[emboss-dev] EMBOSS and mEMBOSS bug-fixes for 6.4.0 released

[ajb at ebi.ac.uk]

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 are appended for easy reference.

1) UNIX

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

ftp://emboss.open-bio.org/pub/EMBOSS/fixes/patches/patch-1-11.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 the bug-fixes listed below.
Uninstall your previous mEMBOSS installation and download and install
the new setup file from:

ftp://emboss.open-bio.org/pub/EMBOSS/windows/mEMBOSS-6.4.0.2-setup.exe


Alan

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Fix 1. EMBOSS-6.4.0/emboss/dbiflat.c
       EMBOSS-6.4.0/emboss/dbxflat.c

10 Aug 2011: The SwissProt description line format includes additional
             tags which interfere with the EMBL parser used in
             previous releases. The fix replaces this with a SwissProt
             parser that strips out the extra tags. After patching the
             release, any existing SwissProt description index files
             should be reindexed. Other indexes are unchanged.

Fix 2. EMBOSS-6.4.0/ajax/core/ajquery.c

10 Aug 2011: For databases with more than one valid format (examples
             include the EBI dbfetch server) this fix allows the
             format to be specified with a qualifier on the command
             line. In the original release, only a format in the query
             string was used.


Fix 3. EMBOSS-6.4.0/ajax/core/ajfeatread.c

10 Aug 2011: When parsing GFF3 format input, long feature tags (for
             example extremely long translations) exceeded limits in
             regular expression parsing. This fix decouples testing for
             escaped quotes from the main task of finding quoted
             strings.


Fix 4. EMBOSS-6.4.0/emboss/data/Etcode.dat

10 Aug 2001: The local data file used by application tcode had a missing
             parameter line.


Fix 5. EMBOSS-6.4.0/ajax/core/ajrange.c

10 Aug 2011: When sequence ranges (and possible highlighting for
             showalign) were in a list file, the parser overwrote
             string values.


Fix 5. EMBOSS-6.4.0/ajax/core/ajseqabi.c

10 Aug 2011: Sample names in ABI format files were stored in
             incompletely defined strings. This fix corrects the
             string object. The sample name is also used as the
             sequence name.


Fix 6. EMBOSS-6.4.0/emboss/dbxresource.c

10 Aug 2011: A future change to the format of Data Resource Catalogue
             entries in DRCAT.dat requires an update to the parsing of
             category lines. The current version is not affected.


Fix 7. EMBOSS-6.4.0/emboss/server.ensemblgenomes
       EMBOSS-6.4.0/emboss/cacheensembl.c
       EMBOSS-6.4.0/ajax/ensembl/ensregistry.c
       EMBOSS-6.4.0/ajax/ensembl/ensregistry.c
       EMBOSS-6.4.0/ajax/ensembl/ensdatabaseadaptor.c
       EMBOSS-6.4.0/ajax/ensembl/ensdatabaseadaptor.h

10 Aug 2011: Microbial genomes use an enumerated species code which
             must be added to the query for data retrieval. This fix
             adds the species code to the comment field. In the next
             release a more complete solution will be implemented.


Fix 8. EMBOSS-6.4.0/ajax/core/ajarch.h

10-Aug-2011: Corrects the size of long integers on Windows systems only.


Fix 9. EMBOSS-6.4.0/emboss/cirdna.c

10-Aug-2011: Cirdna prints text inside solid blocks invisibly. When
             printed outside the text scaling was too small. The text
             scale is now adjusted for the radius and sequence length
             so that labels should be readable outside the box.


Fix 10. EMBOSS-6.4.0/ajax/core/ajpat.c

10-Aug-2011: Fuzznuc, fuzzpro and fuzztran using a pattern file
             ignored the command line -mismatch qualifier for the
             first pattern. The default mismatch is now set to this
             value at the start of the pattern matching loop in the
             library.


Fix 11. EMBOSS-6.4.0/ajax/core/ajfmt.c

11-Aug-2011: The function ajFmtScanF() handled va_list incorrectly. Only
             potentially affected code developers.