c9f02c74337b661effebb021028f73d7a1316565
kate
  Tue Feb 17 21:42:06 2015 -0800
First cut loader of GTEX gene track.  Enough here to test track display. refs #13504

diff --git src/hg/inc/gtexGeneBed.h src/hg/inc/gtexGeneBed.h
new file mode 100644
index 0000000..13ec81e
--- /dev/null
+++ src/hg/inc/gtexGeneBed.h
@@ -0,0 +1,71 @@
+/* gtexGeneBed.h was originally generated by the autoSql program, which also 
+ * generated gtexGeneBed.c and gtexGeneBed.sql.  This header links the database and
+ * the RAM representation of objects. */
+
+#ifndef GTEXGENEBED_H
+#define GTEXGENEBED_H
+
+#define GTEXGENEBED_NUM_COLS 11
+
+extern char *gtexGeneBedCommaSepFieldNames;
+
+struct gtexGeneBed
+/* BED6+ with additional fields for gene and transcript IDs, and expression experiment scores */
+    {
+    struct gtexGeneBed *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;	/* Gene symbol */
+    unsigned score;	/* Score from 0-1000 */
+    char strand[2];	/* + or - for strand */
+    char *geneId;	/* Ensembl gene ID, referenced in GTEx data tables */
+    char *transcriptId;	/* Ensembl ID of Canonical transcript; determines genomic position */
+    char *transcriptClass;	/* GENCODE transcript class (coding, nonCoding, pseudo) */
+    unsigned expCount;	/* Number of experiment values */
+    float *expScores;	/* Comma separated list of experiment scores */
+    };
+
+struct gtexGeneBed *gtexGeneBedLoad(char **row);
+/* Load a gtexGeneBed from row fetched with select * from gtexGeneBed
+ * from database.  Dispose of this with gtexGeneBedFree(). */
+
+struct gtexGeneBed *gtexGeneBedLoadAll(char *fileName);
+/* Load all gtexGeneBed from whitespace-separated file.
+ * Dispose of this with gtexGeneBedFreeList(). */
+
+struct gtexGeneBed *gtexGeneBedLoadAllByChar(char *fileName, char chopper);
+/* Load all gtexGeneBed from chopper separated file.
+ * Dispose of this with gtexGeneBedFreeList(). */
+
+#define gtexGeneBedLoadAllByTab(a) gtexGeneBedLoadAllByChar(a, '\t');
+/* Load all gtexGeneBed from tab separated file.
+ * Dispose of this with gtexGeneBedFreeList(). */
+
+struct gtexGeneBed *gtexGeneBedCommaIn(char **pS, struct gtexGeneBed *ret);
+/* Create a gtexGeneBed out of a comma separated string. 
+ * This will fill in ret if non-null, otherwise will
+ * return a new gtexGeneBed */
+
+void gtexGeneBedFree(struct gtexGeneBed **pEl);
+/* Free a single dynamically allocated gtexGeneBed such as created
+ * with gtexGeneBedLoad(). */
+
+void gtexGeneBedFreeList(struct gtexGeneBed **pList);
+/* Free a list of dynamically allocated gtexGeneBed's */
+
+void gtexGeneBedOutput(struct gtexGeneBed *el, FILE *f, char sep, char lastSep);
+/* Print out gtexGeneBed.  Separate fields with sep. Follow last field with lastSep. */
+
+#define gtexGeneBedTabOut(el,f) gtexGeneBedOutput(el,f,'\t','\n');
+/* Print out gtexGeneBed as a line in a tab-separated file. */
+
+#define gtexGeneBedCommaOut(el,f) gtexGeneBedOutput(el,f,',',',');
+/* Print out gtexGeneBed as a comma separated list including final comma. */
+
+/* -------------------------------- End autoSql Generated Code -------------------------------- */
+void gtexGeneBedCreateTable(struct sqlConnection *conn, char *table);
+/* Create expression record format table of given name. */
+
+#endif /* GTEXGENEBED_H */
+