academic/EMBOSS: Updated with newest patches.

Signed-off-by: Niels Horn <niels.horn@slackbuilds.org>

2 files changed, 126 insertions, 32 deletions

diff --git a/academic/EMBOSS/EMBOSS.SlackBuild b/academic/EMBOSS/EMBOSS.SlackBuild
index 900b1fd602fad..0321ba1146b2b 100644
--- a/academic/EMBOSS/EMBOSS.SlackBuild
+++ b/academic/EMBOSS/EMBOSS.SlackBuild
@@ -10,7 +10,7 @@
 
 PRGNAM=EMBOSS			
 VERSION=${VERSION:-6.4.0}
-BUILD=${BUILD:-2}
+BUILD=${BUILD:-3}
 TAG=${TAG:-_SBo}	
 
 if [ -z "$ARCH" ]; then
@@ -49,8 +49,8 @@ rm -rf $PRGNAM-$VERSION
 tar xvf $CWD/$PRGNAM-$VERSION.tar.gz
 cd $PRGNAM-$VERSION
 
-# Apply EMBOSS bug-fix set 1-21. Thanks to ajb@ebi.ac.uk!
-patch -p1 < $CWD/patch-1-21
+# Apply EMBOSS bug-fix set 1-24. Thanks to Alan at ajb@ebi.ac.uk!
+patch -p1 < $CWD/patch-1-24
 
 chown -R root:root .
 find . \
diff --git a/academic/EMBOSS/patch-1-21 b/academic/EMBOSS/patch-1-24
index cb182c65c8775..04fe05ba2b384 100644
--- a/academic/EMBOSS/patch-1-21
+++ b/academic/EMBOSS/patch-1-24
@@ -1,6 +1,6 @@
 diff -c -N --recursive -a EMBOSS-6.4.0old/ajax/ajaxdb/ajtextdb.c EMBOSS-6.4.0/ajax/ajaxdb/ajtextdb.c
 *** EMBOSS-6.4.0old/ajax/ajaxdb/ajtextdb.c	2011-07-06 17:09:36.000000000 +0100
---- EMBOSS-6.4.0/ajax/ajaxdb/ajtextdb.c	2011-09-05 12:23:43.000000000 +0100
+--- EMBOSS-6.4.0/ajax/ajaxdb/ajtextdb.c	2011-10-05 14:56:07.000000000 +0100
 ***************
 *** 2580,2588 ****
       {
@@ -41,7 +41,7 @@ diff -c -N --recursive -a EMBOSS-6.4.0old/ajax/ajaxdb/ajtextdb.c EMBOSS-6.4.0/aj
               {
 diff -c -N --recursive -a EMBOSS-6.4.0old/ajax/core/ajarch.h EMBOSS-6.4.0/ajax/core/ajarch.h
 *** EMBOSS-6.4.0old/ajax/core/ajarch.h	2011-06-08 11:35:28.000000000 +0100
---- EMBOSS-6.4.0/ajax/core/ajarch.h	2011-09-05 12:23:43.000000000 +0100
+--- EMBOSS-6.4.0/ajax/core/ajarch.h	2011-10-05 14:56:07.000000000 +0100
 ***************
 *** 137,143 ****
   
@@ -68,7 +68,7 @@ diff -c -N --recursive -a EMBOSS-6.4.0old/ajax/core/ajarch.h EMBOSS-6.4.0/ajax/c
 --- 159,161 ----
 diff -c -N --recursive -a EMBOSS-6.4.0old/ajax/core/ajfeatread.c EMBOSS-6.4.0/ajax/core/ajfeatread.c
 *** EMBOSS-6.4.0old/ajax/core/ajfeatread.c	2011-07-07 17:37:21.000000000 +0100
---- EMBOSS-6.4.0/ajax/core/ajfeatread.c	2011-09-05 12:23:43.000000000 +0100
+--- EMBOSS-6.4.0/ajax/core/ajfeatread.c	2011-10-05 14:56:07.000000000 +0100
 ***************
 *** 3035,3041 ****
       AjPStr  TvString  = NULL;
@@ -141,7 +141,7 @@ diff -c -N --recursive -a EMBOSS-6.4.0old/ajax/core/ajfeatread.c EMBOSS-6.4.0/aj
   
