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