GBase.cpp

#include "GBase.h"
#include <ctype.h>
#include <errno.h>

#ifndef S_ISDIR
#define S_ISDIR(mode)  (((mode) & S_IFMT) == S_IFDIR)
#endif

#ifndef S_ISREG
#define S_ISREG(mode)  (((mode) & S_IFMT) == S_IFREG)
#endif

//#ifdef _WIN32
// int (WINAPIV * __vsnprintf)(char *, size_t, const char*, va_list) = _vsnprintf;
//#endif

//************************* Debug helpers **************************
// Assert failed routine
void GAssert(const char* expression, const char* filename, unsigned int lineno){
  char msg[4096];
  sprintf(msg,"%s(%d): ASSERT(%s) failed.\n",filename,lineno,expression);
  fprintf(stderr,"%s",msg);
  #ifdef DEBUG
  // modify here if you [don't] want a core dump
    abort();
  #endif
  exit(1);
}

// Error routine (prints error message and exits!)
void GError(const char* format,...){
  #ifdef _WIN32
    char msg[4096];
    va_list arguments;
    va_start(arguments,format);
    _vsnprintf(msg, 4095, format, arguments);
    vfprintf(stderr, format, arguments); // if a console is available
    msg[4095]=0;
    va_end(arguments);
    OutputDebugString(msg);
    MessageBox(NULL,msg,NULL,MB_OK|MB_ICONEXCLAMATION|MB_APPLMODAL);
  #else
    va_list arguments;
    va_start(arguments,format);
    vfprintf(stderr,format,arguments);
    va_end(arguments);
    #ifdef DEBUG
     // comment this if you do NOT want a core dump
     //abort();
    #endif
  #endif
    exit(1);
  }

// Warning routine (just print message without exiting)
void GMessage(const char* format,...){
  #ifdef _WIN32
    char msg[4096];
    va_list arguments;
    va_start(arguments,format);
    vfprintf(stderr, format , arguments); // if a console is available
    _vsnprintf(msg, 4095, format, arguments);
    msg[4095]=0;
    va_end(arguments);
    fflush(stderr);
    //OutputDebugString(msg);
  #else
    va_list arguments;
    va_start(arguments,format);
    vfprintf(stderr,format,arguments);
    va_end(arguments);
    fflush(stderr);
  #endif
  }


char* Gstrdup(const char* str, int xtracap) {
  if (str==NULL) return NULL;
  char *copy=NULL;
  GMALLOC(copy, strlen(str)+1+xtracap);
  strcpy(copy,str);
  return copy;
  }

char* newEmptyStr() {
  char* zs=NULL;
  GMALLOC(zs,1);
  zs[0]=0;
  return zs;
}

char* Gstrdup(const char* sfrom, const char* sto) {
  if (sfrom==NULL || sto==NULL) return NULL;
  char *copy=NULL;
  if (sfrom[0]==0 || sto<sfrom) return newEmptyStr();
  GMALLOC(copy, sto-sfrom+2);
  strncpy(copy, sfrom, sto-sfrom+1);
  copy[sto-sfrom+1]=0;
  return copy;
  }

int Gstrcmp(const char* a, const char* b, int n) {
 if (a==NULL || b==NULL) {
   return a==NULL ? -1 : 1;
   }
 else {
   if (n<0) return strcmp(a,b);
       else return strncmp(a,b,n);
 }
}

int G_mkdir(const char* path, int perms = (S_IRWXU | S_IRGRP | S_IXGRP | S_IROTH | S_IXOTH) ) {
   //int perms=(S_IRWXU | S_IRGRP | S_IXGRP | S_IROTH | S_IXOTH) ) {
 #ifdef _WIN32
     //return _mkdir(path);
     return !CreateDirectoryA(path, NULL);
 #else
     return mkdir(path, perms);
 #endif
}


void Gmktempdir(char* templ) {
#ifdef _WIN32
  int blen=strlen(templ);
  char* pt=templ+blen-1;
  //on Windows this needs a plain file name template, without directory prefix
  blen=1;
  while (pt!=templ) {
    if (*pt=='/' || *pt=='\\') { pt++; break;}
    --pt; blen++;
  }
  if (_mktemp_s(pt, blen)!=0)
     GError("Error creating template file name %s!\n", pt);
  Gmkdir(templ, true);
#else
  char* cdir=mkdtemp(templ);
  if (cdir==NULL)
	  GError("Error creating temp dir %s!(%s)\n", templ, strerror(errno));
#endif
}

