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#ifndef G_BASE_DEFINED
#define G_BASE_DEFINED
#define GCLIB_VERSION "0.12.7"
#ifdef HAVE_CONFIG_H
#include "config.h"
#endif
#if defined(__WIN32) || defined(__WIN32__) || defined(_WIN32) || defined(_WIN64) || defined(__MINGW64__) || defined(__WINDOWS__)
#ifndef _WIN32
#define _WIN32
#endif
#ifndef _WIN64
#define _WIN64
#endif
#define __USE_MINGW_ANSI_STDIO 1
//#define __ISO_C_VISIBLE 1999
#endif
#define XSTR(x) STR(x)
#define STR(x) #x
#ifdef _WIN32
#include <windows.h>
#include <io.h>
#define CHPATHSEP '\\'
#undef off_t
#define off_t int64_t
#ifndef popen
#define popen _popen
#endif
/*
#ifndef fseeko
#ifdef _fseeki64
#define fseeko(stream, offset, origin) _fseeki64(stream, offset, origin)
#else
#define fseeko fseek
#endif
#endif
#ifndef ftello
#ifdef _ftelli64
#define ftello(stream) _ftelli64(stream)
#else
#define ftello ftell
#endif
#endif
*/
#else
#define CHPATHSEP '/'
#ifdef __CYGWIN__
#define _BSD_SOURCE
#endif
#include <unistd.h>
#endif
#ifdef DEBUG
#undef NDEBUG
#define _DEBUG 1
#define _DEBUG_ 1
#endif
#include <stdlib.h>
#include <stdio.h>
#include <string.h>
#include <math.h>
#include <limits.h>
#include <sys/types.h>
#include <sys/stat.h>
#include <stdint.h>
#include <stdarg.h>
#include <type_traits>
typedef int64_t int64;
typedef uint64_t uint64;
typedef int32_t int32;
typedef uint32_t uint32;
typedef int16_t int16;
typedef uint16_t uint16;
typedef unsigned char uchar;
typedef uint8_t byte;
typedef unsigned int uint;
typedef void* pointer;
#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
/****************************************************************************/
#ifndef EXIT_FAILURE
#define EXIT_FAILURE 1
#endif
#ifndef EXIT_SUCCESS
#define EXIT_SUCCESS 0
#endif
/****************************************************************************/
#define ERR_ALLOC "Error allocating memory.\n"
//-------------------
#define GEXIT(a) { \
fprintf(stderr, "Error: "); fprintf(stderr, a); \
GError("Exiting from line %i in file %s\n",__LINE__,__FILE__); \
}
// Debug helpers
#ifndef NDEBUG
#define GASSERT(exp) ((exp)?((void)0):(void)GAssert(#exp,__FILE__,__LINE__))
#define GVERIFY(condition) \
if (!(condition)) { \
fprintf(stderr, "Assumption \"%s\"\nFailed in file %s: at line:%i\n", \
#condition,__FILE__,__LINE__); \
GEXIT(#condition);}
#ifdef TRACE
#define GTRACE(exp) (GMessage(exp))
#else
#define GTRACE(exp)
#endif
#else
#define GASSERT(exp)
#define GTRACE(exp)
#define GVERIFY(condition)
#endif
#define GERROR(exp) (GError(exp))
// 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 int GCompareProc(const pointer item1, const pointer item2);
typedef long GFStoreProc(const pointer item1, FILE* fstorage); //for serialization
typedef pointer GFLoadProc(FILE* fstorage); //for deserialization
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);
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);
}
char* Grealpath(const char *path, char *resolved_path);
int Gmkdir(const char *path, bool recursive=true, int perms = (S_IRWXU | S_IRGRP | S_IXGRP | S_IROTH | S_IXOTH));
void Gmktempdir(char* templ);
bool haveStdInput(); //if stdin is from a pipe or redirection
/****************************************************************************/
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);
bool GstrEq(const char* a, const char* b);
bool GstriEq(const char* a, const char* b);
//basic swap template function
template<class T> void Gswap(T& lhs, T& rhs) {
T tmp=lhs; //requires copy operator
lhs=rhs;
rhs=tmp;
}
// use std::is_pointer from <type_traits> in C++11 instead
/*
template<typename T>
struct isPointer { static const bool value = false; };
template<typename T>
struct isPointer<T*> { static const bool value = true; };
