From 9d727d9a63166a59006ac6b1687c200fd5a7d771 Mon Sep 17 00:00:00 2001
From: edgrif <edgrif>
Date: Fri, 1 May 2009 15:05:23 +0000
Subject: [PATCH] fix offset problem in gff dumping, we need to set -refseq.
---
src/zmapServer/acedb/acedbServer.c | 15 ++++++---------
1 file changed, 6 insertions(+), 9 deletions(-)
diff --git a/src/zmapServer/acedb/acedbServer.c b/src/zmapServer/acedb/acedbServer.c
index b0b5ceb02..c7275e3d0 100755
--- a/src/zmapServer/acedb/acedbServer.c
+++ b/src/zmapServer/acedb/acedbServer.c
@@ -27,9 +27,9 @@
*
* Exported functions: See zmapServer.h
* HISTORY:
- * Last edited: Apr 30 15:58 2009 (edgrif)
+ * Last edited: May 1 16:04 2009 (edgrif)
* Created: Wed Aug 6 15:46:38 2003 (edgrif)
- * CVS info: $Id: acedbServer.c,v 1.129 2009-04-30 15:00:07 edgrif Exp $
+ * CVS info: $Id: acedbServer.c,v 1.130 2009-05-01 15:05:23 edgrif Exp $
*-------------------------------------------------------------------
*/
@@ -1188,6 +1188,8 @@ static gboolean sequenceRequest(AcedbServer server, GData *styles, ZMapFeatureBl
* for most acedb requests, only images/postscript are not and we aren't asking for them. */
/* -rawmethods makes sure that the server does _not_ use the GFF_source field in the method obj
* to output the source field in the gff, we need to see the raw methods.
+ * -refseq makes sure that the coords returned are relative to the reference sequence, _not_
+ * to the object at the top of the smap tree .
*
* Note that we specify the methods both for the seqget and the seqfeatures to try and exclude
* the parent sequence if it is not required, this is actually quite fiddly to do in the acedb
@@ -1197,19 +1199,14 @@ static gboolean sequenceRequest(AcedbServer server, GData *styles, ZMapFeatureBl
acedb_request = g_strdup_printf("gif seqget %s -coords %d %d %s %s ; "
" %s "
- "seqfeatures -rawmethods -zmap %s",
+ "seqfeatures -refseq %s -rawmethods -zmap %s",
g_quark_to_string(feature_block->original_id),
-
-#ifdef ED_G_NEVER_INCLUDE_THIS_CODE
- feature_block->block_to_sequence.q1,
- feature_block->block_to_sequence.q2,
-#endif /* ED_G_NEVER_INCLUDE_THIS_CODE */
feature_block->features_start,
feature_block->features_end,
-
no_clip ? "-noclip" : "",
methods,
(server->fetch_gene_finder_features ? gene_finder_cmds : ""),
+ g_quark_to_string(feature_block->original_id),
methods) ;
if ((server->last_err_status = AceConnRequest(server->connection, acedb_request, &reply, &reply_len))
--
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