char *to_unix_path(char *p) {
    if (p != NULL) {
        char *pp = p;
        while (*pp != 0) {
            if (*pp == '\\')
                *pp = '/';
            ++pp;
        }
    }
    return p;
}

char* Grealpath(const char *path, char *resolved_path) {
#ifdef _WIN32
  //char *realpath(const char *path, char *resolved_path) {
  char *ret = NULL;
  if (path == NULL) {
     errno = EINVAL;
  } else if (access(path, R_OK) == 0) {
     ret = resolved_path;
     if (ret == NULL) {
         GMALLOC(ret, _MAX_PATH);
     }
     if (ret == NULL) {
       errno = ENOMEM;
     } else {
        ret = _fullpath(ret, path, _MAX_PATH);
        if (ret == NULL)
            errno = EIO;
     }
  }
  return to_unix_path(ret);
  #else
    return realpath(path, resolved_path);
  #endif
}


int Gmkdir(const char *path, bool recursive, int perms) {
	if (path==NULL || path[0]==0) return -1;
	mode_t process_mask = umask(0); //is this really needed?
	if (!recursive) {
	   int r=G_mkdir(path, perms);
	   if (r!=0)
	      GMessage("Warning: G_mkdir(%s) failed: %s\n", path, strerror(errno));
	   umask(process_mask);
	   return r;
	   }
	int plen=strlen(path);
	char* gpath=NULL;
	//make sure gpath ends with /
	if (path[plen-1]=='/') {
		gpath=Gstrdup(path);
	}
	else {
		GMALLOC(gpath, plen+2);
		strcpy(gpath,path);
		strcat(gpath, "/");
		++plen;
	}
	//char* ss=gpath+plen-1;
	char* psep = gpath+plen-1; //start at the last /
	GDynArray<char*> dirstack(4); // stack of directories that should be created
	while (psep>gpath && *(psep-1)=='/') --psep; //skip double slashes
    *psep='\0';
    int fexists=0;
	while ((fexists=fileExists(gpath))==0) {
      dirstack.Push(psep);
      do { --psep; } while (psep>gpath && *psep!='/');
      if (psep<=gpath) { psep=NULL; break; }
      while (psep>gpath && *(psep-1)=='/') --psep;
      *psep='\0';
	}
	if (psep) *psep='/';
	while (dirstack.Count()>0) {
		psep=dirstack.Pop();
		int mkdir_err=0;
		if ((mkdir_err=G_mkdir(gpath, perms))!=0) {
				GMessage("Warning: mkdir(%s) failed: %s\n", gpath, strerror(errno));
			GFREE(gpath);
			umask(process_mask);
			return -1;
		}
		*psep='/';
	}
	GFREE(gpath);
	umask(process_mask);
	return 0;
}

bool haveStdInput() {
#ifdef _WIN32
	HANDLE hIn = GetStdHandle(STD_INPUT_HANDLE);
	DWORD stype = GetFileType(hIn);
	return (stype!=FILE_TYPE_CHAR);
#else
	return !(isatty(fileno(stdin)));
#endif
}

