3afb1ad18d251832c36c02910ba194a3996ab47a
braney
  Mon May 9 14:56:22 2016 -0700
some changes to bigPsl format

diff --git src/hg/inc/bigPsl.h src/hg/inc/bigPsl.h
index 2bbb188..6e4eea1 100644
--- src/hg/inc/bigPsl.h
+++ src/hg/inc/bigPsl.h
@@ -23,31 +23,31 @@
     unsigned score;	/* Score (0-1000) */
     char strand[2];	/* + or - for strand */
     unsigned thickStart;	/* Start of where display should be thick (start codon) */
     unsigned thickEnd;	/* End of where display should be thick (stop codon) */
     unsigned reserved;	/* RGB value (use R,G,B string in input file) */
     int blockCount;	/* Number of blocks */
     int *blockSizes;	/* Comma separated list of block sizes */
     int *chromStarts;	/* Start positions relative to chromStart */
     unsigned oChromStart;	/* Start position in other chromosome */
     unsigned oChromEnd;	/* End position in other chromosome */
     char oStrand[2];	/* + or - for other strand */
     unsigned oChromSize;	/* Size of other chromosome. */
     int *oChromStarts;	/* Start positions relative to oChromStart */
     char *oSequence;	/* Sequence on other chrom (or edit list, or empty) */
     char *oCDS;	/* CDS in NCBI format */
-    unsigned oBlock;	/* Block number on other sequence */
+    unsigned chromSize;	/* Size of target chromosome */
     unsigned match;	/* Number of bases matched. */
     unsigned misMatch;	/*  Number of bases that don't match  */
     unsigned repMatch;	/*  Number of bases that match but are part of repeats  */
     unsigned nCount;	/*  Number of 'N' bases  */
     };
 
 struct bigPsl *bigPslLoad(char **row);
 /* Load a bigPsl from row fetched with select * from bigPsl
  * from database.  Dispose of this with bigPslFree(). */
 
 struct bigPsl *bigPslLoadAll(char *fileName);
 /* Load all bigPsl from whitespace-separated file.
  * Dispose of this with bigPslFreeList(). */
 
 struct bigPsl *bigPslLoadAllByChar(char *fileName, char chopper);
@@ -69,20 +69,20 @@
 
 void bigPslFreeList(struct bigPsl **pList);
 /* Free a list of dynamically allocated bigPsl's */
 
 void bigPslOutput(struct bigPsl *el, FILE *f, char sep, char lastSep);
 /* Print out bigPsl.  Separate fields with sep. Follow last field with lastSep. */
 
 #define bigPslTabOut(el,f) bigPslOutput(el,f,'\t','\n');
 /* Print out bigPsl as a line in a tab-separated file. */
 
 #define bigPslCommaOut(el,f) bigPslOutput(el,f,',',',');
 /* Print out bigPsl as a comma separated list including final comma. */
 
 /* -------------------------------- End autoSql Generated Code -------------------------------- */
 
-struct psl  *pslFromBigPsl( char *chrom, struct bigBedInterval *bb, unsigned chromSize, char **seq, char **cds);
+struct psl  *pslFromBigPsl( char *chrom, struct bigBedInterval *bb,  char **seq, char **cds);
 /* build a psl from a bigPsl */
 #endif /* BIGPSL_H */