int gth_process_intermediate_files(GthInput *input, GtStrArray *consensusfiles,
GthSAProcessFunc saprocessfunc, void *data,
GthShowVerbose showverbose, GtError *err)
{
GtUword i;
GtFile *fp, *genfile;
int had_err = 0;
gt_error_check(err);
/* process all files */
if (gt_str_array_size(consensusfiles)) {
for (i = 0; !had_err && i < gt_str_array_size(consensusfiles); i++) {
/* open file */
fp = gt_file_xopen(gt_str_array_get(consensusfiles, i), "r");
if (showverbose) {
show_parse_file_status(showverbose, i,
gt_str_array_size(consensusfiles),
gt_str_array_get(consensusfiles, i));
}
had_err = gt_parse_intermediate_output(input, saprocessfunc, data,
gt_str_array_get(consensusfiles, i),
fp, err);
/* close file */
gt_file_delete(fp);
}
}
else {
genfile = gt_file_new_from_fileptr(stdin);
had_err = gt_parse_intermediate_output(input, saprocessfunc, data, "stdin",
genfile, err);
gt_file_delete_without_handle(genfile);
}
return had_err;
}
static void hmmsearch_create_fine_fas(GtStr *fine_fasta_filename,
GtRBTree *seqnums,
GtCondenseq *ces) {
GtRBTreeIter *tree_iter;
GtUword *seqnum;
GtFile *gt_outfp;
FILE *outfp;
tree_iter = gt_rbtree_iter_new_from_first(seqnums);
outfp = gt_xtmpfp_generic(fine_fasta_filename, TMPFP_USETEMPLATE);
gt_outfp = gt_file_new_from_fileptr(outfp);
while ((seqnum = gt_rbtree_iter_next(tree_iter)) != NULL) {
const char *seq, *desc;
GtUword seqlen, desclen;
gt_log_log("seqnum: " GT_WU, *seqnum);
seq = gt_condenseq_extract_decoded(ces, &seqlen, *seqnum);
desc = gt_condenseq_description(ces, &desclen, *seqnum);
gt_fasta_show_entry_nt(desc, desclen, seq, seqlen,
GT_FASTA_DEFAULT_WIDTH, gt_outfp);
}
gt_file_delete(gt_outfp);
gt_rbtree_iter_delete(tree_iter);
}