FILE* Gfopen(const char *path, char *mode) {
	FILE* f=NULL;
	if (mode==NULL) f=fopen(path, "rb");
	    	   else f=fopen(path, mode);
	if (f==NULL)
		GMessage("Error opening file '%s':  %s\n", path, strerror(errno));
	return f;
}
#define IS_CHR_DELIM(c) ( c == ' ' || c == '\t' || c == ':' )
void GRangeParser::parse(char* s) {
	 //parses general range format: [+\-|.]refID[+\-\.][ |:][start][-|.\s]end[\s:][+\-\.]
	// if ref ID has ':' a space delimited format is preferred
	//   or just separate the ref ID from the coordinate range: [[+/-]ref<space>start[[-..][end]]
	//the safest way would be to parse from the end in case the ref ID has ':' characters
	//if the whole chromosome is intended (no coordinates to speficy)
	   this->start=0;
	   this->end=0;
	   this->strand=0;
	   int slen=strlen(s);
	   if (slen==0) return;
	   while (isspace(s[slen-1])) { slen--; s[slen]=0; } //trim trailing spaces
	   while (isspace(*s)) { ++s; --slen; } //trim prefix spaces
	   char c=*s;
	   if (c=='+' || c=='-') {
	     strand=c;
	     ++s;slen--;
	   }
	   if (strand && (*s==':' || *s==' ')) //ignore
		   { s++;slen--; }
	   char* p=s; //parsing position for coordinate string
	   char* isep=strpbrk(s, " \t");
	   if (isep==NULL) isep=strchr(s, ':');
	   if (isep) { //chr (ref) ID ending found
		  p=isep+1;
		  *isep=0;
	       //character after the delimiter can only be a strand if it's followed by another delimiter
		   //e.g. chr1 + 134551-204326 or chr1:+:134551-204326
		  c=*(isep+1);
		  if (strand==0 && (c=='+' || c=='-' || c=='.') && IS_CHR_DELIM(*(isep+2))) {
			  strand=c;
			  p=isep+3;
		  }
		  if (strand==0) {
			  c=*(isep-1); //character before the delimiter could be the strand
			  if (c=='+' || c=='-') { //not '.', sorry
				isep--;
				strand=c;
				*isep=0; //ref is now parsable
			  }
		  }
		  this->refName=Gstrdup(s,isep-1);
	   }
	   //here we are after ref ID (and possibly strand) delimiter
	   char* pend=p;
	   if (isdigit(*pend)) {
		 //parse the start coordinate then
		 do { pend++; } while (isdigit(*pend));
		 c=*pend;
		 *pend=0;
		 this->start=atoi(p);
		 p=pend;
		 *p=c;
	   }
	   while (*p=='-' || *p=='.' || *p==' ' || *p=='\t') ++p;
	   pend=p;
	   while (isdigit(*pend)) pend++;
	   if (pend>p) { //parse the 2nd coordinate
		   c=*pend;
		   *pend=0;
		   this->end=atoi(p);
		   *pend=c;
	   }
	   if (start && end && end<start) Gswap(this->start, this->end);
	   //if (strand==0) { ?
	   c=s[slen-1]; //peek at the end of the string for strand
	   if (c=='+' || c=='-' || c=='.') {
		   if (end || IS_CHR_DELIM(s[slen-2]))
		   strand=c;
		   //slen--;s[slen]=0;
	   }
}


bool GstrEq(const char* a, const char* b) {
	 if (a==NULL || b==NULL) return false;
	 return (strcmp(a, b)==0);
}


#ifdef __CYGWIN__
int strcasecmp (const char *s1, const char *s2) {
  int d = 0;
  for ( ; ; ) {
     const int c1 = tolower(*s1++);
     const int c2 = tolower(*s2++);
     if (((d = c1 - c2) != 0) || (c2 == '\0'))
       break;
  }
  return d;
}

int strncasecmp (const char *s1, const char *s2,
                  size_t n) {
  int d = 0;
  for ( ; n != 0; n--) {
     const int c1 = tolower(*s1++);
     const int c2 = tolower(*s2++);
     if (((d = c1 - c2) != 0) || (c2 == '\0'))
       break;
  }
  return d;
}

#endif


bool GstriEq(const char* a, const char* b) {
	 if (a==NULL || b==NULL) return false;
	 return (strcasecmp(a, b)==0);
}

int Gstricmp(const char* a, const char* b, int n) {
 if (a==NULL || b==NULL) return a==NULL ? -1 : 1;
 if (n>=0) return strncasecmp(a,b,n);
      else return strcasecmp(a,b);
}

