[emboss-dev] EMBOSS and mEMBOSS bug-fix set 1-21 released
ajb at ebi.ac.uk
ajb at ebi.ac.uk
Tue Sep 6 08:54:02 UTC 2011
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).
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
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 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
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
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
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
02-Sep-2011: Running with -debug fails. Debug calls used obsolete datatype
for data resource internals. Without -debug there was no problem.
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