static rc_t CommitIndex(KTable* ktbl, const char* name, const SLList* li) { SIndexData data; STSMSG(0, ("Saving index %s", name)); data.rc = KTableCreateIndex(ktbl, &data.kidx, kitU64, kcmInit, name); if( data.rc == 0 ) { if( !SLListDoUntil(li, InsertIndexData, &data) ) { data.rc = KIndexCommit(data.kidx); } KIndexRelease(data.kidx); } return data.rc; }
static rc_t IlluminaLoaderFmt_WriteData(IlluminaLoaderFmt* self, uint32_t argc, const SRALoaderFile* const argv[], int64_t* spots_bad_count) { rc_t rc = 0; uint32_t t, i, k, ftype_q = sizeof(file_types) / sizeof(file_types[0]); SLList files; IlluminaFileInfo* file = NULL; SLListInit(&files); /* group files using spotname, for _prb. file name prefix is used, files reviewed by type detected from name and ordered by file_type array */ for(t = 0; rc == 0 && t < ftype_q; t++) { for(i = 0; rc == 0 && i < argc; i++) { const char* fname, *blk_pfx; int prefix_len = 0; ERunFileType ftype; EIlluminaNativeFileType type = eIlluminaNativeFileTypeNotSet; FGroup_Find_data data; if( (rc = SRALoaderFileName(argv[i], &fname)) != 0 ) { SRALoaderFile_LOG(argv[i], klogErr, rc, "reading file name", NULL); break; } if( (rc = SRALoaderFile_FileType(argv[i], &ftype)) != 0 ) { SRALoaderFile_LOG(argv[i], klogErr, rc, "reading file type", NULL); break; } if( (rc = SRALoaderFileBlockName(argv[i], &blk_pfx)) != 0 ) { SRALoaderFile_LOG(argv[i], klogErr, rc, "reading DATA_BLOCK/@name", NULL); break; } if( blk_pfx == NULL ) { blk_pfx = ""; } {{ /* skip path if present */ const char* p = strrchr(fname, '/'); fname = p ? p + 1 : fname; p = NULL; for(k = 0; type == eIlluminaNativeFileTypeNotSet && k < ftype_q; k++) { const char* const* e = file_types[k].key; while( *e != NULL ) { p = strstr(fname, *e++); if( p != NULL ) { type = file_types[k].type; break; } } } if( p != NULL ) { prefix_len = p - fname; } }} if( ftype == rft_IlluminaNativeSeq ) { type = eIlluminaNativeFileTypeFasta; } else if( ftype == rft_IlluminaNativePrb ) { type = eIlluminaNativeFileTypeQuality4; } else if( ftype == rft_IlluminaNativeInt ) { type = eIlluminaNativeFileTypeIntensity; } else if( ftype == rft_IlluminaNativeQseq ) { type = eIlluminaNativeFileTypeQSeq; } if( type == eIlluminaNativeFileTypeNotSet ) { rc = RC(rcSRA, rcFormatter, rcReading, rcData, rcUnrecognized); SRALoaderFile_LOG(argv[i], klogErr, rc, "detecting file type by file name", NULL); break; } if( type != file_types[t].type ) { /* one type at a time */ continue; } DEBUG_MSG(3, ("file '%s' type set to %d\n", fname, type)); file = calloc(1, sizeof(*file)); if( file == NULL ) { rc = RC(rcSRA, rcFormatter, rcReading, rcMemory, rcExhausted); SRALoaderFile_LOG(argv[i], klogErr, rc, "allocating file object", NULL); break; } IlluminaFileInfo_init(file); file->file = argv[i]; file->type = type; if( file->type == eIlluminaNativeFileTypeQuality4 ) { /* in _prb there is no spotname inside so use file prefix */ rc = pstring_assign(&data.key, fname, prefix_len); } else { /* try to get 1st spot so group can be organized by spot name */ if( (rc = read_next_spot(blk_pfx, file)) != 0 || !file->ready ) { rc = rc ? rc : RC(rcSRA, rcFormatter, rcReading, rcData, rcNotFound); SRALoaderFile_LOG(argv[i], klogErr, rc, "reading 1st spot", NULL); break; } rc = pstring_copy(&data.key, &file->name); } data.found = NULL; if( SLListDoUntil(&files, FGroup_Find, &data) && data.found != NULL ) { IlluminaFileInfo* ss = data.found->files; while( rc == 0 && file != NULL ) { if( ss->type != eIlluminaNativeFileTypeQSeq && ss->type == file->type ) { rc = RC(rcSRA, rcFormatter, rcReading, rcFile, rcDuplicate); SRALoaderFile_LOG(argv[i], klogErr, rc, "type of file for lane", NULL); } else if( ss->next != NULL ) { ss = ss->next; } else { ss->next = file; file->prev = ss; data.found->mask |= file->type; file = NULL; } } } else { data.found = calloc(1, sizeof(*data.found)); if( data.found == NULL ) { rc = RC(rcSRA, rcFormatter, rcReading, rcMemory, rcInsufficient); SRALoaderFile_LOG(argv[i], klogErr, rc, "preparing file group", NULL); break; } else { if( (rc = pstring_assign(&data.found->key, fname, prefix_len)) != 0 ) { SRALoaderFile_LOG(argv[i], klogErr, rc, "setting file group key", NULL); FGroup_Whack(&data.found->dad, NULL); break; } else { FGroup* curr = (FGroup*)SLListHead(&files), *prev = NULL; data.found->blk_pfx = blk_pfx; data.found->files = file; data.found->mask = file->type; /* group inserted into list by coords in 1st spot */ while( curr != NULL ) { if( curr->files[0].coord[0] > file->coord[0] || (curr->files[0].coord[0] == file->coord[0] && curr->files[0].coord[1] > file->coord[1]) ) { data.found->dad.next = &curr->dad; if( prev == NULL ) { files.head = &data.found->dad; } else { prev->dad.next = &data.found->dad; } break; } prev = curr; curr = (FGroup*)curr->dad.next; } if( curr == NULL ) { SLListPushTail(&files, &data.found->dad); } file = NULL; } } } } } if( rc == 0 ) { SLListForEach(&files, FGroup_Validate, &rc); } if( rc == 0 ) { FGroup_Parse_data data; data.self = self; if( SLListDoUntil(&files, FGroup_Parse, &data) ) { rc = data.rc; } } else { free(file); } SLListWhack(&files, FGroup_Whack, NULL); *spots_bad_count = self->spots_bad_count; return rc; }