int strsplit(char* str, GDynArray<char*>& fields, const char* delim, int maxfields) {
 //splits by placing 0 where any of the delim chars are found, setting fields[] to the beginning
 //of each field (stopping after maxfields); returns number of fields parsed
 int tidx=0;
 bool afterdelim=true;
 int i=0;
 fields.Reset();
 while (str[i]!=0 && tidx<maxfields) {
    if (afterdelim) {
       fields.Add(str+i);
       tidx++;
    }
    afterdelim=false;
    if (chrInStr(str[i],(char*)delim)) {
        str[i]=0;
        i++;
        while (str[i]!=0 && chrInStr(str[i], (char*)delim)) i++;
        afterdelim=true;
        continue;
    }
    i++;
 }
 return tidx;
}

int strsplit(char* str, GDynArray<char*>& fields, const char delim, int maxfields) {
  //splits by placing 0 where delim is found, setting fields[] to the beginning
  //of each field (stopping after maxfields); returns number of fields parsed
  int tidx=0;
  bool afterdelim=true;
  int i=0;
  fields.Reset();
  while (str[i]!=0 && tidx<maxfields) {
     if (afterdelim) {
    	 fields.Add(str+i);
         tidx++;
     }
     afterdelim=false;
     if (str[i]==delim) {
         str[i]=0;
         i++;
         while (str[i]!=0 && str[i]==delim) i++;
         afterdelim=true;
         continue;
     }
     i++;
  }
  return tidx;
}

int strsplit(char* str,  GDynArray<char*>& fields, int maxfields) {
  //splits by placing 0 where delim is found, setting fields[] to the beginning
  //of each field (stopping after maxfields); returns number of fields parsed
  int tidx=0;
  bool afterdelim=true;
  int i=0;
  fields.Reset();
  while (str[i]!=0 && tidx<maxfields) {
     if (afterdelim) {
        fields.Add(str+i);
        tidx++;
     }
     afterdelim=false;
     if (str[i]==' ' || str[i]=='\t') {
         str[i]=0;
         i++;
         while (str[i]!=0 && (str[i]=='\t' || str[i]==' ')) i++;
         afterdelim=true;
         continue;
     }
     i++;
  }
  return tidx;
}


char* Gsubstr(const char* str, char* from, char* to) {
 //extract (and allocate) a substring, including boundaries (from/to)
 if (str==NULL || from==NULL) return NULL;
 if (from[0]==0 || str[0]==0) return newEmptyStr();
 if (from<str) return NULL;
 if (to==NULL) {
    to=from;
    while (to[1]) to++;
    }
 if (to<from) return newEmptyStr();
 int newlen=to-from+1;
 char* subs=NULL;
 GMALLOC(subs, newlen);
 memcpy(subs, str, newlen-1);
 subs[newlen]='\0';
 return subs;
 }

char* replaceStr(char* &str, char* newvalue) {
 if (str!=NULL) GFREE(str);
 if (newvalue==NULL) { return NULL; }
 GMALLOC(str, strlen(newvalue)+1);
 strcpy(str,newvalue);
 return str;
 }

void* Gmemscan(void *mem, unsigned int len,
                   void *part, unsigned int partlen) {
char* p;
unsigned int restlen=len-partlen+1;
void* oldp=mem;
while ( (p=(char*)memchr(oldp, ((char*)part)[0], restlen))!=NULL) {
  //located first char, try to match the rest:
  p++;
  if (memcmp(p, &((char*)part)[1], partlen-1)==0) return p-1;
  //no string match, prepare next iteration
  restlen-=(p-(char*)oldp);
  oldp=p;
  }//while
return NULL;
}

//rindex function is missing on some platforms ?
char* rstrchr(char* str, char ch) {  /* returns a pointer to the rightmost
  occurence of ch in str  */
 char *p;
 if (str==NULL) return NULL;
 p=str+strlen(str)-1;
 while (p>=str) {
    if (*p==ch) return p;
    p--;
    }
 return NULL;
}



