gclib/gclib/GBase.h

#ifndef G_BASE_DEFINED
#define G_BASE_DEFINED
#ifndef _POSIX_SOURCE
//mostly for MinGW
#define _POSIX_SOURCE
#endif
#ifdef HAVE_CONFIG_H
#include "config.h"
#endif
#include <string.h>
#include <stdlib.h>
#include <stdio.h>
#include <math.h>
#include <limits.h>
#include <sys/types.h>
#include <sys/stat.h>
#include <stdint.h>

#if defined __WIN32__ || defined WIN32 || defined _WIN32 || defined _WIN32_
  #ifndef __WIN32__
    #define __WIN32__
  #endif
  #include <windows.h>
  #include <io.h>
  #define CHPATHSEP '\\'
  #undef off_t
  #define off_t int64_t
  #ifdef _fseeki64
    #define fseeko(stream, offset, origin) _fseeki64(stream, offset, origin)
  #else
    /*
    #define _DEFINE_WIN32_FSEEKO
    int fseeko(FILE *stream, off_t offset, int whence);
    */
    #define fseeko fseek
  #endif
  #ifdef _ftelli64
    #define ftello(stream) _ftelli64(stream)
  #else
    /*
    #define _DEFINE_WIN32_FTELLO
    off_t ftello(FILE *stream);
    */
    #define ftello ftell
  #endif
 #else
  #define CHPATHSEP '/'
  #include <unistd.h>
#endif

#ifndef fseeko
 #define fseeko fseek
#endif
#ifndef ftello
 #define ftello ftell
#endif

#ifdef DEBUG
#undef NDEBUG
#endif

typedef int32_t int32;
typedef uint32_t uint32;

typedef unsigned char uchar;
typedef unsigned char byte;

#ifndef MAXUINT
#define MAXUINT ((unsigned int)-1)
#endif

#ifndef MAXINT
#define MAXINT INT_MAX
#endif

#ifndef MAX_UINT
#define MAX_UINT ((unsigned int)-1)
#endif

#ifndef MAX_INT
#define MAX_INT INT_MAX
#endif

typedef int64_t int64;
typedef uint64_t uint64;

/****************************************************************************/

#ifndef EXIT_FAILURE
#define EXIT_FAILURE 1
#endif

#ifndef EXIT_SUCCESS
#define EXIT_SUCCESS 0
#endif

/****************************************************************************/
#define ERR_ALLOC "Error allocating memory.\n"

//-------------------

// Debug helpers
#ifndef NDEBUG
 #define GASSERT(exp) ((exp)?((void)0):(void)GAssert(#exp,__FILE__,__LINE__))
 #ifdef TRACE
  #define GTRACE(exp)  (GMessage exp)
 #else
  #define GTRACE(exp)  ((void)0)
 #endif
#else
 #define GASSERT(exp) ((void)0)
 #define GTRACE(exp)  ((void)0)
#endif

#define GERROR(exp) (GError exp)
/**********************************  Macros  ***********************************/
// Abolute value
#define GABS(val) (((val)>=0)?(val):-(val))

// Min and Max
#define GMAX(a,b) (((a)>(b))?(a):(b))
#define GMIN(a,b) (((a)>(b))?(b):(a))

// Min of three
#define GMIN3(x,y,z) ((x)<(y)?GMIN(x,z):GMIN(y,z))

// Max of three
#define GMAX3(x,y,z) ((x)>(y)?GMAX(x,z):GMAX(y,z))

// Return minimum and maximum of a, b
#define GMINMAX(lo,hi,a,b) ((a)<(b)?((lo)=(a),(hi)=(b)):((lo)=(b),(hi)=(a)))

// Clamp value x to range [lo..hi]
#define GCLAMP(lo,x,hi) ((x)<(lo)?(lo):((x)>(hi)?(hi):(x)))

typedef void* pointer;
typedef unsigned int uint;

typedef int GCompareProc(const pointer item1, const pointer item2);
typedef void GFreeProc(pointer item); //usually just delete,
      //but may also support structures with embedded dynamic members

#define GMALLOC(ptr,size)  if (!GMalloc((pointer*)(&ptr),size)) \
                                     GError(ERR_ALLOC)
#define GCALLOC(ptr,size)  if (!GCalloc((pointer*)(&ptr),size)) \
                                     GError(ERR_ALLOC)
#define GREALLOC(ptr,size) if (!GRealloc((pointer*)(&ptr),size)) \
                                     GError(ERR_ALLOC)
#define GFREE(ptr)       GFree((pointer*)(&ptr))

inline char* strMin(char *arg1, char *arg2) {
    return (strcmp(arg1, arg2) < 0)? arg1 : arg2;
}

inline char* strMax(char *arg1, char *arg2) {
    return (strcmp(arg2, arg1) < 0)? arg1 : arg2;
}

inline int iround(double x) {
   return (int)floor(x + 0.5);
}

/****************************************************************************/

inline int Gintcmp(int a, int b) {
 //return (a>b)? 1 : ((a==b)?0:-1);
  return a-b;
}

int Gstrcmp(const char* a, const char* b, int n=-1);
//same as strcmp but doesn't crash on NULL pointers

int Gstricmp(const char* a, const char* b, int n=-1);

