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

diff --git src/hg/lib/bigRmskAlignBed.c src/hg/lib/bigRmskAlignBed.c
new file mode 100644
index 0000000..0283ac0
--- /dev/null
+++ src/hg/lib/bigRmskAlignBed.c
@@ -0,0 +1,212 @@
+/* bigRmskAlignBed.c was originally generated by the autoSql program, which also 
+ * generated bigRmskAlignBed.h and bigRmskAlignBed.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 "bigRmskAlignBed.h"
+
+
+
+char *bigRmskAlignBedCommaSepFieldNames = "chrom,chromStart,chromEnd,chromRemain,score,percSubst,percDel,percIns,strand,repName,repType,repSubtype,repStart,repEnd,repRemain,id,calignData";
+
+void bigRmskAlignBedStaticLoad(char **row, struct bigRmskAlignBed *ret)
+/* Load a row from bigRmskAlignBed 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->chromRemain = sqlUnsigned(row[3]);
+ret->score = sqlFloat(row[4]);
+ret->percSubst = sqlFloat(row[5]);
+ret->percDel = sqlFloat(row[6]);
+ret->percIns = sqlFloat(row[7]);
+safecpy(ret->strand, sizeof(ret->strand), row[8]);
+ret->repName = row[9];
+ret->repType = row[10];
+ret->repSubtype = row[11];
+ret->repStart = sqlUnsigned(row[12]);
+ret->repEnd = sqlUnsigned(row[13]);
+ret->repRemain = sqlUnsigned(row[14]);
+ret->id = sqlUnsigned(row[15]);
+ret->calignData = row[16];
+}
+
+struct bigRmskAlignBed *bigRmskAlignBedLoad(char **row)
+/* Load a bigRmskAlignBed from row fetched with select * from bigRmskAlignBed
+ * from database.  Dispose of this with bigRmskAlignBedFree(). */
+{
+struct bigRmskAlignBed *ret;
+
+AllocVar(ret);
+ret->chrom = cloneString(row[0]);
+ret->chromStart = sqlUnsigned(row[1]);
+ret->chromEnd = sqlUnsigned(row[2]);
+ret->chromRemain = sqlUnsigned(row[3]);
+ret->score = sqlFloat(row[4]);
+ret->percSubst = sqlFloat(row[5]);
+ret->percDel = sqlFloat(row[6]);
+ret->percIns = sqlFloat(row[7]);
+safecpy(ret->strand, sizeof(ret->strand), row[8]);
+ret->repName = cloneString(row[9]);
+ret->repType = cloneString(row[10]);
+ret->repSubtype = cloneString(row[11]);
+ret->repStart = sqlUnsigned(row[12]);
+ret->repEnd = sqlUnsigned(row[13]);
+ret->repRemain = sqlUnsigned(row[14]);
+ret->id = sqlUnsigned(row[15]);
+ret->calignData = cloneString(row[16]);
+return ret;
+}
+
+struct bigRmskAlignBed *bigRmskAlignBedLoadAll(char *fileName) 
+/* Load all bigRmskAlignBed from a whitespace-separated file.
+ * Dispose of this with bigRmskAlignBedFreeList(). */
+{
+struct bigRmskAlignBed *list = NULL, *el;
+struct lineFile *lf = lineFileOpen(fileName, TRUE);
+char *row[17];
+
+while (lineFileRow(lf, row))
+    {
+    el = bigRmskAlignBedLoad(row);
+    slAddHead(&list, el);
+    }
+lineFileClose(&lf);
+slReverse(&list);
+return list;
+}
+
+struct bigRmskAlignBed *bigRmskAlignBedLoadAllByChar(char *fileName, char chopper) 
+/* Load all bigRmskAlignBed from a chopper separated file.
+ * Dispose of this with bigRmskAlignBedFreeList(). */
+{
+struct bigRmskAlignBed *list = NULL, *el;
+struct lineFile *lf = lineFileOpen(fileName, TRUE);
+char *row[17];
+
+while (lineFileNextCharRow(lf, chopper, row, ArraySize(row)))
+    {
+    el = bigRmskAlignBedLoad(row);
+    slAddHead(&list, el);
+    }
+lineFileClose(&lf);
+slReverse(&list);
+return list;
+}
+
+struct bigRmskAlignBed *bigRmskAlignBedCommaIn(char **pS, struct bigRmskAlignBed *ret)
+/* Create a bigRmskAlignBed out of a comma separated string. 
