1bae3cecd9581968ad782c5f932cf8f504363399
kate
  Wed Aug 26 09:02:11 2015 -0700
Expand GTEx sample table.  Now includes all fields except RNA-seqC metrics, which if we decide to include them, will likley be in an auxiliary table. refs #13504

diff --git src/hg/inc/gtexSample.h src/hg/inc/gtexSample.h
index dde1e30..afeef97 100644
--- src/hg/inc/gtexSample.h
+++ src/hg/inc/gtexSample.h
@@ -1,33 +1,41 @@
 /* gtexSample.h was originally generated by the autoSql program, which also 
  * generated gtexSample.c and gtexSample.sql.  This header links the database and
  * the RAM representation of objects. */
 
 #ifndef GTEXSAMPLE_H
 #define GTEXSAMPLE_H
 
-#define GTEXSAMPLE_NUM_COLS 3
+#define GTEXSAMPLE_NUM_COLS 11
 
 extern char *gtexSampleCommaSepFieldNames;
 
 struct gtexSample
 /* GTEx sample description */
     {
     struct gtexSample *next;  /* Next in singly linked list. */
-    char *name;	/* GTEX sample identifier */
-    char *tissue;	/* Tissue name */
-    char *donor;	/* GTEX subject identifier */
+    char *sampleId;	/* GTEx sample identifier */
+    char *tissue;	/* Tissue name. Links to tissue table */
+    char *donor;	/* GTEx subject identifier. Links to donor table */
+    int autolysisScore;	/* Level of tissue self-digestion (0-3; none,mild,moderate,severe, -1 if unknown) */
+    char *ischemicTime;	/* Time from tissue removal to preservation, in 4hr intervals */
+    float rin;	/* RNA Integrity Number */
+    char *collectionSites;	/* GTEx Biospecimen Source Site list */
+    char *batchId;	/* Nucleic acid isolation batch ID */
+    char *isolationType;	/* Type of nucleic acid isolation */
+    char *isolationDate;	/* Date of nucleic acid isolation */
+    char *pathNotes;	/* Pathology report notes */
     };
 
 void gtexSampleStaticLoad(char **row, struct gtexSample *ret);
 /* Load a row from gtexSample table into ret.  The contents of ret will
  * be replaced at the next call to this function. */
 
 struct gtexSample *gtexSampleLoad(char **row);
 /* Load a gtexSample from row fetched with select * from gtexSample
  * from database.  Dispose of this with gtexSampleFree(). */
 
 struct gtexSample *gtexSampleLoadAll(char *fileName);
 /* Load all gtexSample from whitespace-separated file.
  * Dispose of this with gtexSampleFreeList(). */
 
 struct gtexSample *gtexSampleLoadAllByChar(char *fileName, char chopper);
@@ -49,20 +57,19 @@
 
 void gtexSampleFreeList(struct gtexSample **pList);
 /* Free a list of dynamically allocated gtexSample's */
 
 void gtexSampleOutput(struct gtexSample *el, FILE *f, char sep, char lastSep);
 /* Print out gtexSample.  Separate fields with sep. Follow last field with lastSep. */
 
 #define gtexSampleTabOut(el,f) gtexSampleOutput(el,f,'\t','\n');
 /* Print out gtexSample as a line in a tab-separated file. */
 
 #define gtexSampleCommaOut(el,f) gtexSampleOutput(el,f,',',',');
 /* Print out gtexSample as a comma separated list including final comma. */
 
 /* -------------------------------- End autoSql Generated Code -------------------------------- */
 
-void gtexSampleCreateTable(struct sqlConnection *conn, char *table);
-/* Create expression record format table of given name. */
-
 #endif /* GTEXSAMPLE_H */
 
+void gtexSampleCreateTable(struct sqlConnection *conn, char *table);
+/* Create GTEx sample table of given name. */