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|
--- a/src/fchaos.c
+++ b/src/fchaos.c
@@ -985,7 +985,7 @@
SLremove(mylist, tbf->mysles[i]);
}
-inline int CHmatchscore(unsigned char a, unsigned char b) {
+static inline int CHmatchscore(unsigned char a, unsigned char b) {
return substmatrix[a][b];
/*
if (translated)
--- a/src/multial.c
+++ b/src/multial.c
@@ -59,16 +59,16 @@
int normf;
int normprev;
-inline int ismatch(char a, char b) {
+static inline int ismatch(char a, char b) {
return (a == b);
}
-inline int isGap(align* ali, int seqn, int loc) {
+static inline int isGap(align* ali, int seqn, int loc) {
int i = !((ali->algn[loc] >> seqn) & 1);
return i;
}
-inline int scoreLocal(int which, align* ali, int loc) {
+static inline int scoreLocal(int which, align* ali, int loc) {
int i, lets = 0;
for (i=0; i < 4; i++)
lets += ali->cnts[i][loc];
@@ -83,7 +83,7 @@
return lets+ali->cnts[CNTS_GS][loc] * gapcont;
}
-inline hll* reverseHLL(hll* tbr) {
+static inline hll* reverseHLL(hll* tbr) {
hll *nn, *prev=0;
while (tbr) {
nn = tbr->next;
@@ -171,7 +171,7 @@
return res;
}
-inline void reverse (long long int* a, int length) {
+static inline void reverse (long long int* a, int length) {
long long int lft;
int i;
for (i=0; i < length/2; i++) {
@@ -409,7 +409,7 @@
*/
}
-inline int scoreGap(int numgs, int numgc, int numge, int numseq) {
+static inline int scoreGap(int numgs, int numgc, int numge, int numseq) {
return (MIN2(numgc, numseq-numgc) * gapcont) +
(MIN2(numgs, numseq-numgs) * gapstart) +
(MIN2(numge, numseq-numge) * gapend);
@@ -493,7 +493,7 @@
fclose (file);
}
-inline int chmatchscore (unsigned char a, unsigned char b, int substmatrix[256][256]) {
+static inline int chmatchscore (unsigned char a, unsigned char b, int substmatrix[256][256]) {
return substmatrix[a][b];
}
@@ -539,14 +539,14 @@
// printcache();
}
-inline int v (int y){
+static inline int v (int y){
if (y >= 0 && y <= MAX_SEQ) return y;
fprintf(stderr, "Got %d in v\n", y);
assert (0);
return 0;
}
-inline int matchscore (align*a, int ai, align *b, int bi){
+static inline int matchscore (align*a, int ai, align *b, int bi){
return
matchcache[v(a->cnts[0][ai] + b->cnts[0][bi]) |
@@ -559,30 +559,30 @@
(v(a->numseq + b->numseq - (a->cnts[CNTS_CB][ai] + b->cnts[CNTS_CB][bi])) << 18)];
}
-inline int scoreOpp (align *other, int ow, int oppnum){
+static inline int scoreOpp (align *other, int ow, int oppnum){
return matchcache[v(other->cnts[0][ow]) |
(v(other->cnts[1][ow]) << 6) |
(v(other->cnts[2][ow]) << 12) |
(v(other->cnts[3][ow]) << 18)];
}
-inline int endGap0 (align* a, int ai, align* b, int bi){
+static inline int endGap0 (align* a, int ai, align* b, int bi){
return gapcache[(v(a->cnts[CNTS_GE][ai]+b->cnts[CNTS_GE][bi])<<12) |
(v(a->numseq + b->numseq-(b->cnts[CNTS_CB][bi]+a->cnts[CNTS_CB][ai])) << 18)];
}
-inline int endGap1 (align* a, int ai, align* b, int bi){
+static inline int endGap1 (align* a, int ai, align* b, int bi){
return gapcache[(v((b->numseq - b->cnts[CNTS_GS][bi] - b->cnts[CNTS_GC][bi]) + a->cnts[CNTS_GE][ai]) << 12) |
(v(a->numseq + b->numseq - (b->cnts[CNTS_CB][bi]+a->cnts[CNTS_CB][ai])) << 18)];
}
-inline int endGap2 (align* a, int ai, align* b, int bi){
+static inline int endGap2 (align* a, int ai, align* b, int bi){
return gapcache[(v((a->numseq - a->cnts[CNTS_GS][ai] - a->cnts[CNTS_GC][ai]) + b->cnts[CNTS_GE][bi])<<12) |
(v(a->numseq + b->numseq - (b->cnts[CNTS_CB][bi]+a->cnts[CNTS_CB][ai])) << 18)];
}
-inline int contGap(align* ali, int myw, align* other, int ow, int *sopp) {
+static inline int contGap(align* ali, int myw, align* other, int ow, int *sopp) {
return gapcache[(v(other->cnts[CNTS_GS][ow])) |
