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

[jalview.git] / THIRDPARTYLIBS

diff --git a/THIRDPARTYLIBS b/THIRDPARTYLIBS
index 7779627..c7c9b5d 100644 (file)
--- a/THIRDPARTYLIBS
+++ b/THIRDPARTYLIBS
@@ -30,7 +30,6 @@ httpclient-4.0.3.jar
 httpcore-4.0.1.jar
 httpmime-4.0.3.jar
 jaxrpc.jar
-jdas-1.0.4.jar : Apache License - built from http://code.google.com/p/jdas/ (29th Feb 2012)
 jhall.jar
 jswingreader-0.3.jar : Apache license - built from http://jswingreader.sourceforge.net/ svn/trunk v12
 log4j-1.2.8.jar
@@ -39,8 +38,8 @@ miglayout-4.0-swing.jar       BSD http://www.migcalendar.com/miglayout/versions/4.0/li
 min-jaba-client.jar
 regex.jar
 saaj.jar
-spring-core-3.0.5.RELEASE.jar : Apache License: jdas runtime dependencies retrieved via maven
-spring-web-3.0.5.RELEASE.jar : Apache License: jdas runtime dependencies retrieved via maven
+spring-core-3.0.5.RELEASE.jar : Apache License: jdas runtime dependencies retrieved via maven - TODO: JAL-3035 remove if no longer needed ?
+spring-web-3.0.5.RELEASE.jar : Apache License: jdas runtime dependencies retrieved via maven - TODO: JAL-3035 remove if no longer needed ?
 vamsas-client.jar
 wsdl4j.jar
 xercesImpl.jar
@@ -50,9 +49,9 @@ jfreesvg-2.1.jar : GPL v3 licensed library from the JFree suite: http://www.jfre
 
 quaqua: v.8.0 (latest stable) by Randel S Hofer. LGPL and BSD Modified license: downloaded from http://www.randelshofer.ch/quaqua/ 
 
-vaqua: v5 (latest stable) by Alan Snyder et al. GPLv2 with Classpath exception, also includes contributions from Quaqua: downloaded from http://violetlib.org/vaqua/overview.html
+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