[emboss-dev] EMBOSS and mEMBOSS bug-fix set 1-21 released

[ajb at ebi.ac.uk]

New bug-fixes 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 (12-21), listed below,
and all those fixed by previous patches (1-11).

1) UNIX

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

ftp://emboss.open-bio.org/pub/EMBOSS/fixes/patches/patch-1-21.gz

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'.

2) mEMBOSS

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

ftp://emboss.open-bio.org/pub/EMBOSS/windows/mEMBOSS-6.4.0.3-setup.exe


Alan

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Fix 12. EMBOSS-6.4.0/nucleus/embgroup.c

18-Aug-2011: An internal string variable should be initialised as NULL.


Fix 13. EMBOSS-6.4.0/ajax/core/ajseqread.c

18-Aug-2011: Reading protein GFF3 files ignored the EMBOSS type comment.
	     This appears to be the only way to detect a protein GFF3 file.

Fix 14. EMBOSS-6.4.0/emboss/data/Efeatures.gff3protein

18-Aug-2011: In writing GFF3 protein file, uses the current term name
	     from the Sequence Ontology to clear errors from the GFF3
	     online validator.

Fix 15. EMBOSS-6.4.0/ajax/core/ajfeatwrite.c

18-Aug-2011: When writing GFF3 format, tags names are explicitly
  	     converted to lower case as required by the GFF3
  	     standard. This includes EC_number and /PCR_conditions in
  	     EMBL/GenBank/DDBJ and several RefseqP tags. The score is
  	     written using g format to represent very low values.

Fix 16. EMBOSS-6.4.0/ajax/core/ajnexus.c
        EMBOSS-6.4.0/ajax/core/ajseqread.c

22-Aug-2011: When reading nexus data format with no taxlabels block
	     the attempt to read the taxa (sequence names) from the
	     matrix block failed.

Fix 17. EMBOSS-6.4.0/ajax/ajaxdb/ajtextdb.c

22-Aug-2011: The SRS access method added a stray '+' character to the
	     getz command line.

Fix 18. EMBOSS-6.4.0/ajax/core/ajquery.c

25-Aug-2011: In some cases a query using a simple identifier
	     could try to test an undefined "sv" field.


Fix 19. EMBOSS-6.4.0/ajax/core/ajseqread.c

02-Sep-2011: Reading "raw" sequence format failed when piped from
	     standard input. In release 6.4.0 "raw" format was
	     redefined as a binary format to catch binary files that
	     start with one or more sequence characters followed by a
	     NULL character. This fix continues to check binary files,
	     but has to drop the check for data piped through standard
	     input which is read as text and cannot be reread as
	     binary.

Fix 20. EMBOSS-6.4.0/ajax/core/ajnam.c

02-Sep-2011: Complex database definitions with more than one type or
	     format are allowed in 6.4.0 but caused an error message
	     from showdb when the type and format were tested.

Fix 21. EMBOSS-6.4.0/emboss/drfinddata.c
    	EMBOSS-6.4.0/emboss/drfindformat.c
    	EMBOSS-6.4.0/emboss/drfindid.c
    	EMBOSS-6.4.0/emboss/drfindresource.c

02-Sep-2011: Running with -debug fails. Debug calls used obsolete datatype
	     for data resource internals. Without -debug there was no problem.