7bd3ab2b92d48520bf463fd43eeda13318dbe7cb
braney
  Wed Aug 3 12:13:27 2016 -0700
make the doc and AS file for bigPsl a little more explicit about the
file contents

diff --git src/hg/inc/bigPsl.h src/hg/inc/bigPsl.h
index 6e4eea1..831004f 100644
--- src/hg/inc/bigPsl.h
+++ src/hg/inc/bigPsl.h
@@ -1,88 +1,86 @@
 /* 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 */
+    char strand[2];	/* + or - indicates whether the query aligns to the + or - strand on the reference */
     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 */
+    char oStrand[2];	/* + or -, - implies doing a reverse complement on the psl on output */
     unsigned oChromSize;	/* Size of other chromosome. */
-    int *oChromStarts;	/* Start positions relative to oChromStart */
+    int *oChromStarts;	/* Start positions relative to oChromStart or from oChromStart+oChromSize depending on strand */
     char *oSequence;	/* Sequence on other chrom (or edit list, or empty) */
     char *oCDS;	/* CDS in NCBI format */
     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);
 /* 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,  char **seq, char **cds);
 /* build a psl from a bigPsl */
 #endif /* BIGPSL_H */
-
-