b7cb97d2942575d92f6385055e172dcbd979ee05
angie
  Tue Oct 1 13:09:29 2019 -0700
Adding new data type bigDbSnp.as with associated dbSnpDetails.as, for a track based on the new "dbSNP 2.0" schema and JSON downloads.  refs #23283

diff --git src/hg/lib/bigDbSnp.c src/hg/lib/bigDbSnp.c
new file mode 100644
index 0000000..71c30b7
--- /dev/null
+++ src/hg/lib/bigDbSnp.c
@@ -0,0 +1,299 @@
+/* bigDbSnp.c was originally generated by the autoSql program, which also 
+ * generated bigDbSnp.h and bigDbSnp.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 "bigDbSnp.h"
+
+
+
+char *bigDbSnpCommaSepFieldNames = "chrom,chromStart,chromEnd,name,ref,altCount,alts,shiftBases,freqSourceCount,minorAlleleFreq,majorAllele,minorAllele,maxFuncImpact,class,ucscNotes,_dataOffset,_dataLen";
+
+/* definitions for class column */
+static char *values_class[] = {"snv", "mnv", "ins", "del", "delins", "identity", NULL};
+static struct hash *valhash_class = NULL;
+
+struct bigDbSnp *bigDbSnpLoad(char **row)
+/* Load a bigDbSnp from row fetched with select * from bigDbSnp
+ * from database.  Dispose of this with bigDbSnpFree(). */
+{
+struct bigDbSnp *ret;
+
+AllocVar(ret);
+ret->altCount = sqlSigned(row[5]);
+ret->freqSourceCount = sqlSigned(row[8]);
+ret->chrom = cloneString(row[0]);
+ret->chromStart = sqlUnsigned(row[1]);
+ret->chromEnd = sqlUnsigned(row[2]);
+ret->name = cloneString(row[3]);
+ret->ref = cloneString(row[4]);
+{
+int sizeOne;
+sqlStringDynamicArray(row[6], &ret->alts, &sizeOne);
+assert(sizeOne == ret->altCount);
+}
+ret->shiftBases = sqlUnsigned(row[7]);
+{
+int sizeOne;
+sqlDoubleDynamicArray(row[9], &ret->minorAlleleFreq, &sizeOne);
+assert(sizeOne == ret->freqSourceCount);
+}
+{
+int sizeOne;
+sqlStringDynamicArray(row[10], &ret->majorAllele, &sizeOne);
+assert(sizeOne == ret->freqSourceCount);
+}
+{
+int sizeOne;
+sqlStringDynamicArray(row[11], &ret->minorAllele, &sizeOne);
+assert(sizeOne == ret->freqSourceCount);
+}
+ret->maxFuncImpact = sqlUnsigned(row[12]);
+ret->class = sqlEnumParse(row[13], values_class, &valhash_class);
+ret->ucscNotes = cloneString(row[14]);
+ret->_dataOffset = sqlLongLong(row[15]);
+ret->_dataLen = sqlSigned(row[16]);
+return ret;
+}
+
+struct bigDbSnp *bigDbSnpLoadAll(char *fileName) 
+/* Load all bigDbSnp from a whitespace-separated file.
+ * Dispose of this with bigDbSnpFreeList(). */
+{
+struct bigDbSnp *list = NULL, *el;
+struct lineFile *lf = lineFileOpen(fileName, TRUE);
+char *row[17];
+
+while (lineFileRow(lf, row))
+    {
+    el = bigDbSnpLoad(row);
+    slAddHead(&list, el);
+    }
+lineFileClose(&lf);
+slReverse(&list);
+return list;
+}
+
+struct bigDbSnp *bigDbSnpLoadAllByChar(char *fileName, char chopper) 
+/* Load all bigDbSnp from a chopper separated file.
+ * Dispose of this with bigDbSnpFreeList(). */
+{
+struct bigDbSnp *list = NULL, *el;
+struct lineFile *lf = lineFileOpen(fileName, TRUE);
+char *row[17];
+
+while (lineFileNextCharRow(lf, chopper, row, ArraySize(row)))
+    {
+    el = bigDbSnpLoad(row);
+    slAddHead(&list, el);
+    }
+lineFileClose(&lf);
+slReverse(&list);
+return list;
+}
+
+struct bigDbSnp *bigDbSnpCommaIn(char **pS, struct bigDbSnp *ret)
+/* Create a bigDbSnp out of a comma separated string. 
