diff --git a/biology/ncbi-toolkit/files/patch-algo_blast_core_jumper.h b/biology/ncbi-toolkit/files/patch-algo_blast_core_jumper.h new file mode 100644 index 000000000000..52992b964820 --- /dev/null +++ b/biology/ncbi-toolkit/files/patch-algo_blast_core_jumper.h @@ -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); +