//basic swap template function
template<class T> void Gswap(T& lhs, T& rhs) {
 //register T tmp=lhs;
 T tmp=lhs; //requires copy operator
 lhs=rhs;
 rhs=tmp;
}

/// bitCount_32 - this function counts the number of set bits in a value.
/// Ex. CountPopulation(0xF000F000) = 8
/// Returns 0 if the word is zero.
inline uint bitCount_32(uint32_t Value) {
#if __GNUC__ >= 4
    return __builtin_popcount(Value);
#else
    uint32_t v = Value - ((Value >> 1) & 0x55555555);
    v = (v & 0x33333333) + ((v >> 2) & 0x33333333);
    return ((v + (v >> 4) & 0xF0F0F0F) * 0x1010101) >> 24;
#endif
  }

/// bitCount_64 - this function counts the number of set bits in a value,
/// (64 bit edition.)
inline uint bitCount_64(uint64_t Value) {
#if __GNUC__ >= 4
    return __builtin_popcountll(Value);
#else
    uint64_t v = Value - ((Value >> 1) & 0x5555555555555555ULL);
    v = (v & 0x3333333333333333ULL) + ((v >> 2) & 0x3333333333333333ULL);
    v = (v + (v >> 4)) & 0x0F0F0F0F0F0F0F0FULL;
    return uint((uint64_t)(v * 0x0101010101010101ULL) >> 56);
#endif
  }

/// CountTrailingZeros_32 - this function performs the platform optimal form of
/// counting the number of zeros from the least significant bit to the first one
/// bit.  Ex. CountTrailingZeros_32(0xFF00FF00) == 8.
/// Returns 32 if the word is zero.
inline unsigned bitCountTrailingZeros_32(uint32_t Value) {
#if __GNUC__ >= 4
  return Value ? __builtin_ctz(Value) : 32;
#else
  static const unsigned Mod37BitPosition[] = {
    32, 0, 1, 26, 2, 23, 27, 0, 3, 16, 24, 30, 28, 11, 0, 13,
    4, 7, 17, 0, 25, 22, 31, 15, 29, 10, 12, 6, 0, 21, 14, 9,
    5, 20, 8, 19, 18
  };
  return Mod37BitPosition[(-Value & Value) % 37];
#endif
}

// CountTrailingZeros_64 - This function performs the platform optimal form
/// of counting the number of zeros from the least significant bit to the first
/// one bit (64 bit edition.)
/// Returns 64 if the word is zero.
inline unsigned bitCountTrailingZeros_64(uint64_t Value) {
#if __GNUC__ >= 4
  return Value ? __builtin_ctzll(Value) : 64;
#else
  static const unsigned Mod67Position[] = {
    64, 0, 1, 39, 2, 15, 40, 23, 3, 12, 16, 59, 41, 19, 24, 54,
    4, 64, 13, 10, 17, 62, 60, 28, 42, 30, 20, 51, 25, 44, 55,
    47, 5, 32, 65, 38, 14, 22, 11, 58, 18, 53, 63, 9, 61, 27,
    29, 50, 43, 46, 31, 37, 21, 57, 52, 8, 26, 49, 45, 36, 56,
    7, 48, 35, 6, 34, 33, 0
  };
  return Mod67Position[(-Value & Value) % 67];
#endif
}

/**************** Memory management ***************************/

bool GMalloc(pointer* ptr, unsigned long size); // Allocate memory
bool GCalloc(pointer* ptr, unsigned long size); // Allocate and initialize memory
bool GRealloc(pointer* ptr,unsigned long size); // Resize memory
void GFree(pointer* ptr); // Free memory, resets ptr to NULL


int saprintf(char **retp, const char *fmt, ...);

void GError(const char* format,...); // Error routine (aborts program)
void GMessage(const char* format,...);// Log message to stderr
// Assert failed routine:- usually not called directly but through GASSERT
void GAssert(const char* expression, const char* filename, unsigned int lineno);

// ****************** string manipulation *************************
char *Gstrdup(const char* str);
//duplicate a string by allocating a copy for it and returning it
char* Gstrdup(const char* sfrom, const char* sto);
//same as GStrdup, but with an early termination (e.g. on delimiter)

char* Gsubstr(const char* str, char* from, char* to=NULL);
//extracts a substring, allocating it, including boundaries (from/to)

int strsplit(char* str, char** fields, int maxfields, const char* delim);
int strsplit(char* str, char** fields, int maxfields, const char delim);
int strsplit(char* str, char** fields, int maxfields); //splits by tab or space

char* replaceStr(char* &str, char* newvalue);

