gentoo-overlay/sci-biology/bfast/files/bfast-0.7.0a-C99-inline.patch

--- a/bfast/AlignNTSpace.c
+++ b/bfast/AlignNTSpace.c
@@ -478,7 +478,7 @@
 	}
 }
 
-inline void AlignNTSpaceFillInCell(char *read,
+void AlignNTSpaceFillInCell(char *read,
 		int32_t readLength,
 		char *reference,
 		int32_t referenceLength,
--- a/bfast/AlignNTSpace.h
+++ b/bfast/AlignNTSpace.h
@@ -10,5 +10,5 @@
 void AlignNTSpaceRecoverAlignmentFromMatrix(AlignedEntry*, AlignMatrix*, char*, int, char*, int, int32_t, int32_t, int, int32_t, char, int);
 void AlignNTSpaceInitializeAtStart(AlignMatrix*, ScoringMatrix*, int32_t, int32_t);
 void AlignNTSpaceInitializeToExtend(AlignMatrix*, ScoringMatrix*, int32_t, int32_t, int32_t, int32_t);
-inline void AlignNTSpaceFillInCell(char*, int32_t, char*, int32_t, ScoringMatrix*, AlignMatrix*, int32_t, int32_t, int32_t, int32_t);
+void AlignNTSpaceFillInCell(char*, int32_t, char*, int32_t, ScoringMatrix*, AlignMatrix*, int32_t, int32_t, int32_t, int32_t);
 #endif
--- a/bfast/BLib.c
+++ b/bfast/BLib.c
@@ -90,7 +90,7 @@
 }
 
 /* TODO */
-inline char ToUpper(char a)
+char ToUpper(char a)
 {
   if(97 <= a && a < 122) return (char)(a - 32);
   return a;
--- a/bfast/BLib.h
+++ b/bfast/BLib.h
@@ -16,7 +16,7 @@
 int ParseFastaHeaderLine(char*);
 char ToLower(char);
 void ToLowerRead(char*, int);
-inline char ToUpper(char);
+char ToUpper(char);
 void ToUpperRead(char*, int);
 void ReverseRead(char*, char*, int);
 void ReverseReadFourBit(int8_t*, int8_t*, int);
--- a/bfast/ScoringMatrix.c
+++ b/bfast/ScoringMatrix.c
@@ -98,14 +98,14 @@
 	return 1;
 }
 
-inline int32_t ScoringMatrixGetNTScore(char a,
+int32_t ScoringMatrixGetNTScore(char a,
 		char b,
 		ScoringMatrix *sm)
 {
 	return (ToUpper(a) == ToUpper(b)) ? sm->ntMatch : sm->ntMismatch;
 }
 
-inline int32_t ScoringMatrixGetColorScore(char a, 
+int32_t ScoringMatrixGetColorScore(char a, 
 		char b, 
 		ScoringMatrix *sm) 
 {
--- a/bfast/ScoringMatrix.h
+++ b/bfast/ScoringMatrix.h
@@ -3,8 +3,8 @@
 
 #include "BLibDefinitions.h"
 
-inline int32_t ScoringMatrixGetNTScore(char, char, ScoringMatrix*);
-inline int32_t ScoringMatrixGetColorScore(char, char, ScoringMatrix*);
+int32_t ScoringMatrixGetNTScore(char, char, ScoringMatrix*);
+int32_t ScoringMatrixGetColorScore(char, char, ScoringMatrix*);
 
 int ScoringMatrixRead(char*, ScoringMatrix*, int);
 void ScoringMatrixInitialize(ScoringMatrix*);