 diff -c -N --recursive -a EMBOSS-6.4.0old/ajax/core/ajfeatwrite.c EMBOSS-6.4.0/ajax/core/ajfeatwrite.c
 *** EMBOSS-6.4.0old/ajax/core/ajfeatwrite.c	2011-06-23 11:56:06.000000000 +0100
---- EMBOSS-6.4.0/ajax/core/ajfeatwrite.c	2011-09-05 12:23:43.000000000 +0100
+--- EMBOSS-6.4.0/ajax/core/ajfeatwrite.c	2011-10-05 14:56:07.000000000 +0100
 ***************
 *** 4134,4140 ****
           tmpid = owner->Seqid;
@@ -169,9 +169,52 @@ diff -c -N --recursive -a EMBOSS-6.4.0old/ajax/core/ajfeatwrite.c EMBOSS-6.4.0/a
   	outtag = tv->Tag;
   	
   	if(!outtag)
+diff -c -N --recursive -a EMBOSS-6.4.0old/ajax/core/ajfileio.c EMBOSS-6.4.0/ajax/core/ajfileio.c
+*** EMBOSS-6.4.0old/ajax/core/ajfileio.c	2011-05-24 13:51:54.000000000 +0100
+--- EMBOSS-6.4.0/ajax/core/ajfileio.c	2011-10-05 14:56:07.000000000 +0100
+***************
+*** 2006,2025 ****
+  {
+      AjBool ret;
+      ajlong fpos = 0;
+-     AjPStr dest;
+  
+      ret = ajBuffreadLinePos(buff, Pdest, &fpos);
+      
+      /* trim any trailing newline */
+  
+-     dest = *Pdest;
+- 
+      /*ajDebug("Remove carriage-return characters from PC-style files\n");*/
+!     if(ajStrGetCharLast(dest) == '\n')
+  	ajStrCutEnd(Pdest, 1);
+  
+      /* PC files have \r\n Macintosh files have just \r : this fixes both */
+!     if(ajStrGetCharLast(dest) == '\r')
+  	ajStrCutEnd(Pdest, 1);
+  
+      return ret;
+--- 2006,2022 ----
+  {
+      AjBool ret;
+      ajlong fpos = 0;
+  
+      ret = ajBuffreadLinePos(buff, Pdest, &fpos);
+      
+      /* trim any trailing newline */
+  
+      /*ajDebug("Remove carriage-return characters from PC-style files\n");*/
+!     if(ajStrGetCharLast(*Pdest) == '\n')
+  	ajStrCutEnd(Pdest, 1);
+  
+      /* PC files have \r\n Macintosh files have just \r : this fixes both */
+!     if(ajStrGetCharLast(*Pdest) == '\r')
+  	ajStrCutEnd(Pdest, 1);
+  
+      return ret;
 diff -c -N --recursive -a EMBOSS-6.4.0old/ajax/core/ajfmt.c EMBOSS-6.4.0/ajax/core/ajfmt.c
 *** EMBOSS-6.4.0old/ajax/core/ajfmt.c	2011-05-16 11:31:26.000000000 +0100
---- EMBOSS-6.4.0/ajax/core/ajfmt.c	2011-09-05 12:24:01.000000000 +0100