//conversion: to Lower/Upper case
// creating a new string:
char* upCase(const char* str);
char* loCase(const char* str);
// changing string in place:
char* strlower(char * str);
char* strupper(char * str);

//strstr but for memory zones: scans a memory region
//for a substring:
void* Gmemscan(void *mem, unsigned int len,
                  void *part, unsigned int partlen);

// test if a char is in a string:
bool chrInStr(char c, const char* str);

char* rstrchr(char* str, char ch);
/* returns a pointer to the rightmost
  occurence of ch in str - like rindex for platforms missing it*/

char* strchrs(const char* s, const char* chrs);
//strchr but with a set of chars instead of only one

char* rstrfind(const char* str, const char *substr); 
// like rindex() but for strings;  right side version of strstr()

char* reverseChars(char* str, int slen=0); //in place reversal of string 

char* rstrstr(const char* rstart, const char *lend, const char* substr);
/*the reversed, rightside equivalent of strstr: starts searching
 from right end (rstart), going back to left end (lend) and returns
 a pointer to the last (right) matching character in str */

char* strifind(const char* str,  const char* substr);
// the case insensitive version of strstr -- finding a string within a strin


//Determines if a string begins with a given prefix
//(returns false when any of the params is NULL,
// but true when prefix is '' (empty string)!)
bool startsWith(const char* s, const char* prefix);

bool endsWith(const char* s, const char* suffix);
//Note: returns true if suffix is empty string, but false if it's NULL


// ELF hash function for strings
int strhash(const char* str);


//---- generic base GSeg : genomic segment (interval) --
// coordinates are considered 1-based (so 0 is invalid)
class GSeg {
 public:
  uint start; //start<end always!
  uint end;
  GSeg(uint s=0,uint e=0) {
    if (s>e) { start=e;end=s; }
        else { start=s;end=e; }
    }
  //check for overlap with other segment
  uint len() { return end-start+1; }
  bool overlap(GSeg* d) {
     //return start<d->start ? (d->start<=end) : (start<=d->end);
     return (start<=d->end && end>=d->start);
     }

  bool overlap(GSeg& d) {
     //return start<d.start ? (d.start<=end) : (start<=d.end);
     return (start<=d.end && end>=d.start);
     }

  bool overlap(GSeg& d, int fuzz) {
     //return start<d.start ? (d.start<=end+fuzz) : (start<=d.end+fuzz);
     return (start<=d.end+fuzz && end+fuzz>=d.start);
     }

  bool overlap(uint s, uint e) {
     if (s>e) { Gswap(s,e); }
     //return start<s ? (s<=end) : (start<=e);
     return (start<=e && end>=s);
     }

  //return the length of overlap between two segments
  int overlapLen(GSeg* r) {
     if (start<r->start) {
        if (r->start>end) return 0;
        return (r->end>end) ? end-r->start+1 : r->end-r->start+1;
        }
       else { //r->start<=start
        if (start>r->end) return 0;
        return (r->end<end)? r->end-start+1 : end-start+1;
        }
     }
  int overlapLen(uint rstart, uint rend) {
     if (rstart>rend) { Gswap(rstart,rend); }
     if (start<rstart) {
        if (rstart>end) return 0;
        return (rend>end) ? end-rstart+1 : rend-rstart+1;
        }
       else { //rstart<=start
        if (start>rend) return 0;
        return (rend<end)? rend-start+1 : end-start+1;
        }
     }

  //fuzzy coordinate matching:
  bool coordMatch(GSeg* s, uint fuzz=0) {
    if (fuzz==0) return (start==s->start && end==s->end);
    uint sd = (start>s->start) ? start-s->start : s->start-start;
    uint ed = (end>s->end) ? end-s->end : s->end-end;
    return (sd<=fuzz && ed<=fuzz);
    }
  //comparison operators required for sorting
  bool operator==(GSeg& d){
      return (start==d.start && end==d.end);
      }
  bool operator<(GSeg& d){
     return (start==d.start)?(end<d.end):(start<d.start);
     }
};


//--------------------------------------------------------
// ************** simple line reading class for text files

