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.