JAL-3111 drop hts-1.33 as a dependency (in favour of htsjdk-2.12)

diff --git a/.classpath b/.classpath
index ad1fa86..f4d788d 100644 (file)
--- a/.classpath
+++ b/.classpath
@@ -47,7 +47,6 @@
        <classpathentry kind="lib" path="lib/VARNAv3-93.jar"/>
        <classpathentry kind="lib" path="lib/jfreesvg-2.1.jar"/>
        <classpathentry kind="lib" path="lib/quaqua-filechooser-only-8.0.jar"/>
-       <classpathentry kind="lib" path="lib/htsjdk-1.133.jar"/>
        <classpathentry kind="lib" path="lib/VAqua5-patch.jar"/>
        <classpathentry kind="con" path="org.eclipse.jdt.USER_LIBRARY/plugin"/>
        <classpathentry kind="lib" path="lib/xml-apis.jar"/>

diff --git a/THIRDPARTYLIBS b/THIRDPARTYLIBS
index 40d0f6c..c7c9b5d 100644 (file)
--- a/THIRDPARTYLIBS
+++ b/THIRDPARTYLIBS
@@ -51,7 +51,7 @@ quaqua: v.8.0 (latest stable) by Randel S Hofer. LGPL and BSD Modified license:
 
 vaqua5-patch: This is a patched version of VAqua v5 (latest stable) by Alan Snyder et al. GPLv3 with Classpath exception, also includes contributions from Quaqua: http://violetlib.org/vaqua/overview.html - see doc/patching-vaqua.txt for patch details, and http://issues.jalview.org/browse/JAL-2988 for details of the bug that the patch addresses.
 
-lib/htsjdk-1.120-SNAPSHOT.jar: (currently not required for 2.10) built from maven master at https://github.com/samtools/htsjdk MIT License to Broad Institute
+lib/htsjdk-2.12.jar: built from maven master at https://github.com/samtools/htsjdk MIT License to Broad Institute
 
 lib/biojava-core-4.1.0.jar LGPLv2.1 - latest license at https://github.com/biojava/biojava/blob/master/LICENSE
 

diff --git a/lib/htsjdk-1.133.jar b/lib/htsjdk-1.133.jar
deleted file mode 100644 (file)
index f084258..0000000
Binary files a/lib/htsjdk-1.133.jar and /dev/null differ