/* DOS/UNIX safer fgets : reads a text line from a (binary) file and
  update the file position accordingly and the buffer capacity accordingly.
  The given buf is resized to read the entire line in memory
    -- even when it's abnormally long
  */
char* fgetline(char* & buf, int& buf_cap, FILE *stream, off_t* f_pos, int* linelen) {
  //reads a char at a time until \n and/or \r are encountered
  int c=0;
  GDynArray<char> arr(buf, buf_cap);
  off_t fpos=(f_pos!=NULL) ? *f_pos : 0;
  while ((c=getc(stream))!=EOF) {
    if (c=='\n' || c=='\r') {
       if (c=='\r') {
         if ((c=getc(stream))!='\n') ungetc(c,stream);
                                else fpos++;
         }
       fpos++;
       break;
       }
    fpos++;
    arr.Push((char)c);
    } //while i<buf_cap-1
  //if (linelen!=NULL) *linelen=i;
  if (linelen!=NULL) *linelen=arr.Count();
  if (f_pos!=NULL) *f_pos=fpos;
  //if (c==EOF && i==0) return NULL;
  if (c==EOF && arr.Count()==0) return NULL;
  arr.Push('\0');
  buf=arr();
  buf_cap=arr.Capacity();
  return buf;
  }

char* GLineReader::getLine(FILE* stream, off_t& f_pos) {
   if (pushed) { pushed=false; return buf(); }
   //reads a char at a time until \n and/or \r are encountered
   int c=0;
   textlen=0;
   buf.Reset(); //len = 0
   while ((c=getc(stream))!=EOF) {
     if (c=='\n' || c=='\r') {
       textlen=buf.Count();
       buf.Push('\0');
       if (c=='\r') { //DOS file -- special case
         if ((c=getc(stream))!='\n') ungetc(c,stream);
                                else f_pos++;
         }
       f_pos++;
       lcount++;
       return buf();
     }
     f_pos++;
     buf.Push(c);
     } //while i<buf_cap-1
   if (c==EOF) {
     isEOF=true;
     textlen=buf.Count();
     if (buf.Count()==0) return NULL;
     }
   textlen=buf.Count();
   buf.Push('\0');
   lcount++;
   return buf();
}


//strchr but with a set of chars instead of only one
char* strchrs(const char* s, const char* chrs) {
  if (s==NULL || chrs==NULL || *chrs=='\0' || *s=='\0')
         return NULL;
  unsigned int l=strlen(s);
  unsigned int r=strcspn(s, chrs);
  if (r==l) return NULL;
  return ((char*)s+r);
}

char* upCase(const char* str) {
 if (str==NULL) return NULL;
 int len=strlen(str);
 char* upstr=NULL;
 GMALLOC(upstr, len+1);
 upstr[len]='\0';
 for (int i=0;i<len;i++) upstr[i]=toupper(str[i]);
 return upstr;
 }

char* loCase(const char* str) {
 if (str==NULL) return NULL;
 int len=strlen(str);
 char* lostr=NULL;
 GMALLOC(lostr, len+1);
 lostr[len]='\0';
 for (int i=0;i<len;i++) lostr[i]=tolower(str[i]);
 return lostr;
 }

char* strlower(char * str) {//changes string in place
  if (str==NULL) return NULL;
  int i=0;
  while (str[i]!=0) { str[i]=tolower(str[i]); i++; }
  return str;
}

char* strupper(char * str) {//changes string in place
  if (str==NULL) return NULL;
  int i=0;
  while (str[i]!=0) { str[i]=toupper(str[i]); i++; }
  return str;
}

//test if a char is in a given string (set)
bool chrInStr(char c, const char* str) {
 if (str==NULL || *str=='\0') return false;
 for (const char* p=str; (*p)!='\0'; p++) {
   if ((*p)==c) return true;
   }
 return false;
 }



char* rstrfind(const char* str, const char* substr) {
/* like rindex() for a string */
 int l,i;
 if (str==NULL || *str=='\0') return NULL;
 if (substr==NULL || *substr=='\0') return NULL;
 l=strlen(substr);
 char* p=(char*)str+strlen(str)-l;
   //rightmost position that could match

 while (p>=str) {
    for (i=0; i<l && *(p+i) == *(substr+i); i++) ;
    if (i==l) return p; //found!
    p--;
    }
 return NULL;
}

char* strifind(const char* str,  const char* substr) {
 // case insensitive version of strstr -- finding a string within another
  int l,i;
  if (str==NULL || *str==0) return NULL;
  if (substr==NULL || *substr==0) return NULL;
  l=strlen(substr);
  char* smax=(char*)str+strlen(str)-l;
  //rightmost position that could match
  char* p=(char*)str;
  while (p<=smax) {
     for (i=0; i<l && tolower(*(p+i))==tolower(*(substr+i)); i++) ;
     if (i==l) return p;
     p++;
     }
  return NULL;
}

