42ccdd815277a3dc7d78b48fa0ac36d469ab628a
markd
  Mon Feb 28 19:07:04 2022 -0800
added bigRmsk autoSql files from Robert Hubley

diff --git src/hg/lib/bigRmskBed.c src/hg/lib/bigRmskBed.c
new file mode 100644
index 0000000..b37ce78
--- /dev/null
+++ src/hg/lib/bigRmskBed.c
@@ -0,0 +1,197 @@
+/* bigRmskBed.c was originally generated by the autoSql program, which also 
+ * generated bigRmskBed.h and bigRmskBed.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 "bigRmskBed.h"
+
+
+
+char *bigRmskBedCommaSepFieldNames = "chrom,chromStart,chromEnd,name,score,strand,thickStart,thickEnd,reserved,blockCount,blockSizes,blockStarts,id,description";
+
+void bigRmskBedStaticLoad(char **row, struct bigRmskBed *ret)
+/* Load a row from bigRmskBed 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->reserved = sqlUnsigned(row[8]);
+ret->blockCount = sqlUnsigned(row[9]);
+ret->blockSizes = row[10];
+ret->blockStarts = row[11];
+ret->id = sqlUnsigned(row[12]);
+ret->description = row[13];
+}
+
+struct bigRmskBed *bigRmskBedLoad(char **row)
+/* Load a bigRmskBed from row fetched with select * from bigRmskBed
+ * from database.  Dispose of this with bigRmskBedFree(). */
+{
+struct bigRmskBed *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->reserved = sqlUnsigned(row[8]);
+ret->blockCount = sqlUnsigned(row[9]);
+ret->blockSizes = cloneString(row[10]);
+ret->blockStarts = cloneString(row[11]);
+ret->id = sqlUnsigned(row[12]);
+ret->description = cloneString(row[13]);
+return ret;
+}
+
+struct bigRmskBed *bigRmskBedLoadAll(char *fileName) 
+/* Load all bigRmskBed from a whitespace-separated file.
+ * Dispose of this with bigRmskBedFreeList(). */
+{
+struct bigRmskBed *list = NULL, *el;
+struct lineFile *lf = lineFileOpen(fileName, TRUE);
+char *row[14];
+
+while (lineFileRow(lf, row))
+    {
+    el = bigRmskBedLoad(row);
+    slAddHead(&list, el);
+    }
+lineFileClose(&lf);
+slReverse(&list);
+return list;
+}
+
+struct bigRmskBed *bigRmskBedLoadAllByChar(char *fileName, char chopper) 
+/* Load all bigRmskBed from a chopper separated file.
+ * Dispose of this with bigRmskBedFreeList(). */
+{
+struct bigRmskBed *list = NULL, *el;
+struct lineFile *lf = lineFileOpen(fileName, TRUE);
+char *row[14];
+
+while (lineFileNextCharRow(lf, chopper, row, ArraySize(row)))
+    {
+    el = bigRmskBedLoad(row);
+    slAddHead(&list, el);
+    }
+lineFileClose(&lf);
+slReverse(&list);
+return list;
+}
+
+struct bigRmskBed *bigRmskBedCommaIn(char **pS, struct bigRmskBed *ret)
+/* Create a bigRmskBed out of a comma separated string. 
+ * This will fill in ret if non-null, otherwise will
+ * return a new bigRmskBed */
+{
+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->reserved = sqlUnsignedComma(&s);
+ret->blockCount = sqlUnsignedComma(&s);
+ret->blockSizes = sqlStringComma(&s);
+ret->blockStarts = sqlStringComma(&s);
+ret->id = sqlUnsignedComma(&s);
+ret->description = sqlStringComma(&s);
+*pS = s;
+return ret;
+}
+
+void bigRmskBedFree(struct bigRmskBed **pEl)
+/* Free a single dynamically allocated bigRmskBed such as created
+ * with bigRmskBedLoad(). */
+{
+struct bigRmskBed *el;
+
+if ((el = *pEl) == NULL) return;
+freeMem(el->chrom);
+freeMem(el->name);
+freeMem(el->blockSizes);
+freeMem(el->blockStarts);
+freeMem(el->description);
+freez(pEl);
+}
+
+void bigRmskBedFreeList(struct bigRmskBed **pList)
+/* Free a list of dynamically allocated bigRmskBed's */
+{
+struct bigRmskBed *el, *next;
+
+for (el = *pList; el != NULL; el = next)
+    {
+    next = el->next;
+    bigRmskBedFree(&el);
+    }
+*pList = NULL;
+}
+
+void bigRmskBedOutput(struct bigRmskBed *el, FILE *f, char sep, char lastSep) 
+/* Print out bigRmskBed.  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->reserved);
+fputc(sep,f);
+fprintf(f, "%u", el->blockCount);
+fputc(sep,f);
+if (sep == ',') fputc('"',f);
+fprintf(f, "%s", el->blockSizes);
+if (sep == ',') fputc('"',f);
+fputc(sep,f);
+if (sep == ',') fputc('"',f);
+fprintf(f, "%s", el->blockStarts);
+if (sep == ',') fputc('"',f);
+fputc(sep,f);
+fprintf(f, "%u", el->id);
+fputc(sep,f);
+if (sep == ',') fputc('"',f);
+fprintf(f, "%s", el->description);
+if (sep == ',') fputc('"',f);
+fputc(lastSep,f);
+}
+
+/* -------------------------------- End autoSql Generated Code -------------------------------- */
+