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/lib/dgvPlus.c src/hg/lib/dgvPlus.c
new file mode 100644
index 0000000..7379746
--- /dev/null
+++ src/hg/lib/dgvPlus.c
@@ -0,0 +1,255 @@
+/* dgvPlus.c was originally generated by the autoSql program, which also 
+ * generated dgvPlus.h and dgvPlus.sql.  This module links the database and
+ * the RAM representation of objects. */
+
+#include "common.h"
+#include "linefile.h"
+#include "dystring.h"
+#include "jksql.h"
+#include "dgvPlus.h"
+
+
+
+char *dgvPlusCommaSepFieldNames = "chrom,chromStart,chromEnd,name,score,strand,thickStart,thickEnd,itemRgb,varType,reference,pubMedId,method,platform,mergedVariants,supportingVariants,sampleSize,observedGains,observedLosses,cohortDescription,genes,samples";
+
+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. */
+{
+
+ret->chrom = row[0];
+ret->chromStart = sqlUnsigned(row[1]);
+ret->chromEnd = sqlUnsigned(row[2]);
+ret->name = row[3];
+ret->score = sqlUnsigned(row[4]);
+safecpy(ret->strand, sizeof(ret->strand), row[5]);
+ret->thickStart = sqlUnsigned(row[6]);
+ret->thickEnd = sqlUnsigned(row[7]);
+ret->itemRgb = sqlUnsigned(row[8]);
+ret->varType = row[9];
+ret->reference = row[10];
+ret->pubMedId = sqlUnsigned(row[11]);
+ret->method = row[12];
+ret->platform = row[13];
+ret->mergedVariants = row[14];
+ret->supportingVariants = row[15];
+ret->sampleSize = sqlUnsigned(row[16]);
+ret->observedGains = sqlUnsigned(row[17]);
+ret->observedLosses = sqlUnsigned(row[18]);
+ret->cohortDescription = row[19];
+ret->genes = row[20];
+ret->samples = row[21];
+}
+
+struct dgvPlus *dgvPlusLoad(char **row)
+/* Load a dgvPlus from row fetched with select * from dgvPlus
+ * from database.  Dispose of this with dgvPlusFree(). */
+{
+struct dgvPlus *ret;
+
+AllocVar(ret);
+ret->chrom = cloneString(row[0]);
+ret->chromStart = sqlUnsigned(row[1]);
+ret->chromEnd = sqlUnsigned(row[2]);
+ret->name = cloneString(row[3]);
+ret->score = sqlUnsigned(row[4]);
+safecpy(ret->strand, sizeof(ret->strand), row[5]);
+ret->thickStart = sqlUnsigned(row[6]);
+ret->thickEnd = sqlUnsigned(row[7]);
+ret->itemRgb = sqlUnsigned(row[8]);
+ret->varType = cloneString(row[9]);
+ret->reference = cloneString(row[10]);
+ret->pubMedId = sqlUnsigned(row[11]);
+ret->method = cloneString(row[12]);
+ret->platform = cloneString(row[13]);
+ret->mergedVariants = cloneString(row[14]);
+ret->supportingVariants = cloneString(row[15]);
+ret->sampleSize = sqlUnsigned(row[16]);
+ret->observedGains = sqlUnsigned(row[17]);
+ret->observedLosses = sqlUnsigned(row[18]);
+ret->cohortDescription = cloneString(row[19]);
+ret->genes = cloneString(row[20]);
+ret->samples = cloneString(row[21]);
+return ret;
+}
+
+struct dgvPlus *dgvPlusLoadAll(char *fileName) 
+/* Load all dgvPlus from a whitespace-separated file.
+ * Dispose of this with dgvPlusFreeList(). */
+{
+struct dgvPlus *list = NULL, *el;
+struct lineFile *lf = lineFileOpen(fileName, TRUE);
+char *row[22];
+
+while (lineFileRow(lf, row))
+    {
+    el = dgvPlusLoad(row);
+    slAddHead(&list, el);
+    }
+lineFileClose(&lf);
+slReverse(&list);
+return list;
+}
+
+struct dgvPlus *dgvPlusLoadAllByChar(char *fileName, char chopper) 
+/* Load all dgvPlus from a chopper separated file.
