4ac9486a77f0ed4e87de2e946f29e203b354398b
markd
  Thu Jun 13 13:56:46 2024 -0700
added chainToBigChain command

diff --git src/hg/lib/bigLink.c src/hg/lib/bigLink.c
new file mode 100644
index 0000000..22f11bc
--- /dev/null
+++ src/hg/lib/bigLink.c
@@ -0,0 +1,152 @@
+/* bigLink.c was originally generated by the autoSql program, which also 
+ * generated bigLink.h and bigLink.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 "bigLink.h"
+
+
+
+char *bigLinkCommaSepFieldNames = "chrom,chromStart,chromEnd,name,qStart";
+
+void bigLinkStaticLoad(char **row, struct bigLink *ret)
+/* Load a row from bigLink 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->qStart = sqlUnsigned(row[4]);
+}
+
+struct bigLink *bigLinkLoad(char **row)
+/* Load a bigLink from row fetched with select * from bigLink
+ * from database.  Dispose of this with bigLinkFree(). */
+{
+struct bigLink *ret;
+
+AllocVar(ret);
+ret->chrom = cloneString(row[0]);
+ret->chromStart = sqlUnsigned(row[1]);
+ret->chromEnd = sqlUnsigned(row[2]);
+ret->name = cloneString(row[3]);
+ret->qStart = sqlUnsigned(row[4]);
+return ret;
+}
+
+struct bigLink *bigLinkLoadAll(char *fileName) 
+/* Load all bigLink from a whitespace-separated file.
+ * Dispose of this with bigLinkFreeList(). */
+{
+struct bigLink *list = NULL, *el;
+struct lineFile *lf = lineFileOpen(fileName, TRUE);
+char *row[5];
+
+while (lineFileRow(lf, row))
+    {
+    el = bigLinkLoad(row);
+    slAddHead(&list, el);
+    }
+lineFileClose(&lf);
+slReverse(&list);
+return list;
+}
+
+struct bigLink *bigLinkLoadAllByChar(char *fileName, char chopper) 
+/* Load all bigLink from a chopper separated file.
+ * Dispose of this with bigLinkFreeList(). */
+{
+struct bigLink *list = NULL, *el;
+struct lineFile *lf = lineFileOpen(fileName, TRUE);
+char *row[5];
+
+while (lineFileNextCharRow(lf, chopper, row, ArraySize(row)))
+    {
+    el = bigLinkLoad(row);
+    slAddHead(&list, el);
+    }
+lineFileClose(&lf);
+slReverse(&list);
+return list;
+}
+
+struct bigLink *bigLinkCommaIn(char **pS, struct bigLink *ret)
+/* Create a bigLink out of a comma separated string. 
+ * This will fill in ret if non-null, otherwise will
+ * return a new bigLink */
+{
+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->qStart = sqlUnsignedComma(&s);
+*pS = s;
+return ret;
+}
+
+void bigLinkFree(struct bigLink **pEl)
+/* Free a single dynamically allocated bigLink such as created
+ * with bigLinkLoad(). */
+{
+struct bigLink *el;
+
+if ((el = *pEl) == NULL) return;
+freeMem(el->chrom);
+freeMem(el->name);
+freez(pEl);
+}
+
+void bigLinkFreeList(struct bigLink **pList)
+/* Free a list of dynamically allocated bigLink's */
+{
+struct bigLink *el, *next;
+
+for (el = *pList; el != NULL; el = next)
+    {
+    next = el->next;
+    bigLinkFree(&el);
+    }
+*pList = NULL;
+}
+
+void bigLinkOutput(struct bigLink *el, FILE *f, char sep, char lastSep) 
+/* Print out bigLink.  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->qStart);
+fputc(lastSep,f);
+}
+
+/* -------------------------------- End autoSql Generated Code -------------------------------- */
+
+int bigLinkCmpTarget(const void *va, const void *vb)
+/* Compare to sort based on target position. */
+{
+const struct bigLink *a = *((struct bigLink **)va);
+const struct bigLink *b = *((struct bigLink **)vb);
+int dif = strcmp(a->chrom, b->chrom);
+if (dif == 0)
+    dif = a->chromStart - b->chromStart;
+return dif;
+}
+