static void gt_seqorder_output(unsigned long seqnum, GtEncseq *encseq) { GtEncseqReader *esr; unsigned long startpos, len, desclen = 0; const char *desc = NULL; unsigned long i; startpos = gt_encseq_seqstartpos(encseq, seqnum); len = gt_encseq_seqlength(encseq, seqnum); gt_xfputc(GT_FASTA_SEPARATOR, stdout); if (gt_encseq_has_description_support(encseq)) { desc = gt_encseq_description(encseq, &desclen, seqnum); gt_xfwrite(desc, (size_t)1, (size_t)desclen, stdout); } gt_xfputc('\n', stdout); esr = gt_encseq_create_reader_with_readmode(encseq, GT_READMODE_FORWARD, startpos); for (i = 0; i < len; i++) { gt_xfputc(gt_encseq_reader_next_decoded_char(esr), stdout); } gt_encseq_reader_delete(esr); gt_xfputc('\n', stdout); }
static int encseq_reader_lua_next_decoded_char(lua_State *L) { GtEncseqReader **reader; char cc; reader = check_encseq_reader(L, 1); cc = gt_encseq_reader_next_decoded_char(*reader); lua_pushlstring(L, &cc, sizeof (char)); return 1; }
static int output_sequence(GtEncseq *encseq, GtEncseqDecodeArguments *args, const char *filename, GtError *err) { GtUword i, j, sfrom, sto; int had_err = 0; bool has_desc; GtEncseqReader *esr; gt_assert(encseq); if (!(has_desc = gt_encseq_has_description_support(encseq))) gt_warning("Missing description support for file %s", filename); if (strcmp(gt_str_get(args->mode), "fasta") == 0) { /* specify a single sequence to extract */ if (args->seq != GT_UNDEF_UWORD) { if (args->seq >= gt_encseq_num_of_sequences(encseq)) { gt_error_set(err, "requested sequence "GT_WU" exceeds number of sequences " "("GT_WU")", args->seq, gt_encseq_num_of_sequences(encseq)); return -1; } sfrom = args->seq; sto = args->seq + 1; } else if (args->seqrng.start != GT_UNDEF_UWORD && args->seqrng.end != GT_UNDEF_UWORD) { /* specify a sequence range to extract */ if (args->seqrng.start >= gt_encseq_num_of_sequences(encseq) || args->seqrng.end >= gt_encseq_num_of_sequences(encseq)) { gt_error_set(err, "range "GT_WU"-"GT_WU" includes a sequence number " "exceeding the total number of sequences ("GT_WU")", args->seqrng.start, args->seqrng.end, gt_encseq_num_of_sequences(encseq)); return -1; } sfrom = args->seqrng.start; sto = args->seqrng.end + 1; } else { /* extract all sequences */ sfrom = 0; sto = gt_encseq_num_of_sequences(encseq); } for (i = sfrom; i < sto; i++) { GtUword desclen, startpos, len; char buf[BUFSIZ]; const char *desc = NULL; /* XXX: maybe make this distinction in the functions via readmode? */ if (!GT_ISDIRREVERSE(args->rm)) { startpos = gt_encseq_seqstartpos(encseq, i); len = gt_encseq_seqlength(encseq, i); if (has_desc) { desc = gt_encseq_description(encseq, &desclen, i); } else { (void) snprintf(buf, BUFSIZ, "sequence "GT_WU"", i); desclen = strlen(buf); desc = buf; } } else { startpos = gt_encseq_seqstartpos(encseq, i); len = gt_encseq_seqlength(encseq, gt_encseq_num_of_sequences(encseq)-1-i); startpos = gt_encseq_total_length(encseq) - (gt_encseq_seqstartpos(encseq, gt_encseq_num_of_sequences( encseq)-1-i) + len); if (has_desc) { desc = gt_encseq_description(encseq, &desclen, gt_encseq_num_of_sequences(encseq)-1-i); } else { (void) snprintf(buf, BUFSIZ, "sequence "GT_WU"", i); desclen = strlen(buf); desc = buf; } } gt_assert(desc); /* output description */ gt_xfputc(GT_FASTA_SEPARATOR, stdout); gt_xfwrite(desc, 1, desclen, stdout); gt_xfputc('\n', stdout); /* XXX: make this more efficient by writing in a buffer first and then showing the result */ if (args->singlechars) { for (j = 0; j < len; j++) { gt_xfputc(gt_encseq_get_decoded_char(encseq, startpos + j, args->rm), stdout); } } else { esr = gt_encseq_create_reader_with_readmode(encseq, args->rm, startpos); for (j = 0; j < len; j++) { gt_xfputc(gt_encseq_reader_next_decoded_char(esr), stdout); } gt_encseq_reader_delete(esr); } gt_xfputc('\n', stdout); } } if (strcmp(gt_str_get(args->mode), "concat") == 0) { GtUword from = 0, to = gt_encseq_total_length(encseq) - 1; if (args->rng.start != GT_UNDEF_UWORD && args->rng.end != GT_UNDEF_UWORD) { if (args->rng.end > to) { had_err = -1; gt_error_set(err, "end of range ("GT_WU") exceeds encoded sequence length " "("GT_WU")", args->rng.end, to); } if (!had_err) { from = args->rng.start; to = args->rng.end; } } if (!had_err) { if (args->singlechars) { for (j = from; j <= to; j++) { char cc = gt_encseq_get_decoded_char(encseq, j, args->rm); if (cc == (char) SEPARATOR) cc = gt_str_get(args->sepchar)[0]; gt_xfputc(cc, stdout); } } else { esr = gt_encseq_create_reader_with_readmode(encseq, args->rm, from); if (esr) { for (j = from; j <= to; j++) { char cc = gt_encseq_reader_next_decoded_char(esr); if (cc == (char) SEPARATOR) cc = gt_str_get(args->sepchar)[0]; gt_xfputc(cc, stdout); } gt_encseq_reader_delete(esr); } } gt_xfputc('\n', stdout); } } return had_err; }