7ab28d1f5d3428156b5d5831426591e9df121b08
angie
  Fri Sep 13 12:19:12 2013 -0700
New and improved Database of Genomic Variants (DGV).  It is now acomposite track as requested by the submitter, and the tables have
more columns than the older dgv tables.
The track description needs to be updated to make more clear what
DGV gets from dbVar/DGVa and what it adds.
refs #11200

diff --git src/hg/inc/dgvPlus.h src/hg/inc/dgvPlus.h
new file mode 100644
index 0000000..055ad03
--- /dev/null
+++ src/hg/inc/dgvPlus.h
@@ -0,0 +1,84 @@
+/* dgvPlus.h was originally generated by the autoSql program, which also 
+ * generated dgvPlus.c and dgvPlus.sql.  This header links the database and
+ * the RAM representation of objects. */
+
+#ifndef DGVPLUS_H
+#define DGVPLUS_H
+
+#define DGVPLUS_NUM_COLS 22
+
+extern char *dgvPlusCommaSepFieldNames;
+
+struct dgvPlus
+/* Database of Genomic Variants incorporating dbVar, July 2013 and later */
+    {
+    struct dgvPlus *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;	/* ID of merged variant or supporting variant */
+    unsigned score;	/* Score from 0-1000 (placeholder for BED 9+ format) */
+    char strand[2];	/* + or - (placeholder for BED 9+ format) */
+    unsigned thickStart;	/* Same as chromStart (placeholder for BED 9+ format) */
+    unsigned thickEnd;	/* Same as chromEnd (placeholder for BED 9+ format) */
+    unsigned itemRgb;	/* Item R,G,B color. */
+    char *varType;	/* Type of variation */
+    char *reference;	/* Literature reference for the study that included this variant */
+    unsigned pubMedId;	/* For linking to pubMed abstract of reference */
+    char *method;	/* Brief description of method */
+    char *platform;	/* Sequencing platform (if specified) */
+    char *mergedVariants;	/* If this is a supporting variant, ID of merged variant */
+    char *supportingVariants;	/* If this is a merged variant, IDs of supporting variants */
+    unsigned sampleSize;	/* Number of samples in study */
+    unsigned observedGains;	/* Number of samples with copy number gains */
+    unsigned observedLosses;	/* Number of samples with copy number losses */
+    char *cohortDescription;	/* Description of sample population for the study */
+    char *genes;	/* Genes overlapping this variant */
+    char *samples;	/* Sample IDs if available */
+    };
+
+void dgvPlusStaticLoad(char **row, struct dgvPlus *ret);
+/* Load a row from dgvPlus table into ret.  The contents of ret will
+ * be replaced at the next call to this function. */
+
+struct dgvPlus *dgvPlusLoad(char **row);
+/* Load a dgvPlus from row fetched with select * from dgvPlus
+ * from database.  Dispose of this with dgvPlusFree(). */
+
+struct dgvPlus *dgvPlusLoadAll(char *fileName);
+/* Load all dgvPlus from whitespace-separated file.
+ * Dispose of this with dgvPlusFreeList(). */
+
+struct dgvPlus *dgvPlusLoadAllByChar(char *fileName, char chopper);
+/* Load all dgvPlus from chopper separated file.
+ * Dispose of this with dgvPlusFreeList(). */
+
+#define dgvPlusLoadAllByTab(a) dgvPlusLoadAllByChar(a, '\t');
+/* Load all dgvPlus from tab separated file.
+ * Dispose of this with dgvPlusFreeList(). */
+
+struct dgvPlus *dgvPlusCommaIn(char **pS, struct dgvPlus *ret);
+/* Create a dgvPlus out of a comma separated string. 
+ * This will fill in ret if non-null, otherwise will
+ * return a new dgvPlus */
+
+void dgvPlusFree(struct dgvPlus **pEl);
+/* Free a single dynamically allocated dgvPlus such as created
+ * with dgvPlusLoad(). */
+
+void dgvPlusFreeList(struct dgvPlus **pList);
+/* Free a list of dynamically allocated dgvPlus's */
+
+void dgvPlusOutput(struct dgvPlus *el, FILE *f, char sep, char lastSep);
+/* Print out dgvPlus.  Separate fields with sep. Follow last field with lastSep. */
+
+#define dgvPlusTabOut(el,f) dgvPlusOutput(el,f,'\t','\n');
+/* Print out dgvPlus as a line in a tab-separated file. */
+
+#define dgvPlusCommaOut(el,f) dgvPlusOutput(el,f,',',',');
+/* Print out dgvPlus as a comma separated list including final comma. */
+
+/* -------------------------------- End autoSql Generated Code -------------------------------- */
+
+#endif /* DGVPLUS_H */
+