*/
//check if type T is resolved as a pointer to char
template<class T>
struct is_char_ptr : std::integral_constant <
bool,
std::is_same<char const *, typename std::decay<T>::type>::value ||
std::is_same<char *, typename std::decay<T>::type>::value
> {};
inline void GFree(pointer* ptr){
GASSERT(ptr);
if (*ptr) free(*ptr);
*ptr=NULL;
}
inline bool GMalloc(pointer* ptr,unsigned long size){
//GASSERT(ptr);
if (size!=0)
*ptr=malloc(size);
return *ptr!=NULL;
}
// Allocate 0-filled memory
inline bool GCalloc(pointer* ptr,unsigned long size){
GASSERT(ptr);
*ptr=calloc(size,1);
return *ptr!=NULL;
}
// Resize memory
inline bool GRealloc(pointer* ptr,unsigned long size){
//GASSERT(ptr);
if (size==0) {
GFree(ptr);
return true;
}
if (*ptr==NULL) {//simple malloc
void *p=malloc(size);
if (p != NULL) {
*ptr=p;
return true;
}
else return false;
}//malloc
else {//realloc
void *p=realloc(*ptr,size);
if (p) {
*ptr=p;
return true;
}
return false;
}
}
template<class T> T* GDupAlloc(T& data) {
T* tmp=NULL;
if (!GMalloc((pointer*) tmp, sizeof(T)))
GError(ERR_ALLOC);
memcpy((void*)tmp, (void*)&data, sizeof(T));
return tmp;
}
// ****************** basic string manipulation *************************
char *Gstrdup(const char* str, int xtracap=0); //string duplication with extra capacity added
//duplicate a string by allocating a copy for it (+xtracap heap room) and returning the new pointer
//caller is responsible for deallocating the returned pointer!
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)
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);
FILE* Gfopen(const char *path, char *mode=NULL);
// 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);
// case insensitive version of strstr -- finding a string within another string
// returns NULL if not found
//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 startsiWith(const char* s, const char* prefix); //case insensitive
bool endsWith(const char* s, const char* suffix);
//Note: returns true if suffix is empty string, but false if it's NULL
bool endsiWith(const char* s, const char* suffix); //case insensitive version
//like endsWith but also remove the suffix if found
//returns true if the given suffix was found and removed
bool trimSuffix(char* s, const char* suffix);
//case insensitive version:
bool trimiSuffix(char* s, const char* suffix);
// ELF hash function for strings
int strhash(const char* str);
//alternate hash functions:
int fnv1a_hash(const char* cp);
int djb_hash(const char* cp);
//---- generic base GSeg : genomic segment (interval) --
// coordinates are considered 1-based (so 0 is invalid)
struct GSeg {
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->end && end>=d->start);
}
bool overlap(GSeg& d) {
return (start<=d.end && end>=d.start);
}
bool overlap(GSeg& d, int fuzz) {
return (start<=d.end+fuzz && end+fuzz>=d.start);
}
bool overlap(uint x) {
return (start<=x && x<=end);
}
bool overlap(uint s, uint e) {
if (s>e) { Gswap(s,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;
}
}
bool contains(GSeg* s) {
return (start<=s->start && end>=s->end);
}
bool contained(GSeg* s) {
return (s->start<=start && s->end>=end);
}
bool equals(GSeg& d){
return (start==d.start && end==d.end);
}
bool equals(GSeg* d){
return (start==d->start && end==d->end);
}
//fuzzy coordinate matching:
bool coordMatch(GSeg* s, uint fuzz=0) { //caller must check for s!=NULL
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);
}
void expand(int by) { //expand in both directions
start-=by;
end+=by;
}
void expandInclude(uint rstart, uint rend) { //expand to include given coordinates
if (rstart>rend) { Gswap(rstart,rend); }
if (rstart<start) start=rstart;
if (rend>end) end=rend;
}
//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);
}