//GLineReader -- text line reading/buffering class
class GLineReader {
   bool closeFile;
   int len;
   int allocated;
   char* buf;
   bool isEOF;
   FILE* file;
   off_t filepos; //current position
   bool pushed; //pushed back
   int lcount; //line counter (read lines)
 public:
   char* chars() { return buf; }
   char* line() { return buf; }
   int readcount() { return lcount; } //number of lines read
   void setFile(FILE* stream) { file=stream; }
   int length() { return len; }
   int size() { return len; } //same as size();
   bool isEof() {return isEOF; }
   bool eof() { return isEOF; }
   off_t getfpos() { return filepos; }
   off_t getFpos() { return filepos; }
   char* nextLine() { return getLine(); }
   char* getLine() { if (pushed) { pushed=false; return buf; }
                            else return getLine(file);  }
   char* getLine(FILE* stream) {
                 if (pushed) { pushed=false; return buf; }
                          else return getLine(stream, filepos); }
   char* getLine(FILE* stream, off_t& f_pos); //read a line from a stream and update
                           // the given file position
   void pushBack() { if (lcount>0) pushed=true; } // "undo" the last getLine request
            // so the next call will in fact return the same line
   GLineReader(const char* fname) {
      FILE* f=fopen(fname, "rb");
      if (f==NULL) GError("Error opening file '%s'!\n",fname);
      closeFile=true;
      init(f);
      }
   GLineReader(FILE* stream=NULL, off_t fpos=0) {
     closeFile=false;
     init(stream,fpos);
     }
   void init(FILE* stream, off_t fpos=0) {
     len=0;
     isEOF=false;
     allocated=1024;
     GMALLOC(buf,allocated);
     lcount=0;
     buf[0]=0;
     file=stream;
     filepos=fpos;
     pushed=false;
     }
   ~GLineReader() {
     GFREE(buf);
     if (closeFile) fclose(file);
     }
};


/* extended fgets() -  to read one full line from a file and
  update the file position correctly !
  buf will be reallocated as necessary, to fit the whole line
  */
char* fgetline(char* & buf, int& buflen, FILE* stream, off_t* f_pos=NULL, int* linelen=NULL);


//print int/values nicely formatted in 3-digit groups
char* commaprint(uint64 n);

/*********************** File management functions *********************/

// removes the last part (file or directory name) of a full path
// WARNING: this is a destructive operation for the given string!
void delFileName(char* filepath);

// returns a pointer to the last file or directory name in a full path
const char* getFileName(const char* filepath);
// returns a pointer to the file "extension" part in a filename
const char* getFileExt(const char* filepath);


int fileExists(const char* fname);
//returns 0 if file entry doesn't exist
//        1 if it's a directory
//        2 if it's a regular file
//        3 otherwise (?)

int64 fileSize(const char* fpath);

//write a formatted fasta record, fasta formatted
void writeFasta(FILE *fw, const char* seqid, const char* descr,
        const char* seq, int linelen=60, int seqlen=0);

//parses the next number found in a string at the current position
//until a non-digit (and not a '.', 'e','E','-','+') is encountered;
//updates the char* pointer to be after the last digit parsed
bool parseNumber(char* &p, double& v);
bool parseDouble(char* &p, double& v); //just an alias for parseNumber

bool parseInt(char* &p, int& i);
bool parseUInt(char* &p, uint& i);
bool parseHex(char* &p,  uint& i);