+ * This will fill in ret if non-null, otherwise will
+ * return a new bigDbSnp */
+{
+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->ref = sqlStringComma(&s);
+ret->altCount = sqlSignedComma(&s);
+{
+int i;
+s = sqlEatChar(s, '{');
+AllocArray(ret->alts, ret->altCount);
+for (i=0; i<ret->altCount; ++i)
+    {
+    ret->alts[i] = sqlStringComma(&s);
+    }
+s = sqlEatChar(s, '}');
+s = sqlEatChar(s, ',');
+}
+ret->shiftBases = sqlUnsignedComma(&s);
+ret->freqSourceCount = sqlSignedComma(&s);
+{
+int i;
+s = sqlEatChar(s, '{');
+AllocArray(ret->minorAlleleFreq, ret->freqSourceCount);
+for (i=0; i<ret->freqSourceCount; ++i)
+    {
+    ret->minorAlleleFreq[i] = sqlDoubleComma(&s);
+    }
+s = sqlEatChar(s, '}');
+s = sqlEatChar(s, ',');
+}
+{
+int i;
+s = sqlEatChar(s, '{');
+AllocArray(ret->majorAllele, ret->freqSourceCount);
+for (i=0; i<ret->freqSourceCount; ++i)
+    {
+    ret->majorAllele[i] = sqlStringComma(&s);
+    }
+s = sqlEatChar(s, '}');
+s = sqlEatChar(s, ',');
+}
+{
+int i;
+s = sqlEatChar(s, '{');
+AllocArray(ret->minorAllele, ret->freqSourceCount);
+for (i=0; i<ret->freqSourceCount; ++i)
+    {
+    ret->minorAllele[i] = sqlStringComma(&s);
+    }
+s = sqlEatChar(s, '}');
+s = sqlEatChar(s, ',');
+}
+ret->maxFuncImpact = sqlUnsignedComma(&s);
+ret->class = sqlEnumComma(&s, values_class, &valhash_class);
+ret->ucscNotes = sqlStringComma(&s);
+ret->_dataOffset = sqlLongLongComma(&s);
+ret->_dataLen = sqlSignedComma(&s);
+*pS = s;
+return ret;
+}
+
+void bigDbSnpFree(struct bigDbSnp **pEl)
+/* Free a single dynamically allocated bigDbSnp such as created
+ * with bigDbSnpLoad(). */
+{
+struct bigDbSnp *el;
+
+if ((el = *pEl) == NULL) return;
+freeMem(el->chrom);
+freeMem(el->name);
+freeMem(el->ref);
+/* All strings in alts are allocated at once, so only need to free first. */
+if (el->alts != NULL)
+    freeMem(el->alts[0]);
+freeMem(el->alts);
+freeMem(el->minorAlleleFreq);
+/* All strings in majorAllele are allocated at once, so only need to free first. */
+if (el->majorAllele != NULL)
+    freeMem(el->majorAllele[0]);
+freeMem(el->majorAllele);
+/* All strings in minorAllele are allocated at once, so only need to free first. */
+if (el->minorAllele != NULL)
+    freeMem(el->minorAllele[0]);
+freeMem(el->minorAllele);
+freeMem(el->ucscNotes);
+freez(pEl);
+}
+
+void bigDbSnpFreeList(struct bigDbSnp **pList)
+/* Free a list of dynamically allocated bigDbSnp's */
+{
+struct bigDbSnp *el, *next;
+
+for (el = *pList; el != NULL; el = next)
+    {
+    next = el->next;
+    bigDbSnpFree(&el);
+    }
+*pList = NULL;
+}
+
+void bigDbSnpOutput(struct bigDbSnp *el, FILE *f, char sep, char lastSep) 
+/* Print out bigDbSnp.  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);
+if (sep == ',') fputc('"',f);
+fprintf(f, "%s", el->ref);
+if (sep == ',') fputc('"',f);
+fputc(sep,f);
+fprintf(f, "%d", el->altCount);
+fputc(sep,f);
+{
+int i;
+if (sep == ',') fputc('{',f);
+for (i=0; i<el->altCount; ++i)
+    {
+    if (sep == ',') fputc('"',f);
+    fprintf(f, "%s", el->alts[i]);
+    if (sep == ',') fputc('"',f);
+    fputc(',', f);
+    }
+if (sep == ',') fputc('}',f);
+}
+fputc(sep,f);
+fprintf(f, "%u", el->shiftBases);
+fputc(sep,f);
+fprintf(f, "%d", el->freqSourceCount);
+fputc(sep,f);
+{
+int i;
+if (sep == ',') fputc('{',f);
+for (i=0; i<el->freqSourceCount; ++i)
+    {
+    fprintf(f, "%g", el->minorAlleleFreq[i]);
+    fputc(',', f);
+    }
+if (sep == ',') fputc('}',f);
+}
+fputc(sep,f);
+{
+int i;
+if (sep == ',') fputc('{',f);
+for (i=0; i<el->freqSourceCount; ++i)
+    {
+    if (sep == ',') fputc('"',f);
+    fprintf(f, "%s", el->majorAllele[i]);
+    if (sep == ',') fputc('"',f);
+    fputc(',', f);
+    }
+if (sep == ',') fputc('}',f);
+}
+fputc(sep,f);
+{
+int i;
+if (sep == ',') fputc('{',f);
+for (i=0; i<el->freqSourceCount; ++i)
+    {
+    if (sep == ',') fputc('"',f);
+    fprintf(f, "%s", el->minorAllele[i]);
+    if (sep == ',') fputc('"',f);
+    fputc(',', f);
+    }
+if (sep == ',') fputc('}',f);
+}
+fputc(sep,f);
+fprintf(f, "%u", el->maxFuncImpact);
+fputc(sep,f);
+if (sep == ',') fputc('"',f);
+sqlEnumPrint(f, el->class, values_class);
+if (sep == ',') fputc('"',f);
+fputc(sep,f);
+if (sep == ',') fputc('"',f);
+fprintf(f, "%s", el->ucscNotes);
+if (sep == ',') fputc('"',f);
+fputc(sep,f);
+fprintf(f, "%lld", el->_dataOffset);
+fputc(sep,f);
+fprintf(f, "%d", el->_dataLen);
+fputc(lastSep,f);
+}
+
+/* -------------------------------- End autoSql Generated Code -------------------------------- */