4898794edd81be5285ea6e544acbedeaeb31bf78
max
  Tue Nov 23 08:10:57 2021 -0800
Fixing pointers to README file for license in all source code files. refs #27614

diff --git src/hg/inc/lrg.h src/hg/inc/lrg.h
index 094a6ed..af42d34 100644
--- src/hg/inc/lrg.h
+++ src/hg/inc/lrg.h
@@ -1,112 +1,112 @@
 /* lrg.h was originally generated by the autoSql program, which also 
  * generated lrg.c and lrg.sql.  This header links the database and
  * the RAM representation of objects. */
 
 /* Copyright (C) 2013 The Regents of the University of California 
- * See README in this or parent directory for licensing information. */
+ * See kent/LICENSE or http://genome.ucsc.edu/license/ for licensing information. */
 
 #ifndef LRG_H
 #define LRG_H
 
 #define LRG_NUM_COLS 21
 
 extern char *lrgCommaSepFieldNames;
 
 struct lrg
 /* Locus Reference Genomic regions */
     {
     struct lrg *next;  /* Next in singly linked list. */
     char *chrom;	/* Reference assembly chromosome or scaffold */
     unsigned chromStart;	/* Start position in chromosome */
     unsigned chromEnd;	/* End position in chromosome */
     char *name;	/* LRG ID */
     unsigned score;	/* Placeholder for BED format compatibility (0) */
     char strand[2];	/* Orientation of LRG to reference assembly: + or - */
     unsigned thickStart;	/* Placeholder for BED format compatibility (same as chromStart) */
     unsigned thickEnd;	/* Placeholder for BED format compatibility (same as chromEnd) */
     unsigned reserved;	/* Placeholder for BED format compatibility (0) */
     int blockCount;	/* Number of gapless aligned blocks */
     int *blockSizes;	/* Comma separated list of block sizes */
     int *chromStarts;	/* Start positions relative to chromStart */
     char *mismatches;	/* List of bases that differ between LRG and reference assembly */
     char *indels;	/* List of insertions/deletions in LRG and reference assembly */
     unsigned lrgSize;	/* Length in bases of LRG sequence */
     int hgncId;	/* Numeric HGNC gene identifier */
     char *hgncSymbol;	/* HGNC gene symbol */
     char *ncbiAcc;	/* NCBI accession of LRG sequence */
     char *lrgSource;	/* Source of LRG sequence */
     char *lrgSourceUrl;	/* URL of lrgSource */
     char *creationDate;	/* Date on which this sequence was added as a LRG */
     };
 
 struct lrg *lrgLoad(char **row);
 /* Load a lrg from row fetched with select * from lrg
  * from database.  Dispose of this with lrgFree(). */
 
 struct lrg *lrgLoadAll(char *fileName);
 /* Load all lrg from whitespace-separated file.
  * Dispose of this with lrgFreeList(). */
 
 struct lrg *lrgLoadAllByChar(char *fileName, char chopper);
 /* Load all lrg from chopper separated file.
  * Dispose of this with lrgFreeList(). */
 
 #define lrgLoadAllByTab(a) lrgLoadAllByChar(a, '\t');
 /* Load all lrg from tab separated file.
  * Dispose of this with lrgFreeList(). */
 
 struct lrg *lrgCommaIn(char **pS, struct lrg *ret);
 /* Create a lrg out of a comma separated string. 
  * This will fill in ret if non-null, otherwise will
  * return a new lrg */
 
 void lrgFree(struct lrg **pEl);
 /* Free a single dynamically allocated lrg such as created
  * with lrgLoad(). */
 
 void lrgFreeList(struct lrg **pList);
 /* Free a list of dynamically allocated lrg's */
 
 void lrgOutput(struct lrg *el, FILE *f, char sep, char lastSep);
 /* Print out lrg.  Separate fields with sep. Follow last field with lastSep. */
 
 #define lrgTabOut(el,f) lrgOutput(el,f,'\t','\n');
 /* Print out lrg as a line in a tab-separated file. */
 
 #define lrgCommaOut(el,f) lrgOutput(el,f,',',',');
 /* Print out lrg as a comma separated list including final comma. */
 
 /* -------------------------------- End autoSql Generated Code -------------------------------- */
 
 
 struct psl *lrgToPsl(struct lrg *lrg, uint chromSize);
 /* Use lrg's mismatches and indels to make a PSL. */
 
 struct dnaSeq *lrgReconstructSequence(struct lrg *lrg, char *db);
 /* Use genomic sequence, lrg->mismatches and lrg->indels to reconstruct LRG sequence */
 
 struct lrgDiff
 /* Locus Reference Genomic <mapping><diff> item condensed into coordinates and sequences:
  * an alignment gap block.  When lrg->strand is "-", chromSeq is reverse-complemented
  * but chromosome coordinates are still on + strand. */
 {
     struct lrgDiff *next;
     uint chromStart;
     uint chromEnd;
     char *chromSeq;
     uint lrgStart;
     uint lrgEnd;
     char *lrgSeq;
 };
 
 struct lrgDiff *lrgParseMismatches(struct lrg *lrg);
 /* Parse lrg->mismatches and return a list of lrgDiffs. */
 
 struct lrgDiff *lrgParseIndels(struct lrg *lrg);
 /* Parse lrg->indels and return a list of lrgDiffs. */
 
 void lrgDiffFreeList(struct lrgDiff **pDiff);
 /* Free up a list of parsed diffs. */
 
 #endif /* LRG_H */