987241ea99c99b93aea51bb63bdf579f927e9d2b
kent
  Wed Oct 7 13:46:09 2015 -0700
Fixing copyright on some old essentially public domain files.

diff --git src/inc/nib.h src/inc/nib.h
index 622a213..c755dc3 100644
--- src/inc/nib.h
+++ src/inc/nib.h
@@ -1,113 +1,112 @@
-/*****************************************************************************
- * Copyright (C) 2000 Jim Kent.  This source code may be freely used         *
- * for personal, academic, and non-profit purposes.  Commercial use          *
- * permitted only by explicit agreement with Jim Kent (jim_kent@pacbell.net) *
- *****************************************************************************/
 /* nib.h - interface to nucleotides stored 4 bits per base (so have
- * room for N. */
+ * room for N. 
+ *
+ * This file is copyright 2000 Jim Kent, but license is hereby
+ * granted for all use - public, private or commercial. */
+
 #ifndef NIB_H
 #define NIB_H
 
 #ifndef DNAUTIL_H
 #include "dnautil.h"
 #endif 
 
 #ifndef HASH_H
 #include "hash.h"
 #endif
 
 /** Options for controlling masking  */
 #define NIB_MASK_MIXED    0x01 /* Read uses case to indicate masking.
                                 * Write sets mask bit for lower-case */
 #define NIB_MASK_MAP      0x02 /* Read builds dnaSeq->mask bit map. Write
                                 * uses mask to set mask bases.  Note: the
                                 * bit map indicates which bases are not repeats
                                 */
 #define NIB_BASE_NAME     0x04 /* Return a sequence name that is the base name
                                 * the file. */
 
 void nibOpenVerify(char *fileName, FILE **retFile, int *retSize);
 /* Open file and verify it's in good nibble format. */
 
 struct dnaSeq *nibLoadPart(char *fileName, int start, int size);
 /* Load part of an .nib file. */
 
 struct dnaSeq *nibLoadPartMasked(int options, char *fileName, int start, int size);
 /* Load part of an .nib file, with control over handling of masked positions */
 
 struct dnaSeq *nibLdPart(char *fileName, FILE *f, int seqSize, int start, int size);
 /* Load part of an open .nib file. */
 
 struct dnaSeq *nibLdPartMasked(int options, char *fileName, FILE *f, int seqSize, int start, int size);
 /* Load part of an open .nib file, with control over handling of masked
  * positions. */
 
 struct dnaSeq *nibLoadAll(char *fileName);
 /* Load all of a nib file. */
 
 struct dnaSeq *nibLoadAllMasked(int options, char *fileName);
 /* Load part of a .nib file, with control over handling of masked
  * positions. Subranges of nib files may specified in the file name
  * using the syntax:
  *    /path/file.nib:seqid:start-end
  * or\n"
  *    /path/file.nib:start-end
  * With the first form, seqid becomes the id of the subrange, with the second
  * form, a sequence id of file:start-end will be used.
  */
 
 void nibWrite(struct dnaSeq *seq, char *fileName);
 /* Write out file in format of four bits per nucleotide. */
 
 void nibWriteMasked(int options, struct dnaSeq *seq, char *fileName);
 /* Write out file in format of four bits per nucleotide, with control over
  * handling of masked positions. */
 
 boolean nibIsFile(char *fileName);
 /* Return TRUE if file is a nib file. */
 
 boolean nibIsRange(char *fileName);
 /* Return TRUE if file specifies a subrange of a nib file. */
 
 void nibParseName(unsigned options, char *fileSpec, char *filePath,
                          char *name, unsigned *start, unsigned *end);
 /* Parse the nib name, getting the file name, seq name to use, and
  * optionally the start and end positions. Zero is return for start
  * and end if they are not specified. Return the path to the file
  * and the name to use for the sequence. */
 
 struct nibStream *nibStreamOpen(char *fileName);
 /* Create a new nib stream.  Open file and stuff. */
 
 void nibStreamClose(struct nibStream **pNs);
 /* Close a nib stream.  Flush last nibble if need be.  Fix up header. */
 
 void nibStreamOne(struct nibStream *ns, DNA base);
 /* Write out one base to nibStream. */
 
 void nibStreamMany(struct nibStream *ns, DNA *dna, int size);
 /* Write many bases to nibStream. */
 
 struct nibInfo
 /* Info on a nib file. */
     {
     struct nibInfo *next;
     char *fileName;	/* Name of nib file. */
     int size;		/* Number of bases in nib. */
     FILE *f;		/* Open file. */
     };
 
 struct nibInfo *nibInfoNew(char *path);
 /* Make a new nibInfo with open nib file. */
 
 void nibInfoFree(struct nibInfo **pNib);
 /* Free up nib info and close file if open. */
 
 struct nibInfo *nibInfoFromCache(struct hash *hash, char *nibDir, char *nibName);
 /* Get nibInfo on nibDir/nibName.nib from cache, filling cache if need be. */
 
 int nibGetSize(char* nibFile);
 /* Get the number of nucleotides in a nib */
 
 #endif /* NIB_H */