|
|
e210861 |
The files in this directory are bugfix replacements for files in
|
|
|
177c4d5 |
the EMBOSS-6.4.0 distribution. Just drop the replacement files in
|
|
|
e210861 |
the location shown and redo the 'make install.'
|
|
|
e210861 |
|
|
|
177c4d5 |
Fix 1. EMBOSS-6.4.0/emboss/dbiflat.c
|
|
|
177c4d5 |
EMBOSS-6.4.0/emboss/dbxflat.c
|
|
|
e210861 |
|
|
|
177c4d5 |
10-Aug-2011: The SwissProt description line format includes addtional
|
|
|
177c4d5 |
tags which interfere with the EMBL parser used in
|
|
|
177c4d5 |
previous releases. The fix replaces this with a SwissProt
|
|
|
177c4d5 |
parser that strips out the extra tags. After patching the
|
|
|
177c4d5 |
release, any existing SwissProt description index files
|
|
|
177c4d5 |
should be reindexed. Other indexes are unchanged.
|
|
|
5466a51 |
|
|
|
177c4d5 |
Fix 2. EMBOSS-6.4.0/ajax/core/ajquery.c
|
|
|
5466a51 |
|
|
|
177c4d5 |
10-Aug-2011: For databases with more than one valid format (examples
|
|
|
177c4d5 |
include the EBI dbfetch server) this fix allows the
|
|
|
177c4d5 |
format to be specified with a qualifier on the command
|
|
|
177c4d5 |
line. In the original release only a format in the query
|
|
|
177c4d5 |
string was used.
|
|
|
5466a51 |
|
|
|
5466a51 |
|
|
|
177c4d5 |
Fix 3. EMBOSS-6.4.0/ajax/core/ajfeatread.c
|
|
|
5466a51 |
|
|
|
177c4d5 |
10-Aug-2011: When parsing GFF3 format input, long feature tags (for
|
|
|
177c4d5 |
example extremely long translations) exceeded limits in
|
|
|
177c4d5 |
regular expression parsing. Ths fix decouples testing for
|
|
|
177c4d5 |
escaped quotes from the main task of finding quoted
|
|
|
177c4d5 |
strings.
|
|
|
5466a51 |
|
|
|
5466a51 |
|
|
|
177c4d5 |
Fix 4. EMBOSS-6.4.0/emboss/data/Etcode.dat
|
|
|
177c4d5 |
|
|
|
177c4d5 |
10-Aug-2001: The local data file used by application tcode had a missing
|
|
|
177c4d5 |
parameter line.
|
|
|
177c4d5 |
|
|
|
177c4d5 |
|
|
|
177c4d5 |
Fix 5. EMBOSS-6.4.0/ajax/core/ajrange.c
|
|
|
177c4d5 |
|
|
|
177c4d5 |
10-Aug-2011: When sequence ranges (and possible highlighting for
|
|
|
177c4d5 |
showalign) were in a list file the parser overwrote
|
|
|
177c4d5 |
string values.
|
|
|
177c4d5 |
|
|
|
177c4d5 |
|
|
|
177c4d5 |
Fix 5. EMBOSS-6.4.0/ajax/core/ajseqabi.c
|
|
|
177c4d5 |
|
|
|
177c4d5 |
10-Aug-2011: Sample names in ABI format files were stored in
|
|
|
177c4d5 |
incompletely defined strings. This fix corrects the
|
|
|
177c4d5 |
string object. The sample name is also used as the
|
|
|
177c4d5 |
sequence name.
|
|
|
177c4d5 |
|
|
|
177c4d5 |
|
|
|
177c4d5 |
Fix 6. EMBOSS-6.4.0/emboss/dbxresource.c
|
|
|
177c4d5 |
|
|
|
177c4d5 |
10-Aug-2011: A future change to the format of Data Resource Catalogue
|
|
|
177c4d5 |
entries in DRCAT.dat requires an update to the parsing of
|
|
|
177c4d5 |
category lines. The current version is not affected.
|
|
|
177c4d5 |
|
|
|
177c4d5 |
|
|
|
177c4d5 |
Fix 7. EMBOSS-6.4.0/emboss/server.ensemblgenomes
|
|
|
177c4d5 |
EMBOSS-6.4.0/emboss/cacheensembl.c
|
|
|
177c4d5 |
EMBOSS-6.4.0/ajax/ensembl/ensregistry.c
|
|
|
177c4d5 |
EMBOSS-6.4.0/ajax/ensembl/ensregistry.c
|
|
|
177c4d5 |
EMBOSS-6.4.0/ajax/ensembl/ensdatabaseadaptor.c
|
|
|
177c4d5 |
EMBOSS-6.4.0/ajax/ensembl/ensdatabaseadaptor.h
|
|
|
177c4d5 |
|
|
|
177c4d5 |
10-Aug-2011: Microbial genomes use an enumerated species code which
|
|
|
177c4d5 |
must be added to the query for data retrieval. This fix
|
|
|
177c4d5 |
adds the species code to the comment field. In the next
|
|
|
177c4d5 |
release a more complete solution will be implemented.