+--- EMBOSS-6.4.0/ajax/core/ajfmt.c	2011-10-05 18:22:48.000000000 +0100
 ***************
 *** 50,55 ****
 --- 50,65 ----
@@ -741,9 +784,25 @@ diff -c -N --recursive -a EMBOSS-6.4.0old/ajax/core/ajfmt.c EMBOSS-6.4.0/ajax/co
   /* @funcstatic fmtVscan *******************************************************
   **
   ** Scan a string according to fmt and load the va_list variable pointers
+diff -c -N --recursive -a EMBOSS-6.4.0old/ajax/core/ajindex.c EMBOSS-6.4.0/ajax/core/ajindex.c
+*** EMBOSS-6.4.0old/ajax/core/ajindex.c	2011-07-13 11:59:06.000000000 +0100
+--- EMBOSS-6.4.0/ajax/core/ajindex.c	2011-10-05 14:56:07.000000000 +0100
+***************
+*** 650,655 ****
+--- 650,659 ----
+          ajTablePut(btreeFieldsTable,
+                     field->Name,
+                     (void*) field);
++         field = btreeFieldNewField(&btreeFields[i]);
++         ajTablePut(btreeFieldsTable,
++                    field->Extension,
++                    (void*) field);
+      }
+  
+      return;
 diff -c -N --recursive -a EMBOSS-6.4.0old/ajax/core/ajnam.c EMBOSS-6.4.0/ajax/core/ajnam.c
 *** EMBOSS-6.4.0old/ajax/core/ajnam.c	2011-07-15 08:15:37.000000000 +0100
---- EMBOSS-6.4.0/ajax/core/ajnam.c	2011-09-05 12:23:43.000000000 +0100
+--- EMBOSS-6.4.0/ajax/core/ajnam.c	2011-10-05 14:56:07.000000000 +0100
 ***************
 *** 8172,8177 ****
 --- 8172,8181 ----
@@ -831,7 +890,7 @@ diff -c -N --recursive -a EMBOSS-6.4.0old/ajax/core/ajnam.c EMBOSS-6.4.0/ajax/co
   }
 diff -c -N --recursive -a EMBOSS-6.4.0old/ajax/core/ajnexus.c EMBOSS-6.4.0/ajax/core/ajnexus.c
 *** EMBOSS-6.4.0old/ajax/core/ajnexus.c	2011-03-16 17:14:10.000000000 +0000
---- EMBOSS-6.4.0/ajax/core/ajnexus.c	2011-09-05 12:23:43.000000000 +0100
+--- EMBOSS-6.4.0/ajax/core/ajnexus.c	2011-10-05 14:56:07.000000000 +0100
 ***************
 *** 2,24 ****
   ** @source AJAX nexus file parsing functions
@@ -2028,7 +2087,7 @@ diff -c -N --recursive -a EMBOSS-6.4.0old/ajax/core/ajnexus.c EMBOSS-6.4.0/ajax/
   
