fix method name clash for List.sort() in Java 8

override abstract method close() in CRAMReferenceSequenceFile

switch to older EMBOSS version

Building from source without this patch resulted in the following error:
artemis-16.0.0+dfsg/uk/ac/sanger/artemis/components/alignment/CRAMReferenceSequenceFile.java:35:
error: CRAMReferenceSequenceFile is not abstract and does not override abstract method close() in ReferenceSequenceFile

add new 'alias' qualifier

Added Kim Rutherford

Add TravisCI Support, change README to markdown

Rather than testing the Ant build under multiple JDKs, I've arbitrarily
decided to test it only under openjdk7.  This keeps us to 4 builds
rather than 6 before the build is reported as green which should be a
bit quicker.

ant builds copy everything in the pwd into ant_build and then try to
build all of the java files copied, including those of the dependencies
which are built separately.  This does not end well.

We don't

actually clone the history attribute

add support for eupathdb_uc user comment attributes

Added uORF, sORF and tnaORF as extra keys

extend escaping in qualifier values

Added AUTHORS file

Added LICENSE