};
struct GRangeParser: GSeg {
char* refName=NULL;
char strand=0;
void parse(char* s);
GRangeParser(char* s=NULL):GSeg(0, 0) {
if (s) parse(s);
}
~GRangeParser() {
GFREE(refName);
}
};
//basic dynamic array template for primitive types
//which can only grow (reallocate) as needed
//optimize index test
#define GDynArray_INDEX_ERR "Error: use of index (%d) in GDynArray of size %d!\n"
#if defined(NDEBUG) || defined(NODEBUG) || defined(_NDEBUG) || defined(NO_DEBUG)
#define GDynArray_TEST_INDEX(x)
#else
#define GDynArray_TEST_INDEX(x) \
if (fCount==0 || x>=fCount) GError(GDynArray_INDEX_ERR, x, fCount)
#endif
#define GDynArray_MAXCOUNT UINT_MAX-1
#define GDynArray_NOIDX UINT_MAX
//basic dynamic array (vector) template for simple/primitive types or structs
//Warning: uses malloc so it will never call the item's default constructor when growing
template<class OBJ> class GDynArray {
protected:
bool byptr; //in-place copy (pointer) takeover of existing OBJ[]
OBJ *fArray;
uint fCount;
uint fCapacity; // size of allocated memory
const static uint dyn_array_defcap = 16; // initial capacity (in elements)
public:
GDynArray(int initcap=dyn_array_defcap):byptr(false), fArray(NULL), fCount(0),
fCapacity(initcap) { // constructor
GMALLOC(fArray, fCapacity*sizeof(OBJ));
}
GDynArray(const GDynArray &a):byptr(false), fArray(NULL),
fCount(a.fCount), fCapacity(a.fCapacity) { // copy constructor
GMALLOC(fArray, sizeof(OBJ)*a.fCapacity);
memcpy(fArray, a.fArray, sizeof(OBJ)* a.fCapacity);
}
GDynArray(OBJ* ptr, uint pcap):byptr(true), fArray(ptr), fCount(0), fCapacity(pcap) {
//this will never deallocate the passed pointer
}
virtual ~GDynArray() { if (!byptr) { GFREE(fArray); } }
GDynArray& operator = (const GDynArray &a) { // assignment operator
if (this == &a) return *this;
if (a.fCount == 0) {
Clear();
return *this;
}
growTo(a.fCapacity); //set size
memcpy(fArray, a.fArray, sizeof(OBJ)*a.fCount);
return *this;
}
OBJ& operator[] (uint idx) {// get array item
GDynArray_TEST_INDEX(idx);
return fArray[idx];
}
void Grow() {
int delta = (fCapacity>16) ? (fCapacity>>2) : 2;
if (GDynArray_MAXCOUNT-delta<=fCapacity)
delta=GDynArray_MAXCOUNT-fCapacity;
if (delta<=1) GError("Error at GDynArray::Grow(): max capacity reached!\n");
growTo(fCapacity + delta);
}
#define GDynArray_ADD(item) \
if (fCount==MAX_UINT-1) GError("Error at GDynArray: cannot add item, maximum count reached!\n"); \
if ((++fCount) > fCapacity) Grow(); \
fArray[fCount-1] = item;
uint Add(OBJ* item) { // Add item to the end of array
//element given by pointer
if (item==NULL) return GDynArray_NOIDX;
GDynArray_ADD( (*item) );
return (fCount-1);
}
uint Add(OBJ item) { // Add OBJ copy to the end of array
GDynArray_ADD(item);
return (fCount-1);
}
uint Push(OBJ item) { //same as Add
GDynArray_ADD(item);
return (fCount-1);
}
OBJ Pop() { //shoddy.. Do NOT call this for an empty array!
if (fCount==0) return (OBJ)NULL; //a NULL cast operator is required
--fCount;
return fArray[fCount];
}
uint Count() { return fCount; } // get size of array (elements)
uint Capacity() { return fCapacity; }
void growTo(uint newcap) {
if (newcap==0) { Clear(); return; }
if (newcap <= fCapacity) return; //never shrink! (use Pack() for shrinking)
GREALLOC(fArray, newcap*sizeof(OBJ));
fCapacity=newcap;
}
void append(OBJ* arr, uint count) {
//fast adding of a series of objects
growTo(fCount+count);
memcpy(fArray+fCount, arr, count*sizeof(OBJ));
fCount+=count;
}
void append(GDynArray<OBJ> arr) {
//fast adding of a series of objects
growTo(fCount+arr.fCount);
memcpy(fArray+fCount, arr.fArray, arr.fCount*sizeof(OBJ));
fCount+=arr.fCount;
}
void Trim(int tcount=1) {
//simply cut (discard) the last tcount items
//new Count is now fCount-tcount
//does NOT shrink capacity accordingly!