 diff -c -N --recursive -a EMBOSS-6.4.0old/ajax/core/ajpat.c EMBOSS-6.4.0/ajax/core/ajpat.c
 *** EMBOSS-6.4.0old/ajax/core/ajpat.c	2010-04-14 09:04:16.000000000 +0100
---- EMBOSS-6.4.0/ajax/core/ajpat.c	2011-09-05 12:23:43.000000000 +0100
+--- EMBOSS-6.4.0/ajax/core/ajpat.c	2011-10-05 14:56:07.000000000 +0100
 ***************
 *** 752,757 ****
 --- 752,759 ----
@@ -2059,7 +2118,7 @@ diff -c -N --recursive -a EMBOSS-6.4.0old/ajax/core/ajpat.c EMBOSS-6.4.0/ajax/co
   		    ajStrCutStart(&line,1);
 diff -c -N --recursive -a EMBOSS-6.4.0old/ajax/core/ajquery.c EMBOSS-6.4.0/ajax/core/ajquery.c
 *** EMBOSS-6.4.0old/ajax/core/ajquery.c	2011-07-03 12:39:13.000000000 +0100
---- EMBOSS-6.4.0/ajax/core/ajquery.c	2011-09-05 12:23:43.000000000 +0100
+--- EMBOSS-6.4.0/ajax/core/ajquery.c	2011-10-05 14:56:07.000000000 +0100
 ***************
 *** 1609,1615 ****
 --- 1609,1622 ----
@@ -2118,7 +2177,7 @@ diff -c -N --recursive -a EMBOSS-6.4.0old/ajax/core/ajquery.c EMBOSS-6.4.0/ajax/
                       ajStrTrimWhite(&lastoper);
 diff -c -N --recursive -a EMBOSS-6.4.0old/ajax/core/ajrange.c EMBOSS-6.4.0/ajax/core/ajrange.c
 *** EMBOSS-6.4.0old/ajax/core/ajrange.c	2010-05-21 11:54:40.000000000 +0100
---- EMBOSS-6.4.0/ajax/core/ajrange.c	2011-09-05 12:23:43.000000000 +0100
+--- EMBOSS-6.4.0/ajax/core/ajrange.c	2011-10-05 14:56:07.000000000 +0100
 ***************
 *** 179,185 ****
                                     ajuint minsize, ajuint size)
@@ -2217,9 +2276,23 @@ diff -c -N --recursive -a EMBOSS-6.4.0old/ajax/core/ajrange.c EMBOSS-6.4.0/ajax/
       }
   
   
+diff -c -N --recursive -a EMBOSS-6.4.0old/ajax/core/ajreport.c EMBOSS-6.4.0/ajax/core/ajreport.c
+*** EMBOSS-6.4.0old/ajax/core/ajreport.c	2011-07-08 15:54:59.000000000 +0100
+--- EMBOSS-6.4.0/ajax/core/ajreport.c	2011-10-05 14:56:07.000000000 +0100
+***************
+*** 677,682 ****
+--- 677,684 ----
+  	istart  = feature->Start;
+  	iend    = feature->End;
+  	ilen    = iend - istart + 1;
++         if(ilen == 2 && (feature->Flags & FEATFLAG_BETWEEN_SEQ))
++             ilen = 0;
+  	ajStrAssignSubS(&subseq, seqalias, istart-1, iend-1);
+  	/* ajStrFmtUpper(&subseq); */
