7355201a77e934e6e7f28242d4beb15d694e7c8d
braney
  Sun Oct 11 13:21:05 2020 -0700
initial work on Clinvar Submissions track #26330

diff --git src/hg/inc/clinvarSub.h src/hg/inc/clinvarSub.h
new file mode 100644
index 0000000..bd43989
--- /dev/null
+++ src/hg/inc/clinvarSub.h
@@ -0,0 +1,75 @@
+/* clinvarSub.h was originally generated by the autoSql program, which also 
+ * generated clinvarSub.c and clinvarSub.sql.  This header links the database and
+ * the RAM representation of objects. */
+
+#ifndef CLINVARSUB_H
+#define CLINVARSUB_H
+
+#define CLINVARSUB_NUM_COLS 13
+
+extern char *clinvarSubCommaSepFieldNames;
+
+struct clinvarSub
+/* ClinVar variant submission info */
+    {
+    struct clinvarSub *next;  /* Next in singly linked list. */
+    int varId;	/* the identifier assigned by ClinVar and used to build the URL, namely https://ncbi.nlm.nih.gov/clinvar/VariationID */
+    char *clinSign;	/* interpretation of the variation-condition relationship */
+    char *dateLastEval;	/* the last date the variation-condition relationship was evaluated by this submitter */
+    char *description;	/* an optional free text description of the basis of the interpretation */
+    char *subPhenoInfo;	/* the name(s) or identifier(s)  submitted for the condition that was interpreted relative to the variant */
+    char *repPhenoInfo;	/* the MedGen identifier/name combinations ClinVar uses to report the condition that was interpreted. 'na' means there is no public identifer in MedGen for the condition. */
+    char *revStatus;	/* the level of review for this submission, namely http//www.ncbi.nlm.nih.gov/clinvar/docs/variation_report/#review_status */
+    char *collMethod;	/* the method by which the submitter obtained the information provided */
+    char *originCounts;	/* origin and the number of observations for each origin */
+    char *submitter;	/* the submitter of this record */
+    char *scv;	/* the accession and current version assigned by ClinVar to the submitted interpretation of the variation-condition relationship */
+    char *subGeneSymbol;	/* the gene symbol reported in this record */
+    char *explOfInterp;	/* more details if ClinicalSignificance is 'other' or 'drug response' */
+    };
+
+void clinvarSubStaticLoad(char **row, struct clinvarSub *ret);
+/* Load a row from clinvarSub table into ret.  The contents of ret will
+ * be replaced at the next call to this function. */
+
+struct clinvarSub *clinvarSubLoad(char **row);
+/* Load a clinvarSub from row fetched with select * from clinvarSub
+ * from database.  Dispose of this with clinvarSubFree(). */
+
+struct clinvarSub *clinvarSubLoadAll(char *fileName);
+/* Load all clinvarSub from whitespace-separated file.
+ * Dispose of this with clinvarSubFreeList(). */
+
+struct clinvarSub *clinvarSubLoadAllByChar(char *fileName, char chopper);
+/* Load all clinvarSub from chopper separated file.
+ * Dispose of this with clinvarSubFreeList(). */
+
+#define clinvarSubLoadAllByTab(a) clinvarSubLoadAllByChar(a, '\t');
+/* Load all clinvarSub from tab separated file.
+ * Dispose of this with clinvarSubFreeList(). */
+
+struct clinvarSub *clinvarSubCommaIn(char **pS, struct clinvarSub *ret);
+/* Create a clinvarSub out of a comma separated string. 
+ * This will fill in ret if non-null, otherwise will
+ * return a new clinvarSub */
+
+void clinvarSubFree(struct clinvarSub **pEl);
+/* Free a single dynamically allocated clinvarSub such as created
+ * with clinvarSubLoad(). */
+
+void clinvarSubFreeList(struct clinvarSub **pList);
+/* Free a list of dynamically allocated clinvarSub's */
+
+void clinvarSubOutput(struct clinvarSub *el, FILE *f, char sep, char lastSep);
+/* Print out clinvarSub.  Separate fields with sep. Follow last field with lastSep. */
+
+#define clinvarSubTabOut(el,f) clinvarSubOutput(el,f,'\t','\n');
+/* Print out clinvarSub as a line in a tab-separated file. */
+
+#define clinvarSubCommaOut(el,f) clinvarSubOutput(el,f,',',',');
+/* Print out clinvarSub as a comma separated list including final comma. */
+
+/* -------------------------------- End autoSql Generated Code -------------------------------- */
+
+#endif /* CLINVARSUB_H */
+