build.xml | 8 5 + 3 - 0 !
1 file changed, 5 insertions(+), 3 deletions(-)

 use debian packaged jars

fastqc | 11 5 + 6 - 0 !
1 file changed, 5 insertions(+), 6 deletions(-)

 ensure proper classpath according to location of debian jars

uk/ac/babraham/FastQC/FastQCMenuBar.java | 2 1 + 1 - 0 !
1 file changed, 1 insertion(+), 1 deletion(-)

 the original way to open help text ends up in an exception
 Setting the explicit file name as well as avoiding the call to
   ClassLoader.getSystemResource
 helps fixing this.  Specifically the later is important, see
   https://lists.debian.org/debian-med/2012/11/msg00073.html

uk/ac/babraham/FastQC/Modules/AdapterContent.java | 4 3 + 1 - 0 !
uk/ac/babraham/FastQC/Modules/ModuleConfig.java | 3 2 + 1 - 0 !
uk/ac/babraham/FastQC/Sequence/Contaminant/ContaminentFinder.java | 5 3 + 2 - 0 !
3 files changed, 8 insertions(+), 4 deletions(-)

 use config in debian etc dirs instead of embedding data in jar

uk/ac/babraham/FastQC/Sequence/BAMFile.java | 13 7 + 6 - 0 !
1 file changed, 7 insertions(+), 6 deletions(-)

 path to samtools changed when switching from libsam-java
 to libhtsjdk-java

uk/ac/babraham/FastQC/Sequence/BAMFile.java | 17 10 + 7 - 0 !
1 file changed, 10 insertions(+), 7 deletions(-)

 use correct samreader api

build.xml | 4 2 + 2 - 0 !
1 file changed, 2 insertions(+), 2 deletions(-)

 set java 9 as build target
 No idea whether this has some influence finally but trying to get rid
 of this warning
    [javac] Using javac -source 1.5 is no longer supported, switching to 1.7
    [javac] Using javac -target 1.5 is no longer supported, switching to 1.7
 is intended by this patch.