#endif /* G_BASE_DEFINED */
Revision:	150
Committed:	Fri Jan 13 17:20:39 2012 UTC (7 years, 6 months ago) by gpertea
File size:	15343 byte(s)
Log Message:	fixed parsing bug for extractAttr(); Gstrcmp() and Gstricmp() take a 3rd optional param to make them work like strncmp()
Line	User	Rev	File contents
1	gpertea	2	#ifndef G_BASE_DEFINED
2			#define G_BASE_DEFINED
3	gpertea	16	#ifndef _POSIX_SOURCE
4			//mostly for MinGW
5			#define _POSIX_SOURCE
6			#endif
7			#ifdef HAVE_CONFIG_H
8			#include "config.h"
9			#endif
10	gpertea	2	#include <string.h>
11			#include <stdlib.h>
12			#include <stdio.h>
13			#include <math.h>
14			#include <limits.h>
15			#include <sys/types.h>
16			#include <sys/stat.h>
17	gpertea	16	#include <stdint.h>
18
19			#if defined __WIN32__ \|\| defined WIN32 \|\| defined _WIN32 \|\| defined _WIN32_
20			#ifndef __WIN32__
21			#define __WIN32__
22			#endif
23	gpertea	2	#include <windows.h>
24	gpertea	16	#include <io.h>
25			#define CHPATHSEP '\\'
26			#undef off_t
27			#define off_t int64_t
28			#ifdef _fseeki64
29			#define fseeko(stream, offset, origin) _fseeki64(stream, offset, origin)
30			#else
31			/*
32			#define _DEFINE_WIN32_FSEEKO
33			int fseeko(FILE *stream, off_t offset, int whence);
34			*/
35			#define fseeko fseek
36			#endif
37			#ifdef _ftelli64
38			#define ftello(stream) _ftelli64(stream)
39			#else
40			/*
41			#define _DEFINE_WIN32_FTELLO
42			off_t ftello(FILE *stream);
43			*/
44			#define ftello ftell
45			#endif
46			#else
47			#define CHPATHSEP '/'
48			#include <unistd.h>
49	gpertea	2	#endif
50
51	gpertea	36	#ifndef fseeko
52			#define fseeko fseek
53			#endif
54			#ifndef ftello
55			#define ftello ftell
56			#endif
57	gpertea	16
58	gpertea	2	#ifdef DEBUG
59			#undef NDEBUG
60			#endif
61
62	gpertea	16	typedef int32_t int32;
63			typedef uint32_t uint32;
64
65	gpertea	2	typedef unsigned char uchar;
66			typedef unsigned char byte;
67
68			#ifndef MAXUINT
69			#define MAXUINT ((unsigned int)-1)
70			#endif
71
72	gpertea	16	#ifndef MAXINT
73			#define MAXINT INT_MAX
74	gpertea	2	#endif
75
76	gpertea	16	#ifndef MAX_UINT
77			#define MAX_UINT ((unsigned int)-1)
78			#endif
79
80			#ifndef MAX_INT
81			#define MAX_INT INT_MAX
82			#endif
83
84			typedef int64_t int64;
85			typedef uint64_t uint64;
86
87	gpertea	2	/****************************************************************************/
88
89			#ifndef EXIT_FAILURE
90			#define EXIT_FAILURE 1
91			#endif
92
93			#ifndef EXIT_SUCCESS
94			#define EXIT_SUCCESS 0
95			#endif
96
97			/****************************************************************************/
98			#define ERR_ALLOC "Error allocating memory.\n"
99
100			//-------------------
101
102			// Debug helpers
103			#ifndef NDEBUG
104			#define GASSERT(exp) ((exp)?((void)0):(void)GAssert(#exp,__FILE__,__LINE__))
105			#ifdef TRACE
106			#define GTRACE(exp) (GMessage exp)
107			#else
108			#define GTRACE(exp) ((void)0)
109			#endif
110			#else
111			#define GASSERT(exp) ((void)0)
112			#define GTRACE(exp) ((void)0)
113			#endif
114
115			#define GERROR(exp) (GError exp)
116			/******************************** Macros *********************************/
117			// Abolute value
118			#define GABS(val) (((val)>=0)?(val):-(val))
119
120			// Min and Max
121			#define GMAX(a,b) (((a)>(b))?(a):(b))
122			#define GMIN(a,b) (((a)>(b))?(b):(a))
123
124			// Min of three
125			#define GMIN3(x,y,z) ((x)<(y)?GMIN(x,z):GMIN(y,z))
126
127			// Max of three
128			#define GMAX3(x,y,z) ((x)>(y)?GMAX(x,z):GMAX(y,z))
129
130			// Return minimum and maximum of a, b
131			#define GMINMAX(lo,hi,a,b) ((a)<(b)?((lo)=(a),(hi)=(b)):((lo)=(b),(hi)=(a)))
132
133			// Clamp value x to range [lo..hi]
134			#define GCLAMP(lo,x,hi) ((x)<(lo)?(lo):((x)>(hi)?(hi):(x)))
135
136			typedef void* pointer;
137			typedef unsigned int uint;
138
139			typedef int GCompareProc(const pointer item1, const pointer item2);
140			typedef void GFreeProc(pointer item); //usually just delete,
141			//but may also support structures with embedded dynamic members
142
143			#define GMALLOC(ptr,size) if (!GMalloc((pointer*)(&ptr),size)) \
144			GError(ERR_ALLOC)
145			#define GCALLOC(ptr,size) if (!GCalloc((pointer*)(&ptr),size)) \
146			GError(ERR_ALLOC)
147			#define GREALLOC(ptr,size) if (!GRealloc((pointer*)(&ptr),size)) \
148			GError(ERR_ALLOC)
149			#define GFREE(ptr) GFree((pointer*)(&ptr))
150
151	gpertea	16	inline char* strMin(char arg1, char arg2) {
152	gpertea	2	return (strcmp(arg1, arg2) < 0)? arg1 : arg2;
153			}
154