// tests if string s has the given prefix
bool startsWith(const char* s, const char* prefix) {
 if (prefix==NULL || s==NULL) return false;
 int i=0;
 while (prefix[i]!='\0' && prefix[i]==s[i]) i++;
 return (prefix[i]=='\0');
 }

bool startsiWith(const char* s, const char* prefix) {
 if (prefix==NULL || s==NULL) return false;
 int i=0;
 while (prefix[i]!='\0' && tolower(prefix[i])==tolower(s[i])) i++;
 return (prefix[i]=='\0');
 }


// tests if string s ends with given suffix
bool endsWith(const char* s, const char* suffix) {
 if (suffix==NULL || s==NULL) return false;
 if (suffix[0]==0) return true; //special case: empty suffix
 int j=strlen(suffix)-1;
 int i=strlen(s)-1;
 if (i<j) return false;
 while (j>=0 && s[i]==suffix[j]) { i--; j--; }
 return (j==-1);
}

bool endsiWith(const char* s, const char* suffix) {
 if (suffix==NULL || s==NULL) return false;
 if (suffix[0]==0) return true; //special case: empty suffix
 int j=strlen(suffix)-1;
 int i=strlen(s)-1;
 if (i<j) return false;
 while (j>=0 && tolower(s[i])==tolower(suffix[j])) { i--; j--; }
 return (j==-1);
}

bool trimSuffix(char* s, const char* suffix) {
	if (suffix==NULL || s==NULL) return false;
	if (suffix[0]==0) return true; //special case: empty suffix
	int j=strlen(suffix)-1;
	int i=strlen(s)-1;
	if (i<j) return false;
	while (j>=0 && s[i]==suffix[j]) { i--; j--; }
	if (j==-1) { //suffix found
		s[i+1]='\0'; //cut here
		return true;
	}
	return false;
}

bool trimiSuffix(char* s, const char* suffix) {
	if (suffix==NULL || s==NULL) return false;
	if (suffix[0]==0) return true; //special case: empty suffix
	int j=strlen(suffix)-1;
	int i=strlen(s)-1;
	if (i<j) return false;
	while (j>=0 && tolower(s[i])==tolower(suffix[j])) { i--; j--; }
	if (j==-1) { //suffix found
		s[i+1]='\0'; //cut here
		return true;
	}
	return false;
}


char* reverseChars(char* str, int slen) {
  if (slen==0) slen=strlen(str);
  int l=0;
  int r=slen-1;
  char c;
  while (l<r) {
     c=str[l];str[l]=str[r];
     str[r]=c;
     l++;r--;
     }
  return str;
}

char* rstrstr(const char* rstart, const char *lend, const char* substr) {
 //like strstr, but starts searching from right end, going up to lend and
 //returns a pointer to the last (right) matching character in str
 char *p;
 int l,i;
 l=strlen(substr);
 p=(char*)rstart-l+1;
 while (p>=lend) {
    for (i=0;i<l;i++) if (*(p+i) != *(substr+i)) break;
    if (i==l) return p+l-1;
    p--;
    }
 return NULL;
 }

//hash function used for strings in GHash
int strhash(const char* str){
  int h=0;
  int g;
  while (*str) {
    h=(h<<4)+*str++;
    g=h&0xF0000000;
    if(g) h^=g>>24;
    h&=0x0fffffff;
    }
  GASSERT(h<=0x0fffffff);
  return h;
  }

int djb_hash(const char* cp)
{
    int h = 5381;
    while (*cp)
        h = (int)(33 * h ^ (unsigned char) *cp++);
    return (h & 0x7FFFFFFF); //always positive
    //return h;
    //return absolute value of this int:
    //int mask = (h >> (sizeof(int) * CHAR_BIT - 1));
    //return (h + mask) ^ mask;
}

/* Fowler/Noll/Vo (FNV) hash function, variant 1a */
int fnv1a_hash(const char* cp) {
    int h = 0x811c9dc5;
    while (*cp) {
        h ^= (unsigned char) *cp++;
        h *= 0x01000193;
    }
    //return h;
    return (h & 0x7FFFFFFF);
}