+  	i++;
 diff -c -N --recursive -a EMBOSS-6.4.0old/ajax/core/ajseqabi.c EMBOSS-6.4.0/ajax/core/ajseqabi.c
 *** EMBOSS-6.4.0old/ajax/core/ajseqabi.c	2011-05-19 11:28:09.000000000 +0100
---- EMBOSS-6.4.0/ajax/core/ajseqabi.c	2011-09-05 12:23:43.000000000 +0100
+--- EMBOSS-6.4.0/ajax/core/ajseqabi.c	2011-10-05 14:56:07.000000000 +0100
 ***************
 *** 181,186 ****
 --- 181,187 ----
@@ -2242,7 +2315,7 @@ diff -c -N --recursive -a EMBOSS-6.4.0old/ajax/core/ajseqabi.c EMBOSS-6.4.0/ajax
       return ajTrue;
 diff -c -N --recursive -a EMBOSS-6.4.0old/ajax/core/ajseqread.c EMBOSS-6.4.0/ajax/core/ajseqread.c
 *** EMBOSS-6.4.0old/ajax/core/ajseqread.c	2011-06-27 08:38:44.000000000 +0100
---- EMBOSS-6.4.0/ajax/core/ajseqread.c	2011-09-05 12:23:43.000000000 +0100
+--- EMBOSS-6.4.0/ajax/core/ajseqread.c	2011-10-05 14:56:07.000000000 +0100
 ***************
 *** 5497,5502 ****
 --- 5497,5503 ----
@@ -2612,7 +2685,7 @@ diff -c -N --recursive -a EMBOSS-6.4.0old/ajax/core/ajseqread.c EMBOSS-6.4.0/aja
   	ajFeattableDel(&thys->Fttable);
 diff -c -N --recursive -a EMBOSS-6.4.0old/ajax/ensembl/ensdatabaseadaptor.c EMBOSS-6.4.0/ajax/ensembl/ensdatabaseadaptor.c
 *** EMBOSS-6.4.0old/ajax/ensembl/ensdatabaseadaptor.c	2011-07-06 22:50:28.000000000 +0100
---- EMBOSS-6.4.0/ajax/ensembl/ensdatabaseadaptor.c	2011-09-05 12:23:43.000000000 +0100
+--- EMBOSS-6.4.0/ajax/ensembl/ensdatabaseadaptor.c	2011-10-05 14:56:07.000000000 +0100
 ***************
 *** 156,163 ****
   ** @argrule Ini dbc [EnsPDatabaseconnection] Ensembl Database Connection
@@ -2835,7 +2908,7 @@ diff -c -N --recursive -a EMBOSS-6.4.0old/ajax/ensembl/ensdatabaseadaptor.c EMBO
   ** @argrule Species species [AjPStr] Species
 diff -c -N --recursive -a EMBOSS-6.4.0old/ajax/ensembl/ensdatabaseadaptor.h EMBOSS-6.4.0/ajax/ensembl/ensdatabaseadaptor.h
 *** EMBOSS-6.4.0old/ajax/ensembl/ensdatabaseadaptor.h	2011-07-06 22:50:28.000000000 +0100
---- EMBOSS-6.4.0/ajax/ensembl/ensdatabaseadaptor.h	2011-09-05 12:23:43.000000000 +0100
+--- EMBOSS-6.4.0/ajax/ensembl/ensdatabaseadaptor.h	2011-10-05 14:56:07.000000000 +0100
 ***************
 *** 121,127 ****
   
