d09b392333a2f5d2f943f2f36dad4be0a477381e
kate
  Thu Sep 14 13:55:37 2017 -0700
Add pvalue and TSS distance for each eQTL. Input from Casey Brown, U Penn. refs #15646

diff --git src/hg/inc/gtexEqtlCluster.h src/hg/inc/gtexEqtlCluster.h
index 761b024..f3d6f16 100644
--- src/hg/inc/gtexEqtlCluster.h
+++ src/hg/inc/gtexEqtlCluster.h
@@ -1,87 +1,87 @@
 /* gtexEqtlCluster.h was originally generated by the autoSql program, which also 
  * generated gtexEqtlCluster.c and gtexEqtlCluster.sql.  This header links the database and
  * the RAM representation of objects. */
 
 #ifndef GTEXEQTLCLUSTER_H
 #define GTEXEQTLCLUSTER_H
 
 #include "jksql.h"
-#define GTEXEQTLCLUSTER_NUM_COLS 10
+#define GTEXEQTLCLUSTER_NUM_COLS 12
 
 extern char *gtexEqtlClusterCommaSepFieldNames;
 
 struct gtexEqtlCluster
 /* BED5+ of eQTLs (variants affecting gene expression) with a target (gene or tissue), and lists of secondary targets (e.g. tissues or genes) */
     {
     struct gtexEqtlCluster *next;  /* Next in singly linked list. */
     char *chrom;	/* Reference sequence chromosome or scaffold */
     unsigned chromStart;	/* Start position in chromosome */
     unsigned chromEnd;	/* End position in chromosome */
     char *name;	/* Name of variant (rsID or GTEx identifier if none) */
     unsigned score;	/* Score from 0-1000 */
     char *target;	/* Name of target (gene or tissue) */
+    int distance;	/* Distance from TSS */
     unsigned expCount;	/* Number of experiment values */
     char **expNames;	/* Comma separated list of experiment names (e.g. tissue or gene) */
     float *expScores;	/* Comma separated list of effect size values */
+    float *expPvals;	/* Comma separated list of -log10 transformed p-values */
     float *expProbs;	/* Comma separated list of probability variant is in causal set */
     };
 
 struct gtexEqtlCluster *gtexEqtlClusterLoadByQuery(struct sqlConnection *conn, char *query);
 /* Load all gtexEqtlCluster from table that satisfy the query given.  
  * Where query is of the form 'select * from example where something=something'
  * or 'select example.* from example, anotherTable where example.something = 
  * anotherTable.something'.
  * Dispose of this with gtexEqtlClusterFreeList(). */
 
 void gtexEqtlClusterSaveToDb(struct sqlConnection *conn, struct gtexEqtlCluster *el, char *tableName, int updateSize);
 /* Save gtexEqtlCluster as a row to the table specified by tableName. 
  * As blob fields may be arbitrary size updateSize specifies the approx size
  * of a string that would contain the entire query. Arrays of native types are
  * converted to comma separated strings and loaded as such, User defined types are
  * inserted as NULL. This function automatically escapes quoted strings for mysql. */
 
 struct gtexEqtlCluster *gtexEqtlClusterLoad(char **row);
 /* Load a gtexEqtlCluster from row fetched with select * from gtexEqtlCluster
  * from database.  Dispose of this with gtexEqtlClusterFree(). */
 
 struct gtexEqtlCluster *gtexEqtlClusterLoadAll(char *fileName);
 /* Load all gtexEqtlCluster from whitespace-separated file.
  * Dispose of this with gtexEqtlClusterFreeList(). */
 
 struct gtexEqtlCluster *gtexEqtlClusterLoadAllByChar(char *fileName, char chopper);
 /* Load all gtexEqtlCluster from chopper separated file.
  * Dispose of this with gtexEqtlClusterFreeList(). */
 
 #define gtexEqtlClusterLoadAllByTab(a) gtexEqtlClusterLoadAllByChar(a, '\t');
 /* Load all gtexEqtlCluster from tab separated file.
  * Dispose of this with gtexEqtlClusterFreeList(). */
 
 struct gtexEqtlCluster *gtexEqtlClusterCommaIn(char **pS, struct gtexEqtlCluster *ret);
 /* Create a gtexEqtlCluster out of a comma separated string. 
  * This will fill in ret if non-null, otherwise will
  * return a new gtexEqtlCluster */
 
 void gtexEqtlClusterFree(struct gtexEqtlCluster **pEl);
 /* Free a single dynamically allocated gtexEqtlCluster such as created
  * with gtexEqtlClusterLoad(). */
 
 void gtexEqtlClusterFreeList(struct gtexEqtlCluster **pList);
 /* Free a list of dynamically allocated gtexEqtlCluster's */
 
 void gtexEqtlClusterOutput(struct gtexEqtlCluster *el, FILE *f, char sep, char lastSep);
 /* Print out gtexEqtlCluster.  Separate fields with sep. Follow last field with lastSep. */
 
 #define gtexEqtlClusterTabOut(el,f) gtexEqtlClusterOutput(el,f,'\t','\n');
 /* Print out gtexEqtlCluster as a line in a tab-separated file. */
 
 #define gtexEqtlClusterCommaOut(el,f) gtexEqtlClusterOutput(el,f,',',',');
 /* Print out gtexEqtlCluster as a comma separated list including final comma. */
 
 /* -------------------------------- End autoSql Generated Code -------------------------------- */
 
 #define GTEX_EQTL_GENE_FIELD    "target"
 
-#define GTEX_EFFECT_MIN_DEFAULT 0.0
-
 #endif /* GTEXEQTLCLUSTER_H */