// removes the last part (file or directory name) of a full path
// this is a destructive operation for the given string!!!
// the trailing '/' is guaranteed to be there
void delFileName(char* filepath) {
 char *p, *sep;
 if (filepath==NULL) return;
 for (p=filepath, sep=filepath;*p!='\0';p++)
     if (*p=='/' || *p=='\\') sep=p+1;
 *sep='\0'; // truncate filepath
}

// returns a pointer to the last file or directory name in a full path
const char* getFileName(const char* filepath) {
 const char *p, *sep;
 if (filepath==NULL) return NULL;
 for (p=filepath, sep=filepath;*p!='\0';p++)
     if (*p=='/' || *p=='\\') sep=p+1;
 return sep;
}

// returns a pointer to the file "extension" part in a filename
const char* getFileExt(const char* filepath) {
 const char *p, *dp, *sep;
 if (filepath==NULL) return NULL;
 for (p=filepath, dp=filepath, sep=filepath;*p!='\0';p++) {
     if (*p=='.') dp=p+1;
       else if (*p=='/' || *p=='\\')
                  sep=p+1;
     }
 return (dp>sep) ? dp : NULL ;
}

int fileExists(const char* fname) {
  struct stat stFileInfo;
  int r=0;
  // Attempt to get the path attributes
  int fs = stat(fname,&stFileInfo);
  if (fs == 0) {
      r=3;
      // We were able to get the file attributes
      // so the path exists
      if (S_ISREG (stFileInfo.st_mode)) {
         r=2;
         }
      if (S_ISDIR (stFileInfo.st_mode)) {
          r=1;
          }
      }
  return r;
}

int64 fileSize(const char* fpath) {
#ifdef _WIN32
    WIN32_FILE_ATTRIBUTE_DATA fad;
    if (!GetFileAttributesEx(fpath, GetFileExInfoStandard, &fad))
        return -1; // error condition, could call GetLastError to find out more
    LARGE_INTEGER size;
    size.HighPart = fad.nFileSizeHigh;
    size.LowPart = fad.nFileSizeLow;
    return size.QuadPart;
#else
  struct stat results;
  if (stat(fpath, &results) == 0)
      // The size of the file in bytes is in
      return (int64)results.st_size;
  else
    //An error occurred
    //GMessage("Error at stat(%s)!\n", fpath);
    return -1;
#endif
}

bool parseNumber(char* &p, double& v) {
 //skip any spaces..
 while (*p==' ' || *p=='\t') p++;
 char* start=p;
 /*if (*p=='-') p++;
       else if (*p=='+') { p++;start++; }*/

 /* while ((*p>='1' && *p<='9') || *p=='0' ||
          *p=='.' || *p=='-' || tolower(*p)=='e') p++; */
 int numlen=strspn(start, "0123456789eE.-+");
 p=start+numlen;
 //now p is on a non-digit;
 if (*start=='-' && p==start+1) return false;
 char saved=*p;
 *p='\0';
 char* endptr=p;
 v=strtod(start,&endptr);
 *p=saved;
 if (endptr!=p) return false;
 return true;
}

bool parseDouble(char* &p, double& v) {
 return parseNumber(p,v);
}

bool parseFloat(char* &p, float& v) {
 double dv;
 bool parsed=parseNumber(p,dv);
 if (parsed) v=(float)dv;
 return parsed;
}

bool parseInt(char* &p, int& i) { //pointer p is advanced after the number
 while (*p==' ' || *p=='\t') p++;
 char* start=p;
 char* p0=p;
 if (*p=='-') p++;
      else if (*p=='+') { p++;start++; }
 char* atdigits=p;
 while (*p>='0' && *p<='9') p++;
 //now p should be past the digits
 if (atdigits==p) {//no digits found!
	 p=p0;
	 return false;
 }
 char* endptr=NULL;
 long l=strtol(start,&endptr,10);
 i=(int)l;
 if (endptr!=p || endptr==start || i!=l) {
	 p=p0;
	 return false;
 }
 return true;
}

