int filter_main(int argc, char* argv[]){
FLT_OPTS mopts=getFilterOptions(argc,argv);
int flag_a = detect_filetype(mopts.r1);
if(flag_a & FILE_NONE || flag_a & FILE_UNKN || flag_a & FILE_FASTA)
return 1;
mopts.qualityCutoff += flag_a & FILE_PHRED33 ? BASE_SANGER : BASE_SOLEXA;
mopts.meanQuality += flag_a & FILE_PHRED33 ? BASE_SANGER : BASE_SOLEXA;
if(mkdir_report(mopts.output) != 0) return 1;
if(strcmp(mopts.r2,"none") != 0){
int flag_b = detect_filetype(mopts.r2);
if(flag_a != flag_b){
fprintf(stderr,"This two files:%s,%s are not same type\n",mopts.r1,mopts.r2);
return 1;
}
if( flag_a & FILE_FASTQ ) {
if( flag_a & FILE_BZ2 )
#ifdef HAVE_BZLIB
filter_pe_fastq_bz2(&mopts);
#else
error_msg("Do not support bzip2 file");
#endif
else
filter_pe_fastq(&mopts);
}else{
GretlFileType gretl_detect_filetype (const char *fname)
{
if (fname == NULL) {
return GRETL_UNRECOGNIZED;
}
return detect_filetype((char *) fname, OPT_NONE);
}
static int cli_open_append (CMD *cmd, DATASET *dset,
MODEL *model, PRN *prn)
{
gretlopt opt = cmd->opt;
PRN *vprn = prn;
char newfile[MAXLEN] = {0};
char response[3];
int http = 0, dbdata = 0;
int ftype;
int err = 0;
if (opt & OPT_K) {
/* --frompkg=whatever */
err = get_package_data_path(cmd->param, newfile);
if (err) {
errmsg(err, prn);
return err;
}
} else {
err = cli_try_http(cmd->param, newfile, &http);
if (err) {
errmsg(err, prn);
return err;
}
if (!http && !(opt & OPT_O)) {
/* not using http or ODBC */
err = get_full_filename(cmd->param, newfile, (opt & OPT_W)?
OPT_W : OPT_NONE);
if (err) {
errmsg(err, prn);
return err;
}
}
}
if (opt & OPT_W) {
ftype = GRETL_NATIVE_DB_WWW;
} else if (opt & OPT_O) {
ftype = GRETL_ODBC;
} else {
ftype = detect_filetype(newfile, OPT_P);
}
dbdata = (ftype == GRETL_NATIVE_DB || ftype == GRETL_NATIVE_DB_WWW ||
ftype == GRETL_RATS_DB || ftype == GRETL_PCGIVE_DB ||
ftype == GRETL_ODBC);
if (data_status && !batch && !dbdata && cmd->ci != APPEND &&
strcmp(newfile, datafile)) {
fprintf(stderr, _("Opening a new data file closes the "
"present one. Proceed? (y/n) "));
if (fgets(response, sizeof response, stdin) != NULL &&
*response != 'y' && *response != 'Y') {
pprintf(prn, _("OK, staying with current data set\n"));
return 0;
}
}
if (!dbdata && cmd->ci != APPEND) {
cli_clear_data(cmd, dset, model);
}
if (opt & OPT_Q) {
/* --quiet, but in case we hit any problems below... */
vprn = gretl_print_new(GRETL_PRINT_BUFFER, NULL);
}
if (ftype == GRETL_XML_DATA || ftype == GRETL_BINARY_DATA) {
err = gretl_read_gdt(newfile, dset, opt, vprn);
} else if (ftype == GRETL_CSV) {
err = import_csv(newfile, dset, opt, vprn);
} else if (SPREADSHEET_IMPORT(ftype)) {
err = import_spreadsheet(newfile, ftype, cmd->list, cmd->parm2,
dset, opt, vprn);
} else if (OTHER_IMPORT(ftype)) {
err = import_other(newfile, ftype, dset, opt, vprn);
} else if (ftype == GRETL_ODBC) {
err = set_odbc_dsn(cmd->param, vprn);
} else if (dbdata) {
err = set_db_name(newfile, ftype, vprn);
} else {
err = gretl_get_data(newfile, dset, opt, vprn);
}
if (vprn != prn) {
if (err) {
/* The user asked for --quiet operation, but something
went wrong so let's print any info we got on
vprn.
*/
const char *buf = gretl_print_get_buffer(vprn);
if (buf != NULL && *buf != '\0') {
pputs(prn, buf);
}
} else {
/* print minimal success message */
pprintf(prn, _("Read datafile %s\n"), newfile);
}
gretl_print_destroy(vprn);
}
if (err) {
errmsg(err, prn);
return err;
}
if (!dbdata && !http && cmd->ci != APPEND) {
strncpy(datafile, newfile, MAXLEN - 1);
}
data_status = 1;
if (dset->v > 0 && !dbdata && !(opt & OPT_Q)) {
varlist(dset, prn);
}
if (http) {
remove(newfile);
}
return err;
}
static void handle_datafile (char *filearg, char *runfile,
DATASET *dset, PRN *prn,
PRN *cmdprn)
{
char given_file[MAXLEN];
int load_datafile = 1;
int ftype, err = 0;
strcpy(given_file, filearg);
strcpy(datafile, filearg);
ftype = detect_filetype(datafile, OPT_P);
switch (ftype) {
case GRETL_UNRECOGNIZED:
case GRETL_NATIVE_DB:
case GRETL_RATS_DB:
exit(EXIT_FAILURE);
break;
case GRETL_XML_DATA:
case GRETL_BINARY_DATA:
err = gretl_read_gdt(datafile, dset, OPT_NONE, prn);
break;
case GRETL_CSV:
err = import_csv(datafile, dset, OPT_NONE, prn);
break;
case GRETL_XLS:
case GRETL_GNUMERIC:
case GRETL_ODS:
err = import_spreadsheet(datafile, ftype, NULL, NULL,
dset, OPT_NONE, prn);
break;
case GRETL_DTA:
case GRETL_SAV:
case GRETL_SAS:
case GRETL_JMULTI:
case GRETL_OCTAVE:
case GRETL_WF1:
err = import_other(datafile, ftype, dset,
OPT_NONE, prn);
break;
case GRETL_SCRIPT:
runit = 1;
strcpy(runfile, datafile);
memset(datafile, 0, sizeof datafile);
load_datafile = 0;
break;
default:
break;
}
if (load_datafile) {
if (err) {
errmsg(err, prn);
if (err == E_FOPEN) {
show_paths();
}
exit(EXIT_FAILURE);
}
data_status = 1;
if (!batch) {
pprintf(cmdprn, "open %s\n", given_file);
}
}
}