+ * Dispose of this with dgvPlusFreeList(). */
+{
+struct dgvPlus *list = NULL, *el;
+struct lineFile *lf = lineFileOpen(fileName, TRUE);
+char *row[22];
+
+while (lineFileNextCharRow(lf, chopper, row, ArraySize(row)))
+    {
+    el = dgvPlusLoad(row);
+    slAddHead(&list, el);
+    }
+lineFileClose(&lf);
+slReverse(&list);
+return list;
+}
+
+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 */
+{
+char *s = *pS;
+
+if (ret == NULL)
+    AllocVar(ret);
+ret->chrom = sqlStringComma(&s);
+ret->chromStart = sqlUnsignedComma(&s);
+ret->chromEnd = sqlUnsignedComma(&s);
+ret->name = sqlStringComma(&s);
+ret->score = sqlUnsignedComma(&s);
+sqlFixedStringComma(&s, ret->strand, sizeof(ret->strand));
+ret->thickStart = sqlUnsignedComma(&s);
+ret->thickEnd = sqlUnsignedComma(&s);
+ret->itemRgb = sqlUnsignedComma(&s);
+ret->varType = sqlStringComma(&s);
+ret->reference = sqlStringComma(&s);
+ret->pubMedId = sqlUnsignedComma(&s);
+ret->method = sqlStringComma(&s);
+ret->platform = sqlStringComma(&s);
+ret->mergedVariants = sqlStringComma(&s);
+ret->supportingVariants = sqlStringComma(&s);
+ret->sampleSize = sqlUnsignedComma(&s);
+ret->observedGains = sqlUnsignedComma(&s);
+ret->observedLosses = sqlUnsignedComma(&s);
+ret->cohortDescription = sqlStringComma(&s);
+ret->genes = sqlStringComma(&s);
+ret->samples = sqlStringComma(&s);
+*pS = s;
+return ret;
+}
+
+void dgvPlusFree(struct dgvPlus **pEl)
+/* Free a single dynamically allocated dgvPlus such as created
+ * with dgvPlusLoad(). */
+{
+struct dgvPlus *el;
+
+if ((el = *pEl) == NULL) return;
+freeMem(el->chrom);
+freeMem(el->name);
+freeMem(el->varType);
+freeMem(el->reference);
+freeMem(el->method);
+freeMem(el->platform);
+freeMem(el->mergedVariants);
+freeMem(el->supportingVariants);
+freeMem(el->cohortDescription);
+freeMem(el->genes);
+freeMem(el->samples);
+freez(pEl);
+}
+
+void dgvPlusFreeList(struct dgvPlus **pList)
+/* Free a list of dynamically allocated dgvPlus's */
+{
+struct dgvPlus *el, *next;
+
+for (el = *pList; el != NULL; el = next)
+    {
+    next = el->next;
+    dgvPlusFree(&el);
+    }
+*pList = NULL;
+}
+
+void dgvPlusOutput(struct dgvPlus *el, FILE *f, char sep, char lastSep) 
+/* Print out dgvPlus.  Separate fields with sep. Follow last field with lastSep. */
+{
+if (sep == ',') fputc('"',f);
+fprintf(f, "%s", el->chrom);
+if (sep == ',') fputc('"',f);
+fputc(sep,f);
+fprintf(f, "%u", el->chromStart);
+fputc(sep,f);
+fprintf(f, "%u", el->chromEnd);
+fputc(sep,f);
+if (sep == ',') fputc('"',f);
+fprintf(f, "%s", el->name);
+if (sep == ',') fputc('"',f);
+fputc(sep,f);
+fprintf(f, "%u", el->score);
+fputc(sep,f);
+if (sep == ',') fputc('"',f);
+fprintf(f, "%s", el->strand);
+if (sep == ',') fputc('"',f);
+fputc(sep,f);
+fprintf(f, "%u", el->thickStart);
+fputc(sep,f);
+fprintf(f, "%u", el->thickEnd);
+fputc(sep,f);
+fprintf(f, "%u", el->itemRgb);
+fputc(sep,f);
+if (sep == ',') fputc('"',f);
+fprintf(f, "%s", el->varType);
+if (sep == ',') fputc('"',f);
+fputc(sep,f);
+if (sep == ',') fputc('"',f);
+fprintf(f, "%s", el->reference);
+if (sep == ',') fputc('"',f);
+fputc(sep,f);
+fprintf(f, "%u", el->pubMedId);
+fputc(sep,f);
+if (sep == ',') fputc('"',f);
+fprintf(f, "%s", el->method);
+if (sep == ',') fputc('"',f);
+fputc(sep,f);
+if (sep == ',') fputc('"',f);
+fprintf(f, "%s", el->platform);
+if (sep == ',') fputc('"',f);
+fputc(sep,f);
+if (sep == ',') fputc('"',f);
+fprintf(f, "%s", el->mergedVariants);
+if (sep == ',') fputc('"',f);
+fputc(sep,f);
+if (sep == ',') fputc('"',f);
+fprintf(f, "%s", el->supportingVariants);
+if (sep == ',') fputc('"',f);
+fputc(sep,f);
+fprintf(f, "%u", el->sampleSize);
+fputc(sep,f);
+fprintf(f, "%u", el->observedGains);
+fputc(sep,f);
+fprintf(f, "%u", el->observedLosses);
+fputc(sep,f);
+if (sep == ',') fputc('"',f);
+fprintf(f, "%s", el->cohortDescription);
+if (sep == ',') fputc('"',f);
+fputc(sep,f);
+if (sep == ',') fputc('"',f);
+fprintf(f, "%s", el->genes);
+if (sep == ',') fputc('"',f);
+fputc(sep,f);
+if (sep == ',') fputc('"',f);
+fprintf(f, "%s", el->samples);
+if (sep == ',') fputc('"',f);
+fputc(lastSep,f);
+}
+
+/* -------------------------------- End autoSql Generated Code -------------------------------- */
+