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aarch64 char is unnsigned. force signed #28

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6 changes: 3 additions & 3 deletions SweeD.h
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Original file line number Diff line number Diff line change
Expand Up @@ -345,7 +345,7 @@ void printFloatArray(float *array, int n);

void printCharArray(char *array, int n);

int isEndOfLine(char ent);
int isEndOfLine(signed char ent);

void goToLineEnd(FILE *fp);

Expand Down Expand Up @@ -373,9 +373,9 @@ int isValidDNACharacter(char input);

void parseIndividual(char *word, char** genotype, char delimiter, int token, char* states, char phased, char unphased, int *ploidy, int *max_ploidy);

void ignoreAll(FILE * fp, char * ent);
void ignoreAll(FILE * fp, signed char * ent);

int isSpace(char ent);
int isSpace(signed char ent);

double XchooseY_ln(int x, int y);

Expand Down
42 changes: 22 additions & 20 deletions SweeD_Input.c
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Original file line number Diff line number Diff line change
Expand Up @@ -236,7 +236,7 @@ int flagMatch(FILE *fp, char flag[], int flaglength, char tmp)



void ignoreLineSpaces(FILE *fp, char *ent)
void ignoreLineSpaces(FILE *fp, signed char *ent)
{
while(*ent==' '|| *ent == 9) // horizontal tab
*ent = fgetc(fp);
Expand All @@ -245,7 +245,7 @@ void ignoreLineSpaces(FILE *fp, char *ent)

int getFileFormat (FILE * fp)
{
char tmp;
signed char tmp;

int cnt = 0;

Expand Down Expand Up @@ -1293,7 +1293,7 @@ void commandLineParser(int argc, char** argv,
}
}

void ignoreNewLineChars(FILE *fp, char *ent)
void ignoreNewLineChars(FILE *fp, signed char *ent)
{

int brk = 0;
Expand All @@ -1316,7 +1316,7 @@ void ignoreNewLineChars(FILE *fp, char *ent)

}

int isEndOfLine2(char ent)
int isEndOfLine2(signed char ent)
{
if(ent == 10 || ent == 13)
return 1;
Expand All @@ -1331,7 +1331,7 @@ int getNextString(FILE *fp, char ** word, int *readEOL, int *readEOF, int *wordL

*readEOL = *readEOF = 0;

char ent = fgetc(fp);
signed char ent = fgetc(fp);

/* if( ent == 10 || ent == 13) */
/* iseol++; */
Expand Down Expand Up @@ -1439,7 +1439,7 @@ int getNextString_all_lines(FILE *fp, char ** word, int *readEOL, int *readEOF,

int findFirstAlignment(FILE *fp, int format, FILE *fpVCFsamples, int generateVCFsamplelist, char * vcf_samples_filename, FILE * fpInfo)
{
char tmp;
signed char tmp;
int temp=-1, tip = 0, i;

if(format==FASTA_FORMAT)
Expand Down Expand Up @@ -1692,7 +1692,7 @@ int findFirstAlignment(FILE *fp, int format, FILE *fpVCFsamples, int generateVCF

int findNextAlignment(FILE *fp, int fileFormat)
{
char stop,tmp;
signed char stop,tmp;
int temp=-1;

if (fileFormat == MS_FORMAT || fileFormat == SF_FORMAT)
Expand Down Expand Up @@ -2245,7 +2245,7 @@ int isEOFnear(FILE *fp, char *ent)
return 0;
}

void ignoreSpaces(FILE * fp, char * ent)
void ignoreSpaces(FILE * fp, signed char * ent)
{
while(*ent != EOF && (*ent==10 || *ent==13 || *ent==32 || *ent==9) )
*ent = fgetc(fp);
Expand Down Expand Up @@ -2431,7 +2431,7 @@ int parseInfoVar(char *word, char *type, int start)

void goToLineEnd(FILE *fp)
{
char ent;
signed char ent;
while( (ent = fgetc(fp) ) != EOF )
{