@@ -2855,7 +2928,7 @@ diff -c -N --recursive -a EMBOSS-6.4.0old/ajax/ensembl/ensdatabaseadaptor.h EMBO
   
 diff -c -N --recursive -a EMBOSS-6.4.0old/ajax/ensembl/ensregistry.c EMBOSS-6.4.0/ajax/ensembl/ensregistry.c
 *** EMBOSS-6.4.0old/ajax/ensembl/ensregistry.c	2011-07-08 12:43:41.000000000 +0100
---- EMBOSS-6.4.0/ajax/ensembl/ensregistry.c	2011-09-05 12:23:43.000000000 +0100
+--- EMBOSS-6.4.0/ajax/ensembl/ensregistry.c	2011-10-05 14:56:07.000000000 +0100
 ***************
 *** 569,576 ****
       const RegistryPQualityCheck rqc,
@@ -3327,7 +3400,7 @@ diff -c -N --recursive -a EMBOSS-6.4.0old/ajax/ensembl/ensregistry.c EMBOSS-6.4.
                   alias, species);
 diff -c -N --recursive -a EMBOSS-6.4.0old/ajax/ensembl/ensregistry.h EMBOSS-6.4.0/ajax/ensembl/ensregistry.h
 *** EMBOSS-6.4.0old/ajax/ensembl/ensregistry.h	2011-05-25 20:55:04.000000000 +0100
---- EMBOSS-6.4.0/ajax/ensembl/ensregistry.h	2011-09-05 12:23:43.000000000 +0100
+--- EMBOSS-6.4.0/ajax/ensembl/ensregistry.h	2011-10-05 14:56:07.000000000 +0100
 ***************
 *** 116,122 ****
   AjBool ensRegistryRemoveDatabaseadaptor(EnsPDatabaseadaptor* Pdba);
@@ -3347,7 +3420,7 @@ diff -c -N --recursive -a EMBOSS-6.4.0old/ajax/ensembl/ensregistry.h EMBOSS-6.4.
   AjPStr ensRegistryGetStableidentifierprefix(EnsPDatabaseadaptor dba);
 diff -c -N --recursive -a EMBOSS-6.4.0old/emboss/cacheensembl.c EMBOSS-6.4.0/emboss/cacheensembl.c
 *** EMBOSS-6.4.0old/emboss/cacheensembl.c	2011-07-08 17:29:51.000000000 +0100
---- EMBOSS-6.4.0/emboss/cacheensembl.c	2011-09-05 12:23:43.000000000 +0100
+--- EMBOSS-6.4.0/emboss/cacheensembl.c	2011-10-05 14:56:07.000000000 +0100
 ***************
 *** 181,186 ****
 --- 181,191 ----
@@ -3364,7 +3437,7 @@ diff -c -N --recursive -a EMBOSS-6.4.0old/emboss/cacheensembl.c EMBOSS-6.4.0/emb
               ajFmtPrintF(cachef, "  url:     \"%S\"\n", dbcurl);
 diff -c -N --recursive -a EMBOSS-6.4.0old/emboss/cirdna.c EMBOSS-6.4.0/emboss/cirdna.c
 *** EMBOSS-6.4.0old/emboss/cirdna.c	2011-05-16 11:17:10.000000000 +0100
---- EMBOSS-6.4.0/emboss/cirdna.c	2011-09-05 12:23:43.000000000 +0100
+--- EMBOSS-6.4.0/emboss/cirdna.c	2011-10-05 14:56:07.000000000 +0100
 ***************
 *** 970,976 ****
       {
@@ -3432,7 +3505,7 @@ diff -c -N --recursive -a EMBOSS-6.4.0old/emboss/cirdna.c EMBOSS-6.4.0/emboss/ci
   	cirdna_HorTextPile(xDraw, yDraw,
 diff -c -N --recursive -a EMBOSS-6.4.0old/emboss/data/Efeatures.gff3protein EMBOSS-6.4.0/emboss/data/Efeatures.gff3protein
 *** EMBOSS-6.4.0old/emboss/data/Efeatures.gff3protein	2009-03-06 12:37:43.000000000 +0000
---- EMBOSS-6.4.0/emboss/data/Efeatures.gff3protein	2011-09-05 12:23:43.000000000 +0100
+--- EMBOSS-6.4.0/emboss/data/Efeatures.gff3protein	2011-10-05 14:56:08.000000000 +0100
 ***************
 *** 193,199 ****
   