bool strToInt(char* p, int& i) {
	 while (*p==' ' || *p=='\t') p++;
	 char* start=p;
	 if (*p=='-') p++;
	      else if (*p=='+') { p++;start++; }
	 char* atdigits=p;
	 while (*p>='0' && *p<='9') p++;
	 //now p should be past the digits
	 if (atdigits==p) //no digits found!
		 return false;
	 char* endptr=NULL;
	 long l=strtol(start,&endptr,10);
	 i=(int)l;
	 if (endptr!=p || endptr==start || i!=l)
		 return false;
	 return true;
}

bool strToUInt(char* p, uint& i) {
	while (*p==' ' || *p=='\t') p++;
	char* start=p;
	if (*p=='-') return false;
	else if (*p=='+') { p++;start++; }
	while (*p>='0' && *p<='9') p++;
	//now p is on a non-digit;
	if (start==p) return false;
	char* endptr=NULL;
	unsigned long l=strtoul(start,&endptr,10);
	i=(uint) l;
	if (endptr!=p || endptr==start || i!=l)
		return false;
	return true;
}


bool parseUInt(char* &p, uint& i) { //pointer p is advanced after the number
 while (*p==' ' || *p=='\t') p++;
 char* p0=p;
 char* start=p;
 if (*p=='-') return false;
       else if (*p=='+') { p++;start++; }
 while (*p>='0' && *p<='9') p++;
 //now p is on a non-digit;
 if (start==p) {
	 p=p0;
	 return false;
 }
 char* endptr=NULL;
 unsigned long l=strtoul(start,&endptr,10);
 i=(uint) l;
 if (endptr!=p || endptr==start || i!=l) {
	 p=p0;
	 return false;
 }
 return true;
}

bool parseHex(char* &p, uint& i) {
 //skip initial spaces/prefix
 while (*p==' ' || *p=='\t' || *p=='0' || *p=='x') p++;
 char* start=p;
 if (*p=='-') return false;
       else if (*p=='+') { p++;start++; }
 while (isxdigit(*p)) p++;
 //now p is on a non-hexdigit;
 if (p==start+1) return false;
 char saved=*p;
 *p='\0';
 char* endptr=p;
 unsigned long l=strtoul(start,&endptr,16);
 i=(uint) l;
 *p=saved;
 if (endptr!=p || i!=l) return false;
 return true;
}

//write a formatted fasta record, fasta formatted
void writeFasta(FILE *fw, const char* seqid, const char* descr,
        const char* seq, int linelen, int seqlen) {
  fflush(fw);
  // write header line only if given!
  if (seqid!=NULL) {
    if (descr==NULL || descr[0]==0)
             fprintf(fw,">%s\n",seqid);
        else fprintf(fw,">%s %s\n",seqid, descr);
    }
  fflush(fw);
  if (seq==NULL || *seq==0) return; //nothing to print
  if (linelen==0) { //unlimited line length: write the whole sequence on a line
     if (seqlen>0)
             fwrite((const void*)seq, 1, seqlen,fw);
        else fprintf(fw,"%s",seq);
     fprintf(fw,"\n");
     fflush(fw);
     return;
     }
  int ilen=0;
  if (seqlen>0) { //seq length given, so we know when to stop
    for (int i=0; i < seqlen; i++, ilen++) {
            if (ilen == linelen) {
                 fputc('\n', fw);
                 ilen = 0;
                 }
            fputc(seq[i], fw);
            }
    fputc('\n', fw);
    }
  else { //seq length not given, stop when 0 encountered
    for (int i=0; seq[i]!=0; i++, ilen++) {
            if (ilen == linelen) {
                 fputc('\n', fw);
                 ilen = 0;
                 }
            fputc(seq[i], fw);
            } //for
    fputc('\n', fw);
    }
  fflush(fw);
 }



char* commaprintnum(uint64 n) {
  char retbuf[48];
  int comma = ',';
  char *p = &retbuf[sizeof(retbuf)-1];
  int i = 0;
  *p = '\0';
  do {
    if(i%3 == 0 && i != 0)
        *--p = comma;
    *--p = '0' + n % 10;
    n /= 10;
    i++;
  } while(n != 0);
  return Gstrdup(p);
}