(v(ali->numseq + other->cnts[CNTS_GC][ow]) << 6) |
(v(other->cnts[CNTS_GE][ow]) << 12) |
@@ -590,7 +590,7 @@
sopp[ow];
}
-inline int openGap(align* ali, int w, align* other, int ow, int *sopp, char *desc) {
+static inline int openGap(align* ali, int w, align* other, int ow, int *sopp, char *desc) {
int alopen, pen, sav, i;
alopen = ali->cnts[CNTS_GC][w] + ali->cnts[CNTS_GE][w];
--- a/src/order.c
+++ b/src/order.c
@@ -454,11 +454,11 @@
}
-inline int ismatch(char a, char b) {
+static inline int ismatch(char a, char b) {
return a == b;
}
-inline int matchscore (unsigned char a, unsigned char b) {
+static inline int matchscore (unsigned char a, unsigned char b) {
return substmatrix[a][b];
/*
--- a/src/utils/cstat.c
+++ b/src/utils/cstat.c
@@ -121,7 +121,7 @@
return res;
}
-inline int getScore (align* a, int i){
+static inline int getScore (align* a, int i){
return
((a->cnts[0][i] * (a->cnts[0][i] - 1)) +
(a->cnts[1][i] * (a->cnts[1][i] - 1)) +
--- a/src/utils/getbounds.c
+++ b/src/utils/getbounds.c
@@ -6,8 +6,8 @@
#define EXPAND 2
-inline int max (int a, int b){ if (a > b) return a; return b; }
-inline int min (int a, int b){ if (a < b) return a; return b; }
+static inline int max (int a, int b){ if (a > b) return a; return b; }
+static inline int min (int a, int b){ if (a < b) return a; return b; }
int getLength (char *filename){
FILE *file;
--- a/src/utils/scorealign.c
+++ b/src/utils/scorealign.c
@@ -18,17 +18,17 @@
int matchscore[256][256];
int gapopen = -1500, gapcont = -50;
-inline int min (int a, int b){
+static inline int min (int a, int b){
if (a < b) return a;
return b;
}
-inline int max (int a, int b){
+static inline int max (int a, int b){
if (a > b) return a;
return b;
}
-inline int scoreMatch (char c, char d){
+static inline int scoreMatch (char c, char d){
if (c == '-' && d == '-') return 0;
if (c == '-' || d == '-') return gapcont;
return matchscore[(unsigned char) c][(unsigned char) d];
@@ -235,7 +235,7 @@
}
}
-inline int issymbol (char ch){
+static inline int issymbol (char ch){
return ch == 'A' || ch == 'C' || ch == 'G' || ch == 'T' || ch == 'N' || ch == '.' || ch == '-';
}
--- a/src/utils/scorecontigs.c
+++ b/src/utils/scorecontigs.c
@@ -133,7 +133,7 @@
return res;
}
-inline int getstate (char c, char d){
+static inline int getstate (char c, char d){
if (c == '-' || d == '-') return 2;
if (c == 'N' || d == 'N') return 3;
return c == d;
@@ -235,7 +235,7 @@
return r;
}
-inline int getdata (rangelist **ranges, int *offs, int j, int i){
+static inline int getdata (rangelist **ranges, int *offs, int j, int i){
i -= offs[j];
if (i >= 0 && i < ranges[j]->seqlen)
return ranges[j]->score[i];
@@ -243,14 +243,14 @@
}
-inline int match (rangelist **ranges, int numContigs, int i, int j, int *offs){
+static inline int match (rangelist **ranges, int numContigs, int i, int j, int *offs){
int k;
for (k = 0; k < numContigs; k++)
if ((getdata (ranges, offs, k, i) != 0) != (getdata (ranges, offs, k, j) != 0)) return 0;
return 1;
}
-inline int allzeroes (rangelist **ranges, int numContigs, int pos, int *offs){
+static inline int allzeroes (rangelist **ranges, int numContigs, int pos, int *offs){
int i;
for (i = 0; i < numContigs; i++)
@@ -258,7 +258,7 @@
return 1;
}
-inline void print (int start, int end, int *score, int numContigs){
+static inline void print (int start, int end, int *score, int numContigs){
int j;
printf ("(%7d %7d)", start, end);
@@ -303,7 +303,7 @@
free (pattern);
}
-inline double scoregap (int gaplen){
+static inline double scoregap (int gaplen){
if (gaplen == 0) return 0;
//return (gaplen - 1) * -1 - 50;
return (log (gaplen) / log (10) + 1) * scoreGapOpen;
|
