e70152e44cc66cc599ff6b699eb8adc07f3e656a
kent
  Sat May 24 21:09:34 2014 -0700
Adding Copyright NNNN Regents of the University of California to all files I believe with reasonable certainty were developed under UCSC employ or as part of Genome Browser copyright assignment.
diff --git src/hg/inc/samAlignment.h src/hg/inc/samAlignment.h
index 2b6838f..f54585f 100644
--- src/hg/inc/samAlignment.h
+++ src/hg/inc/samAlignment.h
@@ -1,78 +1,81 @@
 /* samAlignment.h was originally generated by the autoSql program, which also
  * generated samAlignment.c and samAlignment.sql.  This header links the database and
  * the RAM representation of objects. */
 
+/* Copyright (C) 2011 The Regents of the University of California 
+ * See README in this or parent directory for licensing information. */
+
 #ifndef SAMALIGNMENT_H
 #define SAMALIGNMENT_H
 
 #include "asParse.h"
 
 #define SAMALIGNMENT_NUM_COLS 12
 
 struct samAlignment
 /* The fields of a SAM short read alignment, the text version of BAM. */
     {
     struct samAlignment *next;  /* Next in singly linked list. */
     char *qName;	/* Query template name - name of a read */
     unsigned short flag;	/* Flags.  0x10 set for reverse complement.  See SAM docs for others. */
     char *rName;	/* Reference sequence name (often a chromosome) */
     unsigned pos;	/* 1 based position */
     unsigned char mapQ;	/* Mapping quality 0-255, 255 is best */
     char *cigar;	/* CIGAR encoded alignment string. */
     char *rNext;	/* Ref sequence for next (mate) read. '=' if same as rName, '*' if no mate */
     int pNext;	/* Position (1-based) of next (mate) sequence. May be -1 or 0 if no mate */
     int tLen;	/* Size of DNA template for mated pairs.  -size for one of mate pairs */
     char *seq;	/* Query template sequence */
     char *qual;	/* ASCII of Phred-scaled base QUALity+33.  Just '*' if no quality scores */
     char *tagTypeVals;	/* Tab-delimited list of tag:type:value optional extra fields */
     };
 
 void samAlignmentStaticLoad(char **row, struct samAlignment *ret);
 /* Load a row from samAlignment table into ret.  The contents of ret will
  * be replaced at the next call to this function. */
 
 struct samAlignment *samAlignmentLoad(char **row);
 /* Load a samAlignment from row fetched with select * from samAlignment
  * from database.  Dispose of this with samAlignmentFree(). */
 
 struct samAlignment *samAlignmentLoadAll(char *fileName);
 /* Load all samAlignment from whitespace-separated file.
  * Dispose of this with samAlignmentFreeList(). */
 
 struct samAlignment *samAlignmentLoadAllByChar(char *fileName, char chopper);
 /* Load all samAlignment from chopper separated file.
  * Dispose of this with samAlignmentFreeList(). */
 
 #define samAlignmentLoadAllByTab(a) samAlignmentLoadAllByChar(a, '\t');
 /* Load all samAlignment from tab separated file.
  * Dispose of this with samAlignmentFreeList(). */
 
 struct samAlignment *samAlignmentCommaIn(char **pS, struct samAlignment *ret);
 /* Create a samAlignment out of a comma separated string.
  * This will fill in ret if non-null, otherwise will
  * return a new samAlignment */
 
 void samAlignmentFree(struct samAlignment **pEl);
 /* Free a single dynamically allocated samAlignment such as created
  * with samAlignmentLoad(). */
 
 void samAlignmentFreeList(struct samAlignment **pList);
 /* Free a list of dynamically allocated samAlignment's */
 
 void samAlignmentOutput(struct samAlignment *el, FILE *f, char sep, char lastSep);
 /* Print out samAlignment.  Separate fields with sep. Follow last field with lastSep. */
 
 #define samAlignmentTabOut(el,f) samAlignmentOutput(el,f,'\t','\n');
 /* Print out samAlignment as a line in a tab-separated file. */
 
 #define samAlignmentCommaOut(el,f) samAlignmentOutput(el,f,',',',');
 /* Print out samAlignment as a comma separated list including final comma. */
 
 /* -------------------------------- End autoSql Generated Code -------------------------------- */
 
 struct asObject *samAsObj();
 // Return asObject describing fields of SAM/BAM
 #define bamAsObj() samAsObj()
 
 #endif /* SAMALIGNMENT_H */