Makefile | 3 2 + 1 - 0 !
1 file changed, 2 insertions(+), 1 deletion(-)

 look for jars in /usr/share/java rather than ./lib
 The bundled jar files in lib/ have been removed for Debian, so the
 build system ought to find the packaged versions in /usr/share/java.
 This patch allows overriding the CLASSPATH while calling make. This
 way, we can change it from within debian/rules.

Makefile | 36 8 + 28 - 0 !
1 file changed, 8 insertions(+), 28 deletions(-)

 leave out removed files when building jar files
 The recipe to build the jar files looks for some files
 that have been excluded from the source distribution (lib/*).
 Their absence causes "can not stat" errors, so any reference to
 them is removed here.

test/build-test.xml | 15 4 + 11 - 0 !
1 file changed, 4 insertions(+), 11 deletions(-)

 change classpath to use external jars in build-test.xml

uk/ac/sanger/artemis/components/alignment/BamUtils.java | 32 16 + 16 - 0 !
uk/ac/sanger/artemis/components/alignment/BamView.java | 686 343 + 343 - 0 !
2 files changed, 359 insertions(+), 359 deletions(-)

 implement new htsjdk api
 See https://github.com/samtools/htsjdk/issues/767#issuecomment-264864910

uk/ac/sanger/artemis/io/GFF3Encoder.java | 2 1 + 1 - 0 !
1 file changed, 1 insertion(+), 1 deletion(-)

 use lang3

test/build-test.xml | 5 0 + 5 - 0 !
1 file changed, 5 deletions(-)

 build-test

test/evosuite-tests/uk/ac/sanger/artemis/circular/MemoryComboBox_ESTest.java | 31 0 + 31 - 0 !
1 file changed, 31 deletions(-)

 disable tests