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.