06845edb9038bb632170891cebcdc8f477f2ea8d angie Fri Dec 4 08:59:38 2015 -0800 Add dbNSFP v3.1a (including VEST scores) to hg38 for hgVai. Add hgVai options for adding in transcript status info: GENCODE tags when applicable, knownCanonical for knownGene, refSeqStatus for refGene. refs #16502, #16503 diff --git src/hg/inc/annoStreamDb.h src/hg/inc/annoStreamDb.h index dae1e4e..657072f 100644 --- src/hg/inc/annoStreamDb.h +++ src/hg/inc/annoStreamDb.h @@ -1,29 +1,34 @@ /* annoStreamDb -- subclass of annoStreamer for database tables */ /* Copyright (C) 2013 The Regents of the University of California * See README in this or parent directory for licensing information. */ #ifndef ANNOSTREAMDB_H #define ANNOSTREAMDB_H #include "annoStreamer.h" +#include "joiner.h" #include "jsonParse.h" struct annoStreamer *annoStreamDbNew(char *db, char *table, struct annoAssembly *aa, int maxOutRows, struct jsonElement *config); /* Create an annoStreamer (subclass) object from a database table. * If config is NULL, then the streamer produces output from all fields * (except bin, unless table's autoSql includes bin). * Otherwise, config is a json object with a member 'relatedTables' that specifies * related tables and fields to join with table, for example: * config = { "relatedTables": [ { "table": "hg19.kgXref", * "fields": ["geneSymbol", "description"] }, * { "table": "hg19.knownCanonical", * "fields": ["clusterId"] } * ] } * -- the streamer's autoSql will be constructed by appending autoSql column * descriptions to the columns of table. * Caller may free db, table, and dbTableFieldList when done with them, but must keep the * annoAssembly aa alive for the lifetime of the returned annoStreamer. */ +char *annoStreamDbColumnNameFromDtf(char *db, char *mainTable, struct joinerDtf *dtf); +/* Return a string with the autoSql column name that would be assigned according to dtf's + * db, table and field. */ + #endif//ndef ANNOSTREAMDB_H