diff options
author | Petar Petrov <ppetrov@paju.oulu.fi> | 2011-10-19 19:39:37 -0200 |
---|---|---|
committer | Niels Horn <niels.horn@slackbuilds.org> | 2011-10-21 15:59:16 -0200 |
commit | fd8480905d0892cfcb2fb02f548442a80cd41627 (patch) | |
tree | 674f78da1761c9d9335861c22616263f56c01d4d /academic/EMBOSS | |
parent | 8d5c20db4abffdde22060be57b4f9b2fd78c1819 (diff) |
academic/EMBOSS: Updated with newest patches.
Signed-off-by: Niels Horn <niels.horn@slackbuilds.org>
Diffstat (limited to 'academic/EMBOSS')
-rw-r--r-- | academic/EMBOSS/EMBOSS.SlackBuild | 6 | ||||
-rw-r--r-- | academic/EMBOSS/patch-1-24 (renamed from academic/EMBOSS/patch-1-21) | 152 |
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; |