@@ -3507,7 +3580,7 @@ diff -c -N --recursive -a EMBOSS-6.4.0old/emboss/data/Efeatures.gff3protein EMBO
   	/ftid
 diff -c -N --recursive -a EMBOSS-6.4.0old/emboss/data/Etcode.dat EMBOSS-6.4.0/emboss/data/Etcode.dat
 *** EMBOSS-6.4.0old/emboss/data/Etcode.dat	2003-03-07 09:45:22.000000000 +0000
---- EMBOSS-6.4.0/emboss/data/Etcode.dat	2011-09-05 12:23:43.000000000 +0100
+--- EMBOSS-6.4.0/emboss/data/Etcode.dat	2011-10-05 14:56:08.000000000 +0100
 ***************
 *** 22,27 ****
 --- 22,28 ----
@@ -3520,7 +3593,7 @@ diff -c -N --recursive -a EMBOSS-6.4.0old/emboss/data/Etcode.dat EMBOSS-6.4.0/em
   #
 diff -c -N --recursive -a EMBOSS-6.4.0old/emboss/dbiflat.c EMBOSS-6.4.0/emboss/dbiflat.c
 *** EMBOSS-6.4.0old/emboss/dbiflat.c	2011-06-23 19:18:45.000000000 +0100
---- EMBOSS-6.4.0/emboss/dbiflat.c	2011-09-05 12:23:43.000000000 +0100
+--- EMBOSS-6.4.0/emboss/dbiflat.c	2011-10-05 14:56:08.000000000 +0100
 ***************
 *** 91,96 ****
 --- 91,100 ----
@@ -3941,7 +4014,7 @@ diff -c -N --recursive -a EMBOSS-6.4.0old/emboss/dbiflat.c EMBOSS-6.4.0/emboss/d
   ** Parse the ID, accession from an EMBL entry.
 diff -c -N --recursive -a EMBOSS-6.4.0old/emboss/dbxflat.c EMBOSS-6.4.0/emboss/dbxflat.c
 *** EMBOSS-6.4.0old/emboss/dbxflat.c	2011-06-23 19:18:45.000000000 +0100
---- EMBOSS-6.4.0/emboss/dbxflat.c	2011-09-05 12:23:43.000000000 +0100
+--- EMBOSS-6.4.0/emboss/dbxflat.c	2011-10-05 14:56:08.000000000 +0100
 ***************
 *** 32,37 ****
 --- 32,38 ----
@@ -4075,7 +4148,7 @@ diff -c -N --recursive -a EMBOSS-6.4.0old/emboss/dbxflat.c EMBOSS-6.4.0/emboss/d
   ** Parse the next entry from a flatfile
 diff -c -N --recursive -a EMBOSS-6.4.0old/emboss/dbxresource.c EMBOSS-6.4.0/emboss/dbxresource.c
 *** EMBOSS-6.4.0old/emboss/dbxresource.c	2011-06-23 19:18:45.000000000 +0100
---- EMBOSS-6.4.0/emboss/dbxresource.c	2011-09-05 12:23:43.000000000 +0100
+--- EMBOSS-6.4.0/emboss/dbxresource.c	2011-10-05 14:56:08.000000000 +0100
 ***************
 *** 535,540 ****
 --- 535,553 ----
@@ -4098,9 +4171,30 @@ diff -c -N --recursive -a EMBOSS-6.4.0old/emboss/dbxresource.c EMBOSS-6.4.0/embo
       else if(ajStrSuffixC(name, "Cat"))
       {
           if(catfield && !ajStrMatchC(rest, "None"))
+diff -c -N --recursive -a EMBOSS-6.4.0old/emboss/diffseq.c EMBOSS-6.4.0/emboss/diffseq.c
+*** EMBOSS-6.4.0old/emboss/diffseq.c	2010-04-14 09:19:27.000000000 +0100
+--- EMBOSS-6.4.0/emboss/diffseq.c	2011-10-05 14:56:08.000000000 +0100
+***************
+*** 338,344 ****
+  	}
+          else
+          {
+!             gf = ajFeatNewII(ftab, diff->End1, diff->End1-1);
+              ajStrAssignC(&tmp, "");
+          }
+          diffseq_Features("first_feature", gf,
+--- 338,345 ----
+  	}
+          else
+          {
+!             gf = ajFeatNewII(ftab, diff->Start1-1, diff->Start1);
+!             gf->Flags |= FEATFLAG_BETWEEN_SEQ;
+              ajStrAssignC(&tmp, "");
+          }
+          diffseq_Features("first_feature", gf,
 diff -c -N --recursive -a EMBOSS-6.4.0old/emboss/drfinddata.c EMBOSS-6.4.0/emboss/drfinddata.c
