Release 6.5.0

The files in this directory are bugfix replacements for files in
the EMBOSS-6.5.0 distribution. Fixes are available as patches from
ftp://emboss.open-bio.org/pub/EMBOSS/fixes/patches/
to be applied to the original EMBOSS release.

It is also possible to update by hand. Just drop the replacement files
in the location shown, edit the configure file to update the value of
PACKAGE_VERSION so the last number matches the latest fix number and
redo the 'make install.'

Fix 1.  EMBOSS-6.5.0/nucleus/embindex.c

17-Jul-2012: Indexing identifiers (or accessions) used the primary
	     page size in calculations. This crashes dbx indexing
	     applications when secondary pages are smaller and an
	     index page of duplicate ids fills up.

Fix 2.  EMBOSS-6.5.0/ajax/core/ajassemread.c
        EMBOSS-6.5.0/ajax/core/ajfeatread.c
        EMBOSS-6.5.0/ajax/core/ajoboread.c
        EMBOSS-6.5.0/ajax/core/ajrefseqread.c
        EMBOSS-6.5.0/ajax/core/ajresource.c
        EMBOSS-6.5.0/ajax/core/ajresourceread.c
        EMBOSS-6.5.0/ajax/core/ajseqread.c
        EMBOSS-6.5.0/ajax/core/ajtaxread.c
        EMBOSS-6.5.0/ajax/core/ajtextead.c
        EMBOSS-6.5.0/ajax/core/ajurlread.c
        EMBOSS-6.5.0/ajax/core/ajvarread.c

17-Jul-2012: Queries using DRCAT lookup to read entries from
	     seqence databases failed to match the query format
	     in the DRCAT resource entry to the formats available
	     in EMBOSS.

	     For example, if EMBL is not defined as a local database
	     the query "entret embl:x13776" should find the EMBL entry
	     by looking up embl in the data resource catalogue and
	     selecting the query that returns an EMBL format text
	     entry.

	     All EMBOSS formats have an EDAM format term associated
	     with them, and all DRCAT entries have the EDAM format
	     term associated with the query. This fix matches the
	     EDAM format term to the EMBOSS datatype format.

	     As a result of this fix, EDAM format terms become
	     available as EMBOSS format names. For example, a prefix
	     of 1927:: or using -sformat 1927 can replace the embl
	     format name in any application.

Fix 3.  EMBOSS-6.5.0/ajax/core/ajrange.c

17-Jul-2012: Ranges in a file can now use a dash as an alternative to
	     whitespace between the start and end positions of the
	     range.

Fix 4.  EMBOSS-6.5.0/emboss/embossversion.c

18-Jul-2012: Corrected code to report installation on FreeBSD systems.
	     Other systems ignore this code and are unaffected.


Fix 5.  EMBOSS-6.5.0/jemboss/Makefile
    	EMBOSS-6.5.0/jemboss/runJemboss.sh
    	EMBOSS-6.5.0/jemboss/lib/Makefile
    	EMBOSS-6.5.0/jemboss/lib/jemboss.jar
    	EMBOSS-6.5.0/jemboss/resources/resources.jar

20-Jul-2012: Jemboss is now started by a runJemboss.sh script.
	     The previous csh script (runJemboss.csh) is deleted when
	     jemboss is installed as part of executing make install.

	     Jemboss was unintentionally omitted from the original
	     6.5.0 distribution.


Fix 6.  EMBOSS-6.5.0/ajax/core/ajnam.c
    	EMBOSS-6.5.0/emboss/embossupdate.c

21-Jul-2012: Minor memory leaks.

Fix 7.  EMBOSS-6.5.0/emoss/epestfind.c

23-Jul-2012: Missing sequence name in output on 32-bit systems.