155	gpertea	16	inline char* strMax(char arg1, char arg2) {
156			return (strcmp(arg2, arg1) < 0)? arg1 : arg2;
157			}
158
159	gpertea	2	inline int iround(double x) {
160			return (int)floor(x + 0.5);
161			}
162
163			/****************************************************************************/
164
165			inline int Gintcmp(int a, int b) {
166			//return (a>b)? 1 : ((a==b)?0:-1);
167			return a-b;
168			}
169
170	gpertea	150	int Gstrcmp(const char* a, const char* b, int n=-1);
171	gpertea	2	//same as strcmp but doesn't crash on NULL pointers
172
173	gpertea	150	int Gstricmp(const char* a, const char* b, int n=-1);
174	gpertea	2
175	gpertea	144	//basic swap template function
176			template<class T> void Gswap(T& lhs, T& rhs) {
177			//register T tmp=lhs;
178			T tmp=lhs; //requires copy operator
179			lhs=rhs;
180			rhs=tmp;
181			}
182	gpertea	2
183	gpertea	144	/// bitCount_32 - this function counts the number of set bits in a value.
184			/// Ex. CountPopulation(0xF000F000) = 8
185			/// Returns 0 if the word is zero.
186			inline uint bitCount_32(uint32_t Value) {
187			#if __GNUC__ >= 4
188			return __builtin_popcount(Value);
189			#else
190			uint32_t v = Value - ((Value >> 1) & 0x55555555);
191			v = (v & 0x33333333) + ((v >> 2) & 0x33333333);
192			return ((v + (v >> 4) & 0xF0F0F0F) * 0x1010101) >> 24;
193			#endif
194	gpertea	16	}
195	gpertea	2
196	gpertea	144	/// bitCount_64 - this function counts the number of set bits in a value,
197			/// (64 bit edition.)
198			inline uint bitCount_64(uint64_t Value) {
199			#if __GNUC__ >= 4
200			return __builtin_popcountll(Value);
201			#else
202			uint64_t v = Value - ((Value >> 1) & 0x5555555555555555ULL);
203			v = (v & 0x3333333333333333ULL) + ((v >> 2) & 0x3333333333333333ULL);
204			v = (v + (v >> 4)) & 0x0F0F0F0F0F0F0F0FULL;
205			return uint((uint64_t)(v * 0x0101010101010101ULL) >> 56);
206			#endif
207	gpertea	16	}
208	gpertea	2
209	gpertea	144	/// CountTrailingZeros_32 - this function performs the platform optimal form of
210			/// counting the number of zeros from the least significant bit to the first one
211			/// bit. Ex. CountTrailingZeros_32(0xFF00FF00) == 8.
212			/// Returns 32 if the word is zero.
213			inline unsigned bitCountTrailingZeros_32(uint32_t Value) {
214			#if __GNUC__ >= 4
215			return Value ? __builtin_ctz(Value) : 32;
216			#else
217			static const unsigned Mod37BitPosition[] = {
218			32, 0, 1, 26, 2, 23, 27, 0, 3, 16, 24, 30, 28, 11, 0, 13,
219			4, 7, 17, 0, 25, 22, 31, 15, 29, 10, 12, 6, 0, 21, 14, 9,
220			5, 20, 8, 19, 18
221			};
222			return Mod37BitPosition[(-Value & Value) % 37];
223			#endif
224			}
225	gpertea	2
226	gpertea	144	// CountTrailingZeros_64 - This function performs the platform optimal form
227			/// of counting the number of zeros from the least significant bit to the first
228			/// one bit (64 bit edition.)
229			/// Returns 64 if the word is zero.
230			inline unsigned bitCountTrailingZeros_64(uint64_t Value) {
231			#if __GNUC__ >= 4
232			return Value ? __builtin_ctzll(Value) : 64;
233			#else
234			static const unsigned Mod67Position[] = {
235			64, 0, 1, 39, 2, 15, 40, 23, 3, 12, 16, 59, 41, 19, 24, 54,
236			4, 64, 13, 10, 17, 62, 60, 28, 42, 30, 20, 51, 25, 44, 55,
237			47, 5, 32, 65, 38, 14, 22, 11, 58, 18, 53, 63, 9, 61, 27,
238			29, 50, 43, 46, 31, 37, 21, 57, 52, 8, 26, 49, 45, 36, 56,
239			7, 48, 35, 6, 34, 33, 0
240			};
241			return Mod67Position[(-Value & Value) % 67];
242			#endif
243			}
244	gpertea	2
245			/************** Memory management *************************/
246
247			bool GMalloc(pointer* ptr, unsigned long size); // Allocate memory
248			bool GCalloc(pointer* ptr, unsigned long size); // Allocate and initialize memory
249			bool GRealloc(pointer* ptr,unsigned long size); // Resize memory
250			void GFree(pointer* ptr); // Free memory, resets ptr to NULL
251
252
253	gpertea	16	int saprintf(char *retp, const char fmt, ...);
254
255	gpertea	2	void GError(const char* format,...); // Error routine (aborts program)
256			void GMessage(const char* format,...);// Log message to stderr
257			// Assert failed routine:- usually not called directly but through GASSERT
258			void GAssert(const char* expression, const char* filename, unsigned int lineno);
259
260			// **************** string manipulation ***********************
261			char Gstrdup(const char str);
262			//duplicate a string by allocating a copy for it and returning it
263			char* Gstrdup(const char* sfrom, const char* sto);