|
|
|
177c4d5 |
|
|
|
177c4d5 |
|
|
|
177c4d5 |
Fix 8. EMBOSS-6.4.0/ajax/core/ajarch.h
|
|
|
177c4d5 |
|
|
|
177c4d5 |
10-Aug-2011: Corrects the size of long integers on Windows systems only.
|
|
|
177c4d5 |
|
|
|
177c4d5 |
|
|
|
177c4d5 |
Fix 9. EMBOSS-6.4.0/emboss/cirdna.c
|
|
|
177c4d5 |
|
|
|
177c4d5 |
10-Aug-2011: Cirdna prints text inside solid blocks invisibly. When
|
|
|
177c4d5 |
printed outside the text scaling was too small. The text
|
|
|
177c4d5 |
scale is now adjusted for the radius and sequence length
|
|
|
177c4d5 |
so that labels should be readable outside the box.
|
|
|
177c4d5 |
|
|
|
177c4d5 |
|
|
|
177c4d5 |
Fix 10. EMBOSS-6.4.0/ajax/core/ajpat.c
|
|
|
177c4d5 |
|
|
|
177c4d5 |
10-Aug-2011: Fuzznuc, fuzzpro and fuzztran using a pattern file
|
|
|
177c4d5 |
ignored the command line -mismatch qualifier for the
|
|
|
177c4d5 |
first pattern. The default mismatch is now set to this
|
|
|
177c4d5 |
value at the start of the pattern matching loop in the
|
|
|
177c4d5 |
library.
|
|
|
177c4d5 |
|
|
|
177c4d5 |
|
|
|
177c4d5 |
Fix 11. EMBOSS-6.4.0/ajax/core/ajfmt.c
|
|
|
177c4d5 |
|
|
|
177c4d5 |
11-Aug-2011: ajFmtScanF handled va_list incorrectly. Only noticeable by code
|
|
|
177c4d5 |
developers.
|
|
|
177c4d5 |
|
|
|
177c4d5 |
|
|
|
177c4d5 |
Fix 12. EMBOSS-6.4.0/nucleus/embgroup.c
|
|
|
177c4d5 |
|
|
|
177c4d5 |
18-Aug-2011: An internal string variable should be initialised as NULL.
|
|
|
177c4d5 |
|
|
|
177c4d5 |
|
|
|
177c4d5 |
Fix 13. EMBOSS-6.4.0/ajax/core/ajseqread.c
|
|
|
177c4d5 |
|
|
|
177c4d5 |
18-Aug-2011: Reading protein GFF3 files ignored the EMBOSS type comment.
|
|
|
177c4d5 |
This appears to be the only way to detect a protein GFF3 file.
|
|
|
177c4d5 |
|
|
|
177c4d5 |
Fix 14. EMBOSS-6.4.0/emboss/data/Efeatures.gff3protein
|
|
|
177c4d5 |
|
|
|
177c4d5 |
18-Aug-2011: In writing GFF3 protein file, uses the current term name
|
|
|
177c4d5 |
from the Sequence Ontology to clear errors from the GFF3
|
|
|
177c4d5 |
online validator.
|
|
|
177c4d5 |
|
|
|
177c4d5 |
Fix 15. EMBOSS-6.4.0/ajax/core/ajfeatwrite.c
|
|
|
177c4d5 |
|
|
|
177c4d5 |
18-Aug-2011: When writing GFF3 format, tags names are explicitly
|
|
|
177c4d5 |
converted to lower case as required by the GFF3
|
|
|
177c4d5 |
standard. This includes EC_number and /PCR_conditions in
|
|
|
177c4d5 |
EMBL/GenBank/DDBJ and several RefseqP tags. The score is
|
|
|
177c4d5 |
written using g format to represent very low values.
|
|
|
177c4d5 |
|
|
|
177c4d5 |
Fix 16. EMBOSS-6.4.0/ajax/core/ajnexus.c
|
|
|
177c4d5 |
EMBOSS-6.4.0/ajax/core/ajseqread.c
|
|
|
177c4d5 |
|
|
|
177c4d5 |
22-Aug-2011: When reading nexus data format with no taxlabels block
|
|
|
177c4d5 |
the attempt to read the taxa (sequence names) from the
|
|
|
177c4d5 |
matrix block failed.
