a1693312d826bef79bda3d13693a80055d43f705
braney
  Tue Aug 4 12:15:39 2015 -0700
left out bigPsl.c in my earlier bigPsl check in.   #14241

diff --git src/hg/inc/bigPsl.h src/hg/inc/bigPsl.h
new file mode 100644
index 0000000..2bbb188
--- /dev/null
+++ src/hg/inc/bigPsl.h
@@ -0,0 +1,88 @@
+/* bigPsl.h was originally generated by the autoSql program, which also 
+ * generated bigPsl.c and bigPsl.sql.  This header links the database and
+ * the RAM representation of objects. */
+
+#ifndef BIGPSL_H
+#define BIGPSL_H
+
+#include "bigBed.h"
+#include "dnaseq.h"
+
+#define BIGPSL_NUM_COLS 24
+
+extern char *bigPslCommaSepFieldNames;
+
+struct bigPsl
+/* bigPsl pairwise alignment */
+    {
+    struct bigPsl *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 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 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);
+/* Load all bigPsl from chopper separated file.
+ * Dispose of this with bigPslFreeList(). */
+
+#define bigPslLoadAllByTab(a) bigPslLoadAllByChar(a, '\t');
+/* Load all bigPsl from tab separated file.
+ * Dispose of this with bigPslFreeList(). */
+
+struct bigPsl *bigPslCommaIn(char **pS, struct bigPsl *ret);
+/* Create a bigPsl out of a comma separated string. 
+ * This will fill in ret if non-null, otherwise will
+ * return a new bigPsl */
+
+void bigPslFree(struct bigPsl **pEl);
+/* Free a single dynamically allocated bigPsl such as created
+ * with bigPslLoad(). */
+
+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);
+/* build a psl from a bigPsl */
+#endif /* BIGPSL_H */
+
+