eae24c27fd543e049969915b3bb690980e15b7d0
kate
  Wed Jul 5 14:48:11 2017 -0700
Cleanup before merge. refs #15646

diff --git src/hg/inc/gtexEqtlCluster.h src/hg/inc/gtexEqtlCluster.h
new file mode 100644
index 0000000..761b024
--- /dev/null
+++ src/hg/inc/gtexEqtlCluster.h
@@ -0,0 +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
+
+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) */
+    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 *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 */
+