// --------------------------------------------------------------------------------//
// MAIN //
// --------------------------------------------------------------------------------//
int main(int argc, char* argv[])
{
// process command-line arguments
CmdLine *cmdLine = InitCmdLine();
int next_arg = cmdLine->Read(argv,argc);
if (HELP) { cmdLine->Usage("key-expand <STDIN>|FILE"); exit(1); }
MESSAGES(VERBOSE);
char *INPUT = next_arg==argc ? NULL : argv[next_arg];
// process
FileBufferText buffer(INPUT);
for (long int r=0; buffer.Next()!=NULL; r++) {
char *inp = buffer.Get();
char *key = GetNextToken(&inp," \t");
while (inp[0]!=0) {
char *val = GetNextToken(&inp," \t");
printf("%s\t%s\n", key, val);
}
}
// cleanup
delete cmdLine;
return 0;
}
// --------------------------------------------------------------------------------//
// MAIN //
// --------------------------------------------------------------------------------//
int main(int argc, char* argv[])
{
// process command-line arguments
if (argc<2) { Usage(); exit(1); }
char *method = argv[1];
CmdLine *cmdLine = InitCmdLine(method);
//--------------------------------------------------------------------------------------//
// OPTION -permute: permute rows //
//--------------------------------------------------------------------------------------//
if (strcmp(method,"-permute")==0) {
// read options
cmdLine->Read(argv+1,argc-1);
MESSAGES(VERBOSE);
// initialize random generator
unsigned long int seed = RND_SEED+getpid()+time(NULL);
gsl_rng *RANDOM_GENERATOR = InitRandomGenerator(seed);
// read input
long int n_lines;
char **L;
FILE *fp = LoadStdIn(&n_lines,BUFFER_SIZE);
if (n_lines==0) return 0;
ALLOCATE1D(L,n_lines,char *);
FileBufferText *buffer = new FileBufferText(fp,BUFFER_SIZE);
Progress PRG("Reading input rows...",n_lines);
for (long int n=0; n<n_lines; n++) {
L[n] = StrCopy(buffer->Next());
PRG.Check();
}
PRG.Done();
// permute
long int *seq;
ALLOCATE1D(seq,n_lines,long int);
for (long int k=0; k<n_lines; k++) seq[k] = k;
gsl_ran_shuffle(RANDOM_GENERATOR,seq,n_lines,sizeof(long int));
// print output
Progress PRG1("Printing output rows...",n_lines);
for (long int n=0; n<n_lines; n++) {
printf("%s\n", L[seq[n]]);
PRG1.Check();
}
PRG1.Done();
// cleanup
FREE1D(seq);
delete RANDOM_GENERATOR;
delete buffer;
}
//--------------------------------------------------------------------------------------//
// OPTION -resample: resample rows //
//--------------------------------------------------------------------------------------//
else if (strcmp(method,"-resample")==0) {
// read options
cmdLine->Read(argv+1,argc-1);
MESSAGES(VERBOSE);
// initialize random generator
unsigned long int seed = (RND_SEED==0)?(getpid()+time(NULL)):RND_SEED;
gsl_rng *RANDOM_GENERATOR = InitRandomGenerator(seed);
// read input
long int n_lines;
char **L;
FILE *fp = LoadStdIn(&n_lines,BUFFER_SIZE);
if (n_lines==0) return 0;
ALLOCATE1D(L,n_lines,char *);
FileBufferText *buffer = new FileBufferText(fp,BUFFER_SIZE);
Progress PRG("Reading input rows...",n_lines);
for (long int n=0; n<n_lines; n++) {
L[n] = StrCopy(buffer->Next());
PRG.Check();
}
PRG.Done();
// print output
if (N_SAMPLES<=0) N_SAMPLES = n_lines;
