Control: tag -1 + help This looks like it's due to API changes in the picard Java library. I was able to avoid some of the errors by using htsjdk (thereby adding dependency on libhtsjdk-java) instead of picard. We may also be able drop the dependency on libsam-java.
However, there are still some errors: /«BUILDDIR»/artemis-16.0.0+dfsg/uk/ac/sanger/artemis/components/alignment/BamView.java:119: error: cannot find symbol import htsjdk.samtools.SAMFileReader.ValidationStringency; ^ symbol: class ValidationStringency location: class SAMFileReader /«BUILDDIR»/artemis-16.0.0+dfsg/uk/ac/sanger/artemis/components/alignment/BamView.java:494: error: cannot find symbol SAMFileReader.setDefaultValidationStringency(ValidationStringency.LENIENT); ^ symbol: variable ValidationStringency location: class BamView /«BUILDDIR»/artemis-16.0.0+dfsg/uk/ac/sanger/artemis/components/alignment/BamView.java:529: error: package net.sf.picard.util.Log does not exist net.sf.picard.util.Log.LogLevel.ERROR); ^ /«BUILDDIR»/artemis-16.0.0+dfsg/uk/ac/sanger/artemis/components/alignment/BamView.java:528: error: package net.sf.picard.util does not exist net.sf.picard.util.Log.setGlobalLogLevel( ^ /«BUILDDIR»/artemis-16.0.0+dfsg/uk/ac/sanger/artemis/components/alignment/BamView.java:583: error: cannot find symbol samFileReader.setValidationStringency(ValidationStringency.SILENT); ^ symbol: variable ValidationStringency location: class BamView Note: Some input files use or override a deprecated API. Note: Recompile with -Xlint:deprecation for details. Note: Some input files use unchecked or unsafe operations. Note: Recompile with -Xlint:unchecked for details. 5 errors 1 warning make[2]: *** [uk/ac/sanger/artemis/MegaBlastComparisonData.class] Error 1 Artemis already uses log4j in other places and perhaps it can be used here to replace the dropped picard logging functionality. Any help would be appreciated. I'm going to push my latest work and also plan to revisit this. regards Afif -- Afif Elghraoui | عفيف الغراوي http://afif.ghraoui.name