Expand Down Expand Up @@ -2573,7 +2573,7 @@ int isOutgroup (char * seqName, char * outgroup)
}


void updateStateCounters (alignment_struct * alignment, char ent, int index)
void updateStateCounters (alignment_struct * alignment, signed char ent, int index)
{
if(ent==AD || ent == ade)
{
Expand Down Expand Up @@ -2603,7 +2603,7 @@ void updateStateCounters (alignment_struct * alignment, char ent, int index)
int readFASTAsequenceLight(FILE * fp, alignment_struct * alignment, char * seqName, int outgroup)
{
int DIM = 10, i=0, y=0;
char ent;
signed char ent;

if(alignment->segsites==-1)
{
Expand Down Expand Up @@ -3096,7 +3096,7 @@ void checkSNIPPositions (FILE* fp, alignment_struct * alignment, int index)
fprintf(fp,"\n");
}

int isEndOfLine(char ent)
int isEndOfLine(signed char ent)
{
if(ent == 10|| ent == 13 || ent == 32)
return 1;
Expand All @@ -3106,7 +3106,7 @@ int isEndOfLine(char ent)



int isSpace(char ent)
int isSpace(signed char ent)
{
if(ent == 9 || ent == 32)
return 1;
Expand All @@ -3116,15 +3116,15 @@ int isSpace(char ent)



void ignoreAll(FILE * fp, char * ent)
void ignoreAll(FILE * fp, signed char * ent)
{
while(*ent < 33 && *ent != EOF)
*ent = fgetc(fp);
}

int skipLine (FILE * fp)
{
char tmp;
signed char tmp;

while( (tmp = fgetc(fp) ) != EOF)
if(tmp == 10 || tmp == 13)
Expand Down Expand Up @@ -3562,7 +3562,7 @@ int readLine_VCF (FILE * fp, char ** string, int lineIndex, alignment_struct * a
{

int eol=0, eof=0, maxLength=STRINGLENGTH;
char tmp;
signed char tmp;
int elementIndex = -1, lineSkipped=0, isEOF = 1, i,j=0, y, s=0, tip = 0;

char stateVector[MAX_STATES_VCF+1];
Expand Down Expand Up @@ -3754,6 +3754,7 @@ int readLine_VCF (FILE * fp, char ** string, int lineIndex, alignment_struct * a

if(elementIndex == VCF_HLENGTH-1 || eol==1 || eof==1 || lineSkipped==1)
break;

}

if (eof== 1 || position == -1)
Expand Down Expand Up @@ -4227,7 +4228,7 @@ int readAlignmentMACS(FILE *fp, alignment_struct *alignment, FILE *fpInfo, FILE
fprintf(fpInfo," Alignment %d\n",alignmentIndex);

int i, DIM = 2, prevDIM;
char ent;
signed char ent;
int nsnp = 0;
int sitevar;
char siteflag[100];
Expand Down Expand Up @@ -4396,7 +4397,8 @@ int readAlignmentMS(FILE *fp, alignment_struct *alignment, FILE * fpInfo, FILE *
fprintf(stdout," Alignment %d\n",alignmentIndex);
fprintf(fpInfo," Alignment %d\n",alignmentIndex);

char ent, stringtemp[100];
char stringtemp[100];
signed char ent;


/* get rid of the first line information */
Expand Down Expand Up @@ -4558,7 +4560,7 @@ int readAlignmentSF(FILE *fp, FILE * fpInfo, FILE *fpSFo, int minsnps_threshold_
char *fgetsValue = NULL;
double position = 0.;
char tmpString[100];
char ent;
signed char ent;
char line[LEN];

alignment->x = calloc(DIM, sizeof(al_t));
Expand Down Expand Up @@ -4587,7 +4589,7 @@ int readAlignmentSF(FILE *fp, FILE * fpInfo, FILE *fpSFo, int minsnps_threshold_

cnt++;

char charTMP = fgetc(fp);
signed char charTMP = fgetc(fp);

ungetc(charTMP, fp);

Expand Down
1 change: 1 addition & 0 deletions SweeD_SFS.c
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Original file line number Diff line number Diff line change
Expand Up @@ -446,6 +446,7 @@ void createSFS (FILE * fpSFS, FILE * fpSFSo, int alignmentIndex, int * SFSsize)
{
int i;
static int allocSFS = 1;
signed char t;

if(allocSFS==1)
{
Expand Down