Progress PRG1("Printing output rows...",N_SAMPLES);
for (long int n=0; n<N_SAMPLES; n++) {
long int k = gsl_rng_uniform_int(RANDOM_GENERATOR,n_lines);
printf("%s\n", L[k]);
PRG1.Check();
}
PRG1.Done();
// cleanup
delete RANDOM_GENERATOR;
delete buffer;
}
//--------------------------------------------------------------------------------------//
// OPTION -number: do row numbering //
//--------------------------------------------------------------------------------------//
else if (strcmp(method,"-number")==0) {
// read options
cmdLine->Read(argv+1,argc-1);
MESSAGES(VERBOSE);
// read input
FileBufferText buffer((char*)NULL,BUFFER_SIZE);
Progress PRG("Reading input rows...",1);
long int id = HEADER?0:1;
for (char *inp=buffer.Next(); inp!=NULL; inp=buffer.Next()) {
if (id==0) printf("\t");
else printf("%s%012ld\t", PREFIX, id);
printf("%s\n", inp);
id++;
PRG.Check();
}
PRG.Done();
}
//--------------------------------------------------------------------------------------//
// OTHER OPTIONS //
//--------------------------------------------------------------------------------------//
else {
// read options
int next_arg = cmdLine->Read(argv,argc);
MESSAGES(VERBOSE);
// allocate buffer
char *BUFFER = (char *) malloc(BUFFER_SIZE*sizeof(char));
if (BUFFER==NULL) { fprintf(stderr, "Out of memory!\n"); exit(1); }
Sequence rows = strlen(ROW_FILE)==0 ? GetRows(&argv[next_arg],argc-next_arg) : LoadRows(ROW_FILE);
// option 1: use period
if (PERIOD>0) {
int choose = MERGE ? -1 : atoi(argv[next_arg]);
//printf("(PERIOD,NEXTARG,CHOOSE) = (%i,%i,%i)\n", PERIOD, next_arg, choose);
for (int n=0; ; n++) {
if (fgets(BUFFER,BUFFER_SIZE,stdin)==NULL) break;
if (BUFFER[strlen(BUFFER)-1]!='\n') {
fprintf(stderr, "Error: line was only partially read (max chars=%i)!\n", BUFFER_SIZE); exit(1);
}
if (BUFFER[strlen(BUFFER)-1]=='\n') BUFFER[strlen(BUFFER)-1] = 0;
if (MERGE) printf("%s%s", BUFFER, n%PERIOD==PERIOD-1?"\n":SEPARATOR);
else if (n%PERIOD==choose) printf("%s\n", BUFFER);
}
}
// option 2: choose rows
else {
if (EXCLUDE==true) {
for (long int n=0,k=1; k<=rows[0]; n++) {
fgets(BUFFER,BUFFER_SIZE,stdin);
if (feof(stdin)) break;
if (BUFFER[strlen(BUFFER)-1]!='\n') { fprintf(stderr, "Error: line was only partially read (max chars=%i)!\n", BUFFER_SIZE); exit(1); }
if (n<rows[k]) printf("%s", BUFFER);
else { ++k; if (EMPTY) printf("\n"); }
}
while (true) {
fgets(BUFFER,BUFFER_SIZE,stdin);
if (feof(stdin)) break;
if (BUFFER[strlen(BUFFER)-1]!='\n') { fprintf(stderr, "Error: line was only partially read (max chars=%i)!\n", BUFFER_SIZE); exit(1); }
printf("%s", BUFFER);
}
}
else {
for (long int n=0,k=1; k<=rows[0]; n++) {
fgets(BUFFER,BUFFER_SIZE,stdin);
if (feof(stdin)) break;
if (BUFFER[strlen(BUFFER)-1]!='\n') { fprintf(stderr, "Error: line was only partially read (max chars=%i)!\n", BUFFER_SIZE); exit(1); }
if (n==rows[k]) { printf("%s", BUFFER); k++; }
else if (EMPTY) printf("\n");
}
if (EMPTY) {
while (true) {
fgets(BUFFER,BUFFER_SIZE,stdin);
if (feof(stdin)) break;
if (BUFFER[strlen(BUFFER)-1]!='\n') { fprintf(stderr, "Error: line was only partially read (max chars=%i)!\n", BUFFER_SIZE); exit(1); }
printf("\n");
}
}
}
}
// clean up
FREE1D(rows);
FREE1D(BUFFER);
}
// clean up
delete cmdLine;
return 0;
}