if (fCount>=tcount) fCount-=tcount;
}
void Pack() { //shrink capacity to fCount+dyn_array_defcap
if (fCapacity-fCount<=dyn_array_defcap) return;
int newcap=fCount+dyn_array_defcap;
GREALLOC(fArray, newcap*sizeof(OBJ));
fCapacity=newcap;
}
void zPack(OBJ z) { //shrink capacity to fCount+1 and adds a z terminator
if (fCapacity-fCount<=1) { fArray[fCount]=z; return; }
int newcap=fCount+1;
GREALLOC(fArray, newcap*sizeof(OBJ));
fCapacity=newcap;
fArray[fCount]=z;
}
inline void Shrink() { Pack(); }
void Delete(uint idx) {
GDynArray_TEST_INDEX(idx);
--fCount;
if (idx<fCount)
memmove(&fArray[idx], &fArray[idx+1], (fCount-idx)*sizeof(OBJ));
}
inline void Remove(uint idx) { Delete(idx); }
void Clear() { // clear array, shrinking its allocated memory
fCount = 0;
GREALLOC(fArray, sizeof(OBJ)*dyn_array_defcap);
// set initial memory size again
fCapacity = dyn_array_defcap;
}
void Reset() {// fast clear array WITHOUT deallocating it
fCount = 0;
}
OBJ* operator()() { return fArray; }
//use methods below in order to prevent deallocation of fArray pointer on destruct
//could be handy for adopting stack objects (e.g. cheap dynamic strings)
void ForgetPtr() { byptr=true; }
void DetachPtr() { byptr=true; }
};
int strsplit(char* str, GDynArray<char*>& fields, const char* delim, int maxfields=MAX_INT);
//splits a string 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 strsplit(char* str, GDynArray<char*>& fields, const char delim, int maxfields=MAX_INT);
//splits a string by placing 0 where the delim char is found, setting fields[] to the beginning
//of each field (stopping after maxfields); returns number of fields parsed
int strsplit(char* str, GDynArray<char*>& fields, int maxfields=MAX_INT); //splits by tab or space
//splits a string by placing 0 where tab or space is found, setting fields[] to the beginning
//of each field (stopping after maxfields); returns number of fields parsed
// ************** simple line reading class for text files
//GLineReader -- text line reading/buffering class
class GLineReader {
bool closeFile;
//int len;
//int allocated;
GDynArray<char> buf;
int textlen; //length of actual text, without newline character(s)
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 blength() { return buf.Count(); } //binary/buffer length, including newline character(s)
int charcount() { return buf.Count(); } //line length, including newline character(s)
int tlength() { return textlen; } //text length excluding newline character(s)
int linelen() { return textlen; } //line length, excluding newline character(s)
//int size() { return buf.Count(); } //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):closeFile(false),buf(1024), textlen(0),
isEOF(false),file(NULL),filepos(0), pushed(false), lcount(0) {
FILE* f=fopen(fname, "rb");
if (f==NULL) GError("Error opening file '%s'!\n",fname);
closeFile=true;
file=f;
}
GLineReader(FILE* stream=NULL, off_t fpos=0):closeFile(false),buf(1024),
textlen(0), isEOF(false),file(stream),
filepos(fpos), pushed(false), lcount(0) {
}
~GLineReader() {
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* commaprintnum(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 path doesn't exist
// 1 if it's a directory
// 2 if it's a regular file
// 3 something else (but entry exists)
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 parseFloat(char* &p, float& v);
bool strToInt(char* p, int& i);
bool strToUInt(char* p, uint& i);
bool parseInt(char* &p, int& i); //advance pointer p after the number
bool parseUInt(char* &p, uint& i); //advance pointer p after the number
bool parseHex(char* &p, uint& i);
#endif /* G_BASE_DEFINED */
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