264			//same as GStrdup, but with an early termination (e.g. on delimiter)
265
266			char* Gsubstr(const char* str, char* from, char* to=NULL);
267			//extracts a substring, allocating it, including boundaries (from/to)
268
269			int strsplit(char* str, char** fields, int maxfields, const char* delim);
270			int strsplit(char* str, char** fields, int maxfields, const char delim);
271			int strsplit(char* str, char** fields, int maxfields); //splits by tab or space
272
273			char* replaceStr(char* &str, char* newvalue);
274
275			//conversion: to Lower/Upper case
276			// creating a new string:
277			char* upCase(const char* str);
278			char* loCase(const char* str);
279			// changing string in place:
280			char* strlower(char * str);
281			char* strupper(char * str);
282
283			//strstr but for memory zones: scans a memory region
284			//for a substring:
285			void* Gmemscan(void *mem, unsigned int len,
286			void *part, unsigned int partlen);
287
288			// test if a char is in a string:
289	gpertea	16	bool chrInStr(char c, const char* str);
290	gpertea	2
291			char* rstrchr(char* str, char ch);
292			/* returns a pointer to the rightmost
293			occurence of ch in str - like rindex for platforms missing it*/
294
295	gpertea	16	char* strchrs(const char* s, const char* chrs);
296	gpertea	2	//strchr but with a set of chars instead of only one
297
298	gpertea	90	char* rstrfind(const char* str, const char *substr);
299			// like rindex() but for strings; right side version of strstr()
300	gpertea	2
301	gpertea	90	char* reverseChars(char* str, int slen=0); //in place reversal of string
302
303	gpertea	16	char* rstrstr(const char* rstart, const char lend, const char substr);
304	gpertea	2	/*the reversed, rightside equivalent of strstr: starts searching
305			from right end (rstart), going back to left end (lend) and returns
306			a pointer to the last (right) matching character in str */
307
308	gpertea	16	char* strifind(const char* str, const char* substr);
309	gpertea	2	// the case insensitive version of strstr -- finding a string within a strin
310
311
312			//Determines if a string begins with a given prefix
313			//(returns false when any of the params is NULL,
314			// but true when prefix is '' (empty string)!)
315	gpertea	16	bool startsWith(const char* s, const char* prefix);
316	gpertea	2
317	gpertea	16	bool endsWith(const char* s, const char* suffix);
318			//Note: returns true if suffix is empty string, but false if it's NULL
319
320
321	gpertea	2	// ELF hash function for strings
322			int strhash(const char* str);
323
324
325
326			//---- generic base GSeg : genomic segment (interval) --
327			// coordinates are considered 1-based (so 0 is invalid)
328			class GSeg {
329			public:
330			uint start; //start<end always!
331			uint end;
332			GSeg(uint s=0,uint e=0) {
333			if (s>e) { start=e;end=s; }
334			else { start=s;end=e; }
335			}
336			//check for overlap with other segment
337			uint len() { return end-start+1; }
338			bool overlap(GSeg* d) {
339	gpertea	16	//return start<d->start ? (d->start<=end) : (start<=d->end);
340			return (start<=d->end && end>=d->start);
341	gpertea	2	}
342
343			bool overlap(GSeg& d) {
344	gpertea	16	//return start<d.start ? (d.start<=end) : (start<=d.end);
345			return (start<=d.end && end>=d.start);
346	gpertea	2	}
347
348			bool overlap(GSeg& d, int fuzz) {
349	gpertea	16	//return start<d.start ? (d.start<=end+fuzz) : (start<=d.end+fuzz);
350			return (start<=d.end+fuzz && end+fuzz>=d.start);
351	gpertea	2	}
352
353			bool overlap(uint s, uint e) {
354	gpertea	144	if (s>e) { Gswap(s,e); }
355	gpertea	16	//return start<s ? (s<=end) : (start<=e);
356			return (start<=e && end>=s);
357	gpertea	2	}
358
359			//return the length of overlap between two segments
360			int overlapLen(GSeg* r) {
361			if (start<r->start) {
362			if (r->start>end) return 0;
363			return (r->end>end) ? end-r->start+1 : r->end-r->start+1;
364			}
365			else { //r->start<=start
366			if (start>r->end) return 0;
367			return (r->end<end)? r->end-start+1 : end-start+1;
368			}
369			}
370			int overlapLen(uint rstart, uint rend) {
371	gpertea	144	if (rstart>rend) { Gswap(rstart,rend); }
372	gpertea	2	if (start<rstart) {
373			if (rstart>end) return 0;
374			return (rend>end) ? end-rstart+1 : rend-rstart+1;
375			}
376			else { //rstart<=start
377			if (start>rend) return 0;
378			return (rend<end)? rend-start+1 : end-start+1;
379			}
380			}
381
382			//fuzzy coordinate matching:
383			bool coordMatch(GSeg* s, uint fuzz=0) {
384			if (fuzz==0) return (start==s->start && end==s->end);
