static int encseq_loader_lua_require_multiseq_support(lua_State *L) { GtEncseqLoader **loader; loader = check_encseq_loader(L, 1); gt_assert(*loader); gt_encseq_loader_require_multiseq_support(*loader); return 0; }
static int bioseq_fill(GtBioseq *bs, bool recreate, GtError *err) { GtStr *bioseq_index_file = NULL, *bioseq_ois_file = NULL, *bioseq_sds_file = NULL, *bioseq_md5_file = NULL, *bioseq_des_file = NULL; int had_err = 0; GtStr *bioseq_basename; gt_assert(!bs->encseq); if (bs->use_stdin) bioseq_basename = gt_str_new_cstr("stdin"); else bioseq_basename = bs->sequence_file; /* construct file names */ bioseq_index_file = gt_str_clone(bioseq_basename); gt_str_append_cstr(bioseq_index_file, GT_ENCSEQFILESUFFIX); bioseq_ois_file = gt_str_clone(bioseq_basename); gt_str_append_cstr(bioseq_ois_file, GT_OISTABFILESUFFIX); bioseq_sds_file = gt_str_clone(bioseq_basename); gt_str_append_cstr(bioseq_sds_file, GT_SDSTABFILESUFFIX); bioseq_md5_file = gt_str_clone(bioseq_basename); gt_str_append_cstr(bioseq_md5_file, GT_MD5TABFILESUFFIX); bioseq_des_file = gt_str_clone(bioseq_basename); gt_str_append_cstr(bioseq_des_file, GT_DESTABFILESUFFIX); /* construct the bioseq files if necessary */ if (recreate || bs->use_stdin || !gt_file_exists(gt_str_get(bioseq_index_file)) || !gt_file_exists(gt_str_get(bioseq_ois_file)) || !gt_file_exists(gt_str_get(bioseq_sds_file)) || !gt_file_exists(gt_str_get(bioseq_md5_file)) || !gt_file_exists(gt_str_get(bioseq_des_file)) || gt_file_is_newer(gt_str_get(bs->sequence_file), gt_str_get(bioseq_index_file))) { had_err = construct_bioseq_files(bs, bioseq_basename, err); } if (!had_err) { GtEncseqLoader *el = gt_encseq_loader_new(); gt_encseq_loader_disable_autosupport(el); gt_encseq_loader_require_lossless_support(el); gt_encseq_loader_require_description_support(el); gt_encseq_loader_require_md5_support(el); gt_encseq_loader_require_multiseq_support(el); bs->encseq = gt_encseq_loader_load(el, gt_str_get(bioseq_basename), err); if (bs->encseq == NULL) { had_err = -1; gt_assert(gt_error_is_set(err)); } gt_encseq_loader_delete(el); } if (!had_err) { gt_assert(bs->encseq); } /* free */ if (bs->use_stdin) gt_str_delete(bioseq_basename); gt_str_delete(bioseq_index_file); gt_str_delete(bioseq_ois_file); gt_str_delete(bioseq_md5_file); gt_str_delete(bioseq_sds_file); gt_str_delete(bioseq_des_file); return had_err; }
int gt_runidxlocali(const IdxlocaliOptions *idxlocalioptions,GtError *err) { Genericindex *genericindex = NULL; bool haserr = false; GtLogger *logger; const GtEncseq *encseq = NULL; logger = gt_logger_new(idxlocalioptions->verbose, GT_LOGGER_DEFLT_PREFIX, stdout); if (idxlocalioptions->doonline) { GtEncseqLoader *el; el = gt_encseq_loader_new(); gt_encseq_loader_require_multiseq_support(el); gt_encseq_loader_drop_description_support(el); gt_encseq_loader_set_logger(el, logger); encseq = gt_encseq_loader_load(el, gt_str_get(idxlocalioptions->indexname), err); gt_encseq_loader_delete(el); if (encseq == NULL) { haserr = true; } } else { genericindex = genericindex_new(gt_str_get(idxlocalioptions->indexname), idxlocalioptions->withesa, idxlocalioptions->withesa || idxlocalioptions->docompare, false, true, 0, logger, err); if (genericindex == NULL) { haserr = true; } else { encseq = genericindex_getencseq(genericindex); } } if (!haserr) { GtSeqIterator *seqit; const GtUchar *query; unsigned long querylen; char *desc = NULL; int retval; Limdfsresources *limdfsresources = NULL; const AbstractDfstransformer *dfst; SWdpresource *swdpresource = NULL; Showmatchinfo showmatchinfo; ProcessIdxMatch processmatch; GtAlphabet *a; void *processmatchinfoonline, *processmatchinfooffline; Storematchinfo storeonline, storeoffline; a = gt_encseq_alphabet(encseq); if (idxlocalioptions->docompare) { processmatch = storematch; gt_initstorematch(&storeonline,encseq); gt_initstorematch(&storeoffline,encseq); processmatchinfoonline = &storeonline; processmatchinfooffline = &storeoffline; } else { processmatch = showmatch; showmatchinfo.encseq = encseq; showmatchinfo.characters = gt_alphabet_characters(a); showmatchinfo.wildcardshow = gt_alphabet_wildcard_show(a); showmatchinfo.showalignment = idxlocalioptions->showalignment; processmatchinfoonline = processmatchinfooffline = &showmatchinfo; } if (idxlocalioptions->doonline || idxlocalioptions->docompare) { swdpresource = gt_newSWdpresource(idxlocalioptions->matchscore, idxlocalioptions->mismatchscore, idxlocalioptions->gapextend, idxlocalioptions->threshold, idxlocalioptions->showalignment, processmatch, processmatchinfoonline); } dfst = gt_locali_AbstractDfstransformer(); if (!idxlocalioptions->doonline || idxlocalioptions->docompare) { gt_assert(genericindex != NULL); limdfsresources = gt_newLimdfsresources(genericindex, true, 0, 0, /* maxpathlength */ true, /* keepexpandedonstack */ processmatch, processmatchinfooffline, NULL, /* processresult */ NULL, /* processresult info */ dfst); } seqit = gt_seq_iterator_sequence_buffer_new(idxlocalioptions->queryfiles, err); if (!seqit) haserr = true; if (!haserr) { gt_seq_iterator_set_symbolmap(seqit, gt_alphabet_symbolmap(a)); for (showmatchinfo.queryunit = 0; /* Nothing */; showmatchinfo.queryunit++) { retval = gt_seq_iterator_next(seqit, &query, &querylen, &desc, err); if (retval < 0) { haserr = true; break; } if (retval == 0) { break; } printf("process sequence " Formatuint64_t " of length %lu\n", PRINTuint64_tcast(showmatchinfo.queryunit),querylen); if (idxlocalioptions->doonline || idxlocalioptions->docompare) { gt_multiapplysmithwaterman(swdpresource,encseq,query,querylen); } if (!idxlocalioptions->doonline || idxlocalioptions->docompare) { gt_indexbasedlocali(limdfsresources, idxlocalioptions->matchscore, idxlocalioptions->mismatchscore, idxlocalioptions->gapstart, idxlocalioptions->gapextend, idxlocalioptions->threshold, query, querylen, dfst); } if (idxlocalioptions->docompare) { gt_checkandresetstorematch(showmatchinfo.queryunit, &storeonline,&storeoffline); } } if (limdfsresources != NULL) { gt_freeLimdfsresources(&limdfsresources,dfst); } if (swdpresource != NULL) { gt_freeSWdpresource(swdpresource); swdpresource = NULL; } gt_seq_iterator_delete(seqit); } if (idxlocalioptions->docompare) { gt_freestorematch(&storeonline); gt_freestorematch(&storeoffline); } } if (genericindex == NULL) { gt_encseq_delete((GtEncseq *) encseq); encseq = NULL; } else { genericindex_delete(genericindex); } gt_logger_delete(logger); logger = NULL; return haserr ? -1 : 0; }