 *** EMBOSS-6.4.0old/emboss/drfinddata.c	2011-05-25 10:10:32.000000000 +0100
---- EMBOSS-6.4.0/emboss/drfinddata.c	2011-09-05 12:23:43.000000000 +0100
+--- EMBOSS-6.4.0/emboss/drfinddata.c	2011-10-05 14:56:08.000000000 +0100
 ***************
 *** 155,162 ****
                           {
@@ -4123,7 +4217,7 @@ diff -c -N --recursive -a EMBOSS-6.4.0old/emboss/drfinddata.c EMBOSS-6.4.0/embos
                                              (void *) 1);
 diff -c -N --recursive -a EMBOSS-6.4.0old/emboss/drfindformat.c EMBOSS-6.4.0/emboss/drfindformat.c
 *** EMBOSS-6.4.0old/emboss/drfindformat.c	2011-05-25 13:41:47.000000000 +0100
---- EMBOSS-6.4.0/emboss/drfindformat.c	2011-09-05 12:23:43.000000000 +0100
+--- EMBOSS-6.4.0/emboss/drfindformat.c	2011-10-05 14:56:08.000000000 +0100
 ***************
 *** 152,159 ****
                           {
@@ -4146,7 +4240,7 @@ diff -c -N --recursive -a EMBOSS-6.4.0old/emboss/drfindformat.c EMBOSS-6.4.0/emb
                                              (void *) 1);
 diff -c -N --recursive -a EMBOSS-6.4.0old/emboss/drfindid.c EMBOSS-6.4.0/emboss/drfindid.c
 *** EMBOSS-6.4.0old/emboss/drfindid.c	2011-05-25 13:41:47.000000000 +0100
---- EMBOSS-6.4.0/emboss/drfindid.c	2011-09-05 12:23:43.000000000 +0100
+--- EMBOSS-6.4.0/emboss/drfindid.c	2011-10-05 14:56:08.000000000 +0100
 ***************
 *** 152,159 ****
                           {
@@ -4169,7 +4263,7 @@ diff -c -N --recursive -a EMBOSS-6.4.0old/emboss/drfindid.c EMBOSS-6.4.0/emboss/
                                              (void *) 1);
 diff -c -N --recursive -a EMBOSS-6.4.0old/emboss/drfindresource.c EMBOSS-6.4.0/emboss/drfindresource.c
 *** EMBOSS-6.4.0old/emboss/drfindresource.c	2011-04-12 17:30:58.000000000 +0100
---- EMBOSS-6.4.0/emboss/drfindresource.c	2011-09-05 12:23:43.000000000 +0100
+--- EMBOSS-6.4.0/emboss/drfindresource.c	2011-10-05 14:56:08.000000000 +0100
 ***************
 *** 162,170 ****
                           {
@@ -4194,7 +4288,7 @@ diff -c -N --recursive -a EMBOSS-6.4.0old/emboss/drfindresource.c EMBOSS-6.4.0/e
                               }
 diff -c -N --recursive -a EMBOSS-6.4.0old/emboss/server.ensemblgenomes EMBOSS-6.4.0/emboss/server.ensemblgenomes
 *** EMBOSS-6.4.0old/emboss/server.ensemblgenomes	2011-07-06 23:14:17.000000000 +0100
---- EMBOSS-6.4.0/emboss/server.ensemblgenomes	2011-09-05 12:23:43.000000000 +0100
+--- EMBOSS-6.4.0/emboss/server.ensemblgenomes	2011-10-05 14:56:08.000000000 +0100
 ***************
 *** 1,4 ****
 ! # server.ensemblgenomes 2011-07-05 00:00:00
@@ -7212,7 +7306,7 @@ diff -c -N --recursive -a EMBOSS-6.4.0old/emboss/server.ensemblgenomes EMBOSS-6.
     url:     "mysql://anonymous@mysql.ebi.ac.uk:4157/wolbachia_collection_core_9_62_1a"
 diff -c -N --recursive -a EMBOSS-6.4.0old/nucleus/embgroup.c EMBOSS-6.4.0/nucleus/embgroup.c
 *** EMBOSS-6.4.0old/nucleus/embgroup.c	2011-05-16 11:14:30.000000000 +0100
---- EMBOSS-6.4.0/nucleus/embgroup.c	2011-09-05 12:23:43.000000000 +0100
+--- EMBOSS-6.4.0/nucleus/embgroup.c	2011-10-05 14:56:08.000000000 +0100
 ***************
 *** 1173,1179 ****
       AjPStr tail;