385			uint sd = (start>s->start) ? start-s->start : s->start-start;
386			uint ed = (end>s->end) ? end-s->end : s->end-end;
387			return (sd<=fuzz && ed<=fuzz);
388			}
389			//comparison operators required for sorting
390			bool operator==(GSeg& d){
391			return (start==d.start && end==d.end);
392			}
393			bool operator<(GSeg& d){
394			return (start==d.start)?(end<d.end):(start<d.start);
395			}
396			};
397
398
399
400			//--------------------------------------------------------
401			// ************** simple line reading class for text files
402
403			//GLineReader -- text line reading/buffering class
404			class GLineReader {
405	gpertea	16	bool closeFile;
406	gpertea	2	int len;
407			int allocated;
408			char* buf;
409			bool isEOF;
410			FILE* file;
411			off_t filepos; //current position
412			bool pushed; //pushed back
413			int lcount; //line counter (read lines)
414			public:
415			char* chars() { return buf; }
416			char* line() { return buf; }
417			int readcount() { return lcount; } //number of lines read
418	gpertea	16	void setFile(FILE* stream) { file=stream; }
419	gpertea	2	int length() { return len; }
420			int size() { return len; } //same as size();
421			bool isEof() {return isEOF; }
422			bool eof() { return isEOF; }
423			off_t getfpos() { return filepos; }
424			off_t getFpos() { return filepos; }
425			char* nextLine() { return getLine(); }
426			char* getLine() { if (pushed) { pushed=false; return buf; }
427			else return getLine(file); }
428			char* getLine(FILE* stream) {
429			if (pushed) { pushed=false; return buf; }
430			else return getLine(stream, filepos); }
431			char* getLine(FILE* stream, off_t& f_pos); //read a line from a stream and update
432			// the given file position
433			void pushBack() { if (lcount>0) pushed=true; } // "undo" the last getLine request
434			// so the next call will in fact return the same line
435	gpertea	16	GLineReader(const char* fname) {
436			FILE* f=fopen(fname, "rb");
437			if (f==NULL) GError("Error opening file '%s'!\n",fname);
438			closeFile=true;
439			init(f);
440			}
441	gpertea	2	GLineReader(FILE* stream=NULL, off_t fpos=0) {
442	gpertea	16	closeFile=false;
443			init(stream,fpos);
444			}
445			void init(FILE* stream, off_t fpos=0) {
446	gpertea	2	len=0;
447			isEOF=false;
448			allocated=1024;
449			GMALLOC(buf,allocated);
450			lcount=0;
451			buf[0]=0;
452			file=stream;
453			filepos=fpos;
454			pushed=false;
455			}
456			~GLineReader() {
457			GFREE(buf);
458	gpertea	16	if (closeFile) fclose(file);
459	gpertea	2	}
460			};
461
462
463			/* extended fgets() - to read one full line from a file and
464			update the file position correctly !
465			buf will be reallocated as necessary, to fit the whole line
466			*/
467			char* fgetline(char* & buf, int& buflen, FILE* stream, off_t* f_pos=NULL, int* linelen=NULL);
468
469	gpertea	16
470			//print int/values nicely formatted in 3-digit groups
471			char* commaprint(uint64 n);
472
473	gpertea	2	/********************* File management functions *******************/
474
475	gpertea	16	// removes the last part (file or directory name) of a full path
476			// WARNING: this is a destructive operation for the given string!
477	gpertea	2	void delFileName(char* filepath);
478
479	gpertea	16	// returns a pointer to the last file or directory name in a full path
480			const char* getFileName(const char* filepath);
481			// returns a pointer to the file "extension" part in a filename
482			const char* getFileExt(const char* filepath);
483	gpertea	2
484	gpertea	16
485	gpertea	2	int fileExists(const char* fname);
486			//returns 0 if file entry doesn't exist
487			// 1 if it's a directory
488			// 2 if it's a regular file
489			// 3 otherwise (?)
490
491	gpertea	16	int64 fileSize(const char* fpath);
492	gpertea	2
493	gpertea	16	//write a formatted fasta record, fasta formatted
494			void writeFasta(FILE fw, const char seqid, const char* descr,
495			const char* seq, int linelen=60, int seqlen=0);
496
497	gpertea	2	//parses the next number found in a string at the current position
498			//until a non-digit (and not a '.', 'e','E','-','+') is encountered;
499			//updates the char* pointer to be after the last digit parsed
500			bool parseNumber(char* &p, double& v);
501			bool parseDouble(char* &p, double& v); //just an alias for parseNumber
502
503			bool parseInt(char* &p, int& i);
504			bool parseUInt(char* &p, uint& i);
505			bool parseHex(char* &p, uint& i);
506
507			#endif /* G_BASE_DEFINED */