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Date: Tue, 8 Sep 2020 19:23:15 -0400
From: Lennart Sorensen <lsorense@csclub.uwaterloo.ca>
Description: Force signed char on every architecture
Bug-Debian: https://bugs.debian.org/969552
--- a/src/fasta.c
+++ b/src/fasta.c
@@ -36,7 +36,7 @@ along with PhiPack. If not, see <http:/
void read_sequence_name(FILE *in_file,char *name, int capacity)
{
int i=0;
- char ch='\0';
+ signed char ch='\0';
ch=fgetc(in_file);
if(ch != '>')
@@ -97,7 +97,7 @@ char read_seq_part(FILE *in_file, int b
{
int bases_read=0;
int new_limit;
- char ch;
+ signed char ch;
char s[250];
ch=fgetc(in_file);
@@ -175,7 +175,7 @@ void read_fasta(const char* file_name,
int *seq_counter;
int i;
- char ch;
+ signed char ch;
int cur_seqs;
int num_seqs=1,new_num;
--- a/src/global.c
+++ b/src/global.c
@@ -34,7 +34,7 @@ const char AA_AMBIG[] = {'B','Z'};
const int AA_AMBIG_SIZE =2;
const char GAP[] = {'-'};
-const int GAP_SIZE=2;
+const int GAP_SIZE=1;
cbool memberOf(const char *set, const int num, char ch)
{
@@ -79,10 +79,10 @@ cbool missing_ambig_State(alignmentClass
switch(alignKind)
{
case DNA:
- return (memberOf(DNA_MISSING,DNA_MISSING_SIZE,ch) || memberOf(DNA_AMBIG,DNA_AMBIG_SIZE,ch));
+ return (memberOf(DNA_MISSING,DNA_MISSING_SIZE,ch) || memberOf(DNA_AMBIG,DNA_AMBIG_SIZE,ch)) ? TRUE : FALSE;
break;
case AA:
- return (memberOf(AA_MISSING,AA_MISSING_SIZE,ch) || memberOf(AA_AMBIG,AA_AMBIG_SIZE,ch));
+ return (memberOf(AA_MISSING,AA_MISSING_SIZE,ch) || memberOf(AA_AMBIG,AA_AMBIG_SIZE,ch)) ? TRUE : FALSE;
break;
case OTHER:
if(ch == GLOBAL_MISSING)
--- a/src/main.c
+++ b/src/main.c
@@ -71,7 +71,8 @@ void print_usage()
void get_params(int argc, char**argv, options *opt)
{
- char *cur,ch,nextch;
+ char *cur;
+ signed char ch,nextch;
char temp[MAX_SIZE+1];
int i;
cbool inFileFound=FALSE;
--- a/src/mem.c
+++ b/src/mem.c
@@ -96,7 +96,7 @@ FILE *ffopen(char *name,char *mod)
char ffclose(FILE *handle)
{
- char f;
+ signed char f;
char s[MAX_SIZE+1];
f=fclose(handle);
--- a/src/misc.c
+++ b/src/misc.c
@@ -46,7 +46,7 @@ char *strsub(char *s1, const char *s2, i
char skip_all_space(FILE *in_file)
{
- char ch;
+ signed char ch;
ch=fgetc(in_file);
while((ch != EOF) && isspace(ch))
@@ -61,7 +61,7 @@ char skip_all_space(FILE *in_file)
char skip_newlines(FILE *in_file)
{
- char ch;
+ signed char ch;
ch=fgetc(in_file);
while((ch != EOF) && (ch == '\n'))
@@ -76,7 +76,7 @@ char skip_newlines(FILE *in_file)
char skip_non_newline(FILE *in_file)
{
- char ch;
+ signed char ch;
ch=fgetc(in_file);
while((ch != EOF) && (ch != '\n'))
@@ -90,7 +90,7 @@ char skip_non_newline(FILE *in_file)
char skip_non_newline_space(FILE *in_file)
{
- char ch;
+ signed char ch;
ch=fgetc(in_file);
while((ch != EOF) && (ch != '\n') && isspace(ch))
--- a/src/phylip.c
+++ b/src/phylip.c
@@ -30,7 +30,7 @@
void read_strict_name(FILE *in_file,char *name, int capacity)
{
int i;
- char ch='\0';
+ signed char ch='\0';
for(i=0;(i<PHYLIP_SIZE) && (ch!=EOF);i++)
{
ch=fgetc(in_file);
@@ -51,7 +51,7 @@ void read_strict_name(FILE *in_file,char
void read_relaxed_name(FILE *in_file,char *name, int capacity)
{
int i=0;
- char ch='\0',next_ch;
+ signed char ch='\0',next_ch;
cbool double_space=FALSE;
while((i<capacity) && (ch!=EOF) && (double_space == FALSE))
@@ -129,7 +129,7 @@ void write_phylip(FILE* cur_stream, cboo
int read_seq_bit(FILE *in_file, int base_limit, align_type* states, int index, int *num_bases)
{
int bases_read=num_bases[index];
- char ch;
+ signed char ch;
char s[250];
ch=fgetc(in_file);
@@ -213,7 +213,7 @@ void read_phylip(const char* file_name,
int *seq_counter;
int i;
int cur_seq=0;
- char ch;
+ signed char ch;
in_file=fopen(file_name,"r");
if(in_file == NULL)
--- a/src/profile.c
+++ b/src/profile.c
@@ -71,7 +71,8 @@ void print_usage()
void get_params(int argc, char**argv, options *opt)
{
- char *cur,ch,nextch;
+ char *cur;
+ signed char ch,nextch;
char temp[MAX_SIZE+1];
int i;
cbool inFileFound=FALSE;
--- a/src/seqManip.c
+++ b/src/seqManip.c
@@ -190,7 +190,7 @@ void get_informative( align_type **align
cbool validate_alignment(align_type **alignment, alignmentClass alignKind,int num_taxa, int num_sites)
{
int i,j;
- char ch;
+ signed char ch;
char s[MAX_SIZE+1];
for(i=0;i<num_taxa;i++)
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