aio.cpp

#include <cstring>
#include <sys/stat.h>
#include "aio.h"

int aio::fexists(const char* str){///@param str Filename given as a string.
  struct stat buffer ;
  return (stat(str, &buffer )==0 ); /// @return Function returns 1 if file exists.
}

size_t aio::fsize(const char* fname){
  struct stat st ;
  stat(fname,&st);
  return st.st_size;
}

std::vector <char *> dumpedFiles;//small hack for getting a nice vector of outputfiles
FILE *aio::openFile(const char* a,const char* b){
  if(0)
    fprintf(stderr,"[%s] %s %s",__FUNCTION__,a,b);
  char *c = new char[strlen(a)+strlen(b)+1];
  strcpy(c,a);
  strcat(c,b);
  //  fprintf(stderr,"\t-> Dumping file: %s\n",c);
  dumpedFiles.push_back(strdup(c));
  FILE *fp = NULL;
  fp = fopen(c,"w");
  if(fp==NULL){
    fprintf(stderr,"\t-> Problem opening file: \'%s\' check permissions\n",c);
    exit(0);
  }
  delete [] c;
  return fp;
}

BGZF *aio::openFileBG(const char* a,const char* b){

  char *c = new char[strlen(a)+strlen(b)+1];
  strcpy(c,a);
  strcat(c,b);
  dumpedFiles.push_back(strdup(c));
  BGZF *fp = bgzf_open(c,"w6h");
  delete [] c;
  return fp;
}

htsFile *aio::openFileHts(const char* a,const char* b){

  char *c = new char[strlen(a)+strlen(b)+1];
  strcpy(c,a);
  strcat(c,b);
  dumpedFiles.push_back(strdup(c));
  htsFile *fp = hts_open(c,"w");
  delete [] c;
  return fp;
}

htsFile *aio::openFileHtsBcf(const char* a,const char* b){

  char *c = new char[strlen(a)+strlen(b)+1];
  strcpy(c,a);
  strcat(c,b);
  dumpedFiles.push_back(strdup(c));
  htsFile *fp = hts_open(c,"wb");
  delete [] c;
  return fp;
}

FILE *aio::getFILE(const char*fname,const char* mode){
  int writeFile = 0;
  for(size_t i=0;i<strlen(mode);i++)
    if(mode[i]=='w')
      writeFile = 1;
  FILE *fp;
  if(NULL==(fp=fopen(fname,mode))){
    fprintf(stderr,"\t-> Error opening FILE handle for file:%s exiting\n",fname);
    exit(0);
  }
  return fp;
}

//checks that newer is newer than older
int aio::isNewer(const char *newer,const char *older){
   if (strstr(older, "ftp://") == older || strstr(older, "http://") == older)
     return 0;
  //  fprintf(stderr,"newer:%s older:%s\n",newer,older);
  // return 0;
  struct stat one;
  struct stat two;
  stat(newer, &one );
  stat(older, &two );
  
  return one.st_mtime>=two.st_mtime;
}

ssize_t aio::bgzf_write(BGZF *fp, const void *data, size_t length){
  if(length>0)
    return ::bgzf_write(fp,data,length);
  return 0;
}


int aio::tgets(gzFile gz,char**buf,int *l){
  int rlen = 0;
 neverUseGoto:
  char *tok = gzgets(gz,*buf+rlen,*l-rlen);
  if(!tok)
    return rlen;
  int tmp = tok?strlen(tok):0;
  if(tok[tmp-1]!='\n'){
    rlen += tmp;
    *l *= 2;
    *buf = (char*) realloc(*buf,*l);
    goto neverUseGoto;
  }
  rlen += tmp;
  return rlen;
}