svn commit: r484211 - head/biology/ncbi-toolkit/files
Mark Linimon
linimon at FreeBSD.org
Mon Nov 5 19:47:44 UTC 2018
Author: linimon
Date: Mon Nov 5 19:47:42 2018
New Revision: 484211
URL: https://svnweb.freebsd.org/changeset/ports/484211
Log:
Fix build failure with base GCC because of double typedefs.
PR: 232457
Submitted by: Piotr Kubaj
Approved by: portmgr (tier-2 blanket)
Added:
head/biology/ncbi-toolkit/files/patch-algo_blast_core_jumper.h (contents, props changed)
Added: head/biology/ncbi-toolkit/files/patch-algo_blast_core_jumper.h
==============================================================================
--- /dev/null 00:00:00 1970 (empty, because file is newly added)
+++ head/biology/ncbi-toolkit/files/patch-algo_blast_core_jumper.h Mon Nov 5 19:47:42 2018 (r484211)
@@ -0,0 +1,48 @@
+--- algo/blast/core/jumper.h.orig 2018-10-19 17:37:04 UTC
++++ algo/blast/core/jumper.h
+@@ -66,13 +66,13 @@ typedef struct JumperPrelimEditBlock
+
+
+ /** Gapped alignment data needed for jumper */
+-typedef struct JumperGapAlign
++struct JumperGapAlign
+ {
+ JumperPrelimEditBlock* left_prelim_block;
+ JumperPrelimEditBlock* right_prelim_block;
+ Uint4* table; /**< Table used for matching 4 bases in compressed subject
+ to 4 bases in uncompressed query */
+-} JumperGapAlign;
++};
+
+
+ JumperGapAlign* JumperGapAlignFree(JumperGapAlign* jumper_align);
+@@ -90,11 +90,11 @@ typedef struct JumperEdit
+
+
+ /** Alignment edit script for gapped alignment */
+-typedef struct JumperEditsBlock
++struct JumperEditsBlock
+ {
+ JumperEdit* edits;
+ Int4 num_edits;
+-} JumperEditsBlock;
++};
+
+
+ JumperEditsBlock* JumperEditsBlockFree(JumperEditsBlock* block);
+@@ -262,13 +262,13 @@ JumperEditsBlock* JumperEditsBlockCombine(JumperEditsB
+ JumperEditsBlock** append);
+
+ /** Structure to save short unaligned subsequences outside an HSP */
+-typedef struct SequenceOverhangs
++struct SequenceOverhangs
+ {
+ Int4 left_len; /**< Length of the left subsequence */
+ Int4 right_len; /**< Length of the right subsequence */
+ Uint1* left; /**< Left subsequence */
+ Uint1* right; /**< Rught subsequence */
+-} SequenceOverhangs;
++};
+
+ SequenceOverhangs* SequenceOverhangsFree(SequenceOverhangs* overhangs);
+
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