[emboss-dev] EMBOSS patch set 1-24 available. New mEMBOSS available.

ajb at ebi.ac.uk ajb at ebi.ac.uk
Wed Oct 5 15:06:32 UTC 2011

New bug-fix files are available for EMBOSS-6.4.0 and, for Windows
users, a new version of mEMBOSS is available.

The bugs fixed include those recently fixed (22-24), listed below,
and all those fixed by previous patches (1-21).


As usual, the most convenient way of applying the bug-fixes is
to apply the patch file:


to a freshly extracted copy of the EMBOSS-6.4.0.tar.gz source code
and recompiling/installing.

(see ftp://emboss.open-bio.org/pub/EMBOSS/fixes/patches/README.patch
 for instructions on using 'patch').

Alternatively, you can individually copy the patched files
from the ftp://emboss.open-bio.org/pub/EMBOSS/fixes/ directory
if your system does not support 'patch'.


The new version incorporates all new and previous bug-fixes.
Uninstall your previous mEMBOSS installation and download and install
the new setup file from:




Fix 22. EMBOSS-6.4.0/emboss/diffseq.c

14-Sep-2011: Diffseq reports insertions in the second sequence with a
	     length 2 reversed region in the first sequence instead of
	     a length 0 empty sequence. This bug was introduced in
	     release 6.0.0 when reversed sequence features were updated.

Fix 23. EMBOSS-6.4.0/ajax/core/ajindex.c

04-Oct-2011: Dbx index files from earlier releases do not include a
	     type parameter to indicate an Identifier or Secondary
	     index. The code to test index field names failed to
	     define id and acc fields as Identifiers. This fix allows
	     old indexes to work with EMBOSS 6.4.0.

Fix 24. EMBOSS-6.4.0/ajax/core/ajfileio.c

05-Oct-2011: Trimming carriage controls from the ends of lines in a
	     buffer failed when MacOSX-style characters are used and
	     the line buffer is a reference counted string. An example
	     on non-MacOSX systems was processing the data returned by
	     the NCBI Entrez server.

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