72535938e4d91de0bd56e9a3fd77b76f47e0b2da
braney
  Fri Jun 23 13:57:33 2023 -0700
add bigChain parsing code to library

diff --git src/hg/lib/bigChain.c src/hg/lib/bigChain.c
new file mode 100644
index 0000000..462bb7a
--- /dev/null
+++ src/hg/lib/bigChain.c
@@ -0,0 +1,181 @@
+/* bigChain.c was originally generated by the autoSql program, which also 
+ * generated bigChain.h and bigChain.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 "bigChain.h"
+
+
+
+char *bigChainCommaSepFieldNames = "chrom,chromStart,chromEnd,name,score,strand,tSize,qName,qSize,qStart,qEnd,chainScore";
+
+void bigChainStaticLoad(char **row, struct bigChain *ret)
+/* Load a row from bigChain 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->tSize = sqlUnsigned(row[6]);
+ret->qName = row[7];
+ret->qSize = sqlUnsigned(row[8]);
+ret->qStart = sqlUnsigned(row[9]);
+ret->qEnd = sqlUnsigned(row[10]);
+ret->chainScore = sqlDouble(row[11]);
+}
+
+struct bigChain *bigChainLoad(char **row)
+/* Load a bigChain from row fetched with select * from bigChain
+ * from database.  Dispose of this with bigChainFree(). */
+{
+struct bigChain *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->tSize = sqlUnsigned(row[6]);
+ret->qName = cloneString(row[7]);
+ret->qSize = sqlUnsigned(row[8]);
+ret->qStart = sqlUnsigned(row[9]);
+ret->qEnd = sqlUnsigned(row[10]);
+ret->chainScore = sqlDouble(row[11]);
+return ret;
+}
+
+struct bigChain *bigChainLoadAll(char *fileName) 
+/* Load all bigChain from a whitespace-separated file.
+ * Dispose of this with bigChainFreeList(). */
+{
+struct bigChain *list = NULL, *el;
+struct lineFile *lf = lineFileOpen(fileName, TRUE);
+char *row[12];
+
+while (lineFileRow(lf, row))
+    {
+    el = bigChainLoad(row);
+    slAddHead(&list, el);
+    }
+lineFileClose(&lf);
+slReverse(&list);
+return list;
+}
+
+struct bigChain *bigChainLoadAllByChar(char *fileName, char chopper) 
+/* Load all bigChain from a chopper separated file.
+ * Dispose of this with bigChainFreeList(). */
+{
+struct bigChain *list = NULL, *el;
+struct lineFile *lf = lineFileOpen(fileName, TRUE);
+char *row[12];
+
+while (lineFileNextCharRow(lf, chopper, row, ArraySize(row)))
+    {
+    el = bigChainLoad(row);
+    slAddHead(&list, el);
+    }
+lineFileClose(&lf);
+slReverse(&list);
+return list;
+}
+
+struct bigChain *bigChainCommaIn(char **pS, struct bigChain *ret)
+/* Create a bigChain out of a comma separated string. 
+ * This will fill in ret if non-null, otherwise will
+ * return a new bigChain */
+{
+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->tSize = sqlUnsignedComma(&s);
+ret->qName = sqlStringComma(&s);
+ret->qSize = sqlUnsignedComma(&s);
+ret->qStart = sqlUnsignedComma(&s);
+ret->qEnd = sqlUnsignedComma(&s);
+ret->chainScore = sqlDoubleComma(&s);
+*pS = s;
+return ret;
+}
+
+void bigChainFree(struct bigChain **pEl)
+/* Free a single dynamically allocated bigChain such as created
+ * with bigChainLoad(). */
+{
+struct bigChain *el;
+
+if ((el = *pEl) == NULL) return;
+freeMem(el->chrom);
+freeMem(el->name);
+freeMem(el->qName);
+freez(pEl);
+}
+
+void bigChainFreeList(struct bigChain **pList)
+/* Free a list of dynamically allocated bigChain's */
+{
+struct bigChain *el, *next;
+
+for (el = *pList; el != NULL; el = next)
+    {
+    next = el->next;
+    bigChainFree(&el);
+    }
+*pList = NULL;
+}
+
+void bigChainOutput(struct bigChain *el, FILE *f, char sep, char lastSep) 
+/* Print out bigChain.  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->tSize);
+fputc(sep,f);
+if (sep == ',') fputc('"',f);
+fprintf(f, "%s", el->qName);
+if (sep == ',') fputc('"',f);
+fputc(sep,f);
+fprintf(f, "%u", el->qSize);
+fputc(sep,f);
+fprintf(f, "%u", el->qStart);
+fputc(sep,f);
+fprintf(f, "%u", el->qEnd);
+fputc(sep,f);
+fprintf(f, "%g", el->chainScore);
+fputc(lastSep,f);
+}
+
+/* -------------------------------- End autoSql Generated Code -------------------------------- */
+