13d3857bbc66cfaeac0b2b9b1f90340ad7fceff9
braney
  Mon Jun 26 05:58:25 2023 -0700
first pass at a synteny breaks track

diff --git src/hg/lib/bigChain.h src/hg/lib/bigChain.h
deleted file mode 100644
index f0748ba..0000000
--- src/hg/lib/bigChain.h
+++ /dev/null
@@ -1,74 +0,0 @@
-/* bigChain.h was originally generated by the autoSql program, which also 
- * generated bigChain.c and bigChain.sql.  This header links the database and
- * the RAM representation of objects. */
-
-#ifndef BIGCHAIN_H
-#define BIGCHAIN_H
-
-#define BIGCHAIN_NUM_COLS 12
-
-extern char *bigChainCommaSepFieldNames;
-
-struct bigChain
-/* bigChain pairwise alignment */
-    {
-    struct bigChain *next;  /* Next in singly linked list. */
-    char *chrom;	/* Reference sequence chromosome or scaffold */
-    unsigned chromStart;	/* Start position in chromosome */
-    unsigned chromEnd;	/* End position in chromosome */
-    char *name;	/* Name or ID of item, ideally both human readable and unique */
-    unsigned score;	/* Score (0-1000) */
-    char strand[2];	/* + or - for strand */
-    unsigned tSize;	/* size of target sequence */
-    char *qName;	/* name of query sequence */
-    unsigned qSize;	/* size of query sequence */
-    unsigned qStart;	/* start of alignment on query sequence */
-    unsigned qEnd;	/* end of alignment on query sequence */
-    double chainScore;	/* score from chain */
-    };
-
-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. */
-
-struct bigChain *bigChainLoad(char **row);
-/* Load a bigChain from row fetched with select * from bigChain
- * from database.  Dispose of this with bigChainFree(). */
-
-struct bigChain *bigChainLoadAll(char *fileName);
-/* Load all bigChain from whitespace-separated file.
- * Dispose of this with bigChainFreeList(). */
-
-struct bigChain *bigChainLoadAllByChar(char *fileName, char chopper);
-/* Load all bigChain from chopper separated file.
- * Dispose of this with bigChainFreeList(). */
-
-#define bigChainLoadAllByTab(a) bigChainLoadAllByChar(a, '\t');
-/* Load all bigChain from tab separated file.
- * Dispose of this with bigChainFreeList(). */
-
-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 */
-
-void bigChainFree(struct bigChain **pEl);
-/* Free a single dynamically allocated bigChain such as created
- * with bigChainLoad(). */
-
-void bigChainFreeList(struct bigChain **pList);
-/* Free a list of dynamically allocated bigChain's */
-
-void bigChainOutput(struct bigChain *el, FILE *f, char sep, char lastSep);
-/* Print out bigChain.  Separate fields with sep. Follow last field with lastSep. */
-
-#define bigChainTabOut(el,f) bigChainOutput(el,f,'\t','\n');
-/* Print out bigChain as a line in a tab-separated file. */
-
-#define bigChainCommaOut(el,f) bigChainOutput(el,f,',',',');
-/* Print out bigChain as a comma separated list including final comma. */
-
-/* -------------------------------- End autoSql Generated Code -------------------------------- */
-
-#endif /* BIGCHAIN_H */
-