The files in this directory are bugfix replacements for files in
the EMBOSS-6.4.0 distribution. Just drop the replacement files in
the location shown and redo the 'make install.'
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 addtional
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. Ths 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: ajFmtScanF handled va_list incorrectly. Only noticeable by code
developers.
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.
Fix 22. EMBOSS-6.4.0/emboss/diffseq.c
EMBOSS-6.4.0/ajax/core/ajreport.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 control 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.