+ * This will fill in ret if non-null, otherwise will
+ * return a new bigRmskAlignBed */
+{
+char *s = *pS;
+
+if (ret == NULL)
+    AllocVar(ret);
+ret->chrom = sqlStringComma(&s);
+ret->chromStart = sqlUnsignedComma(&s);
+ret->chromEnd = sqlUnsignedComma(&s);
+ret->chromRemain = sqlUnsignedComma(&s);
+ret->score = sqlFloatComma(&s);
+ret->percSubst = sqlFloatComma(&s);
+ret->percDel = sqlFloatComma(&s);
+ret->percIns = sqlFloatComma(&s);
+sqlFixedStringComma(&s, ret->strand, sizeof(ret->strand));
+ret->repName = sqlStringComma(&s);
+ret->repType = sqlStringComma(&s);
+ret->repSubtype = sqlStringComma(&s);
+ret->repStart = sqlUnsignedComma(&s);
+ret->repEnd = sqlUnsignedComma(&s);
+ret->repRemain = sqlUnsignedComma(&s);
+ret->id = sqlUnsignedComma(&s);
+ret->calignData = sqlStringComma(&s);
+*pS = s;
+return ret;
+}
+
+void bigRmskAlignBedFree(struct bigRmskAlignBed **pEl)
+/* Free a single dynamically allocated bigRmskAlignBed such as created
+ * with bigRmskAlignBedLoad(). */
+{
+struct bigRmskAlignBed *el;
+
+if ((el = *pEl) == NULL) return;
+freeMem(el->chrom);
+freeMem(el->repName);
+freeMem(el->repType);
+freeMem(el->repSubtype);
+freeMem(el->calignData);
+freez(pEl);
+}
+
+void bigRmskAlignBedFreeList(struct bigRmskAlignBed **pList)
+/* Free a list of dynamically allocated bigRmskAlignBed's */
+{
+struct bigRmskAlignBed *el, *next;
+
+for (el = *pList; el != NULL; el = next)
+    {
+    next = el->next;
+    bigRmskAlignBedFree(&el);
+    }
+*pList = NULL;
+}
+
+void bigRmskAlignBedOutput(struct bigRmskAlignBed *el, FILE *f, char sep, char lastSep) 
+/* Print out bigRmskAlignBed.  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);
+fprintf(f, "%u", el->chromRemain);
+fputc(sep,f);
+fprintf(f, "%g", el->score);
+fputc(sep,f);
+fprintf(f, "%g", el->percSubst);
+fputc(sep,f);
+fprintf(f, "%g", el->percDel);
+fputc(sep,f);
+fprintf(f, "%g", el->percIns);
+fputc(sep,f);
+if (sep == ',') fputc('"',f);
+fprintf(f, "%s", el->strand);
+if (sep == ',') fputc('"',f);
+fputc(sep,f);
+if (sep == ',') fputc('"',f);
+fprintf(f, "%s", el->repName);
+if (sep == ',') fputc('"',f);
+fputc(sep,f);
+if (sep == ',') fputc('"',f);
+fprintf(f, "%s", el->repType);
+if (sep == ',') fputc('"',f);
+fputc(sep,f);
+if (sep == ',') fputc('"',f);
+fprintf(f, "%s", el->repSubtype);
+if (sep == ',') fputc('"',f);
+fputc(sep,f);
+fprintf(f, "%u", el->repStart);
+fputc(sep,f);
+fprintf(f, "%u", el->repEnd);
+fputc(sep,f);
+fprintf(f, "%u", el->repRemain);
+fputc(sep,f);
+fprintf(f, "%u", el->id);
+fputc(sep,f);
+if (sep == ',') fputc('"',f);
+fprintf(f, "%s", el->calignData);
+if (sep == ',') fputc('"',f);
+fputc(lastSep,f);
+}
+
+/* -------------------------------- End autoSql Generated Code -------------------------------- */
+