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

diff --git src/hg/inc/bigChain.h src/hg/inc/bigChain.h
index f0748ba..bcb9914 100644
--- src/hg/inc/bigChain.h
+++ src/hg/inc/bigChain.h
@@ -1,74 +1,77 @@
 /* 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 -------------------------------- */
 
+int bigChainCmpTarget(const void *va, const void *vb);
+/* Compare to sort based on target position. */
+
 #endif /* BIGCHAIN_H */