|
|
|
177c4d5 |
|
|
|
177c4d5 |
Fix 17. EMBOSS-6.4.0/ajax/ajaxdb/ajtextdb.c
|
|
|
177c4d5 |
|
|
|
177c4d5 |
22-Aug-2011: The SRS access method added a stray '+' character to the
|
|
|
177c4d5 |
getz command line.
|
|
|
177c4d5 |
|
|
|
177c4d5 |
Fix 18. EMBOSS-6.4.0/ajax/core/ajquery.c
|
|
|
177c4d5 |
|
|
|
177c4d5 |
25-Aug-2011: In some cases a query using a simple identifier
|
|
|
177c4d5 |
could try to test an undefined "sv" field.
|
|
|
177c4d5 |
|
|
|
177c4d5 |
Fix 19. EMBOSS-6.4.0/ajax/core/ajseqread.c
|
|
|
177c4d5 |
|
|
|
177c4d5 |
02-Sep-2011: Reading "raw" sequence format failed when piped from
|
|
|
177c4d5 |
standard input. In release 6.4.0 "raw" format was
|
|
|
177c4d5 |
redefined as a binary format to catch binary files that
|
|
|
177c4d5 |
start with one or more sequence characters followed by a
|
|
|
177c4d5 |
NULL character. This fix continues to check binary files,
|
|
|
177c4d5 |
but has to drop the check for data piped through standard
|
|
|
177c4d5 |
input which is read as text and cannot be reread as
|
|
|
177c4d5 |
binary.
|
|
|
177c4d5 |
|
|
|
177c4d5 |
Fix 20. EMBOSS-6.4.0/ajax/core/ajnam.c
|
|
|
177c4d5 |
|
|
|
177c4d5 |
02-Sep-2011: Complex database definitions with more than one type or
|
|
|
177c4d5 |
format are allowed in 6.4.0 but caused an error message
|
|
|
177c4d5 |
from showdb when the type and format were tested.
|
|
|
177c4d5 |
|
|
|
177c4d5 |
Fix 21. EMBOSS-6.4.0/emboss/drfinddata.c
|
|
|
177c4d5 |
EMBOSS-6.4.0/emboss/drfindformat.c
|
|
|
177c4d5 |
EMBOSS-6.4.0/emboss/drfindid.c
|
|
|
177c4d5 |
EMBOSS-6.4.0/emboss/drfindresource.c
|
|
|
177c4d5 |
|
|
|
177c4d5 |
02-Sep-2011: Running with -debug fails. Debug calls used obsolete datatype
|
|
|
177c4d5 |
for data resource internals. Without -debug there was no problem.
|
|
|
177c4d5 |
|
|
|
177c4d5 |
Fix 22. EMBOSS-6.4.0/emboss/diffseq.c
|
|
|
177c4d5 |
EMBOSS-6.4.0/ajax/core/ajreport.c
|
|
|
177c4d5 |
|
|
|
177c4d5 |
14-Sep-2011: Diffseq reports insertions in the second sequence with a
|
|
|
177c4d5 |
length 2 reversed region in the first sequence instead of
|
|
|
177c4d5 |
a length 0 empty sequence. This bug was introduced in
|
|
|
177c4d5 |
release 6.0.0 when reversed sequence features were updated.
|
|
|
177c4d5 |
|
|
|
177c4d5 |
Fix 23. EMBOSS-6.4.0/ajax/core/ajindex.c
|
|
|
177c4d5 |
|
|
|
177c4d5 |
04-Oct-2011: Dbx index files from earlier releases do not include a
|
|
|
177c4d5 |
type parameter to indicate an Identifier or Secondary
|
|
|
177c4d5 |
index. The code to test index field names failed to
|
|
|
177c4d5 |
define id and acc fields as Identifiers. This fix allows
|
|
|
177c4d5 |
old indexes to work with EMBOSS 6.4.0.
|
|
|
177c4d5 |
|
|
|
177c4d5 |
Fix 24. EMBOSS-6.4.0/ajax/core/ajfileio.c
|
|
|
177c4d5 |
|
|
|
177c4d5 |
05-Oct-2011: Trimming carriage control from the ends of lines in a
|
|
|
177c4d5 |
buffer failed when MacOSX-style characters are used and
|
|
|
177c4d5 |
the line buffer is a reference counted string. An example
|
|
|
177c4d5 |
on non-MacOSX systems was processing the data returned by
|
|
|
177c4d5 |
the NCBI Entrez server.
|
|
|
5466a51 |
|