile with -Xdiags:verbose to get full output
2 errors
1 warning

Since upstream jar came with htsjdk-1.128.jar included and the build was
done agains libhtsjdk-java 2.0.1 I suspect an API change. Any hint how
to fix this?

Kind regards

Andreas.

[1] https://anonscm.debian.org/git/debian-med/surankco.git

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