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/zoo/pslToFa/pslToFa.c src/hg/zoo/pslToFa/pslToFa.c
index de0bff3..9acf500 100644
--- src/hg/zoo/pslToFa/pslToFa.c
+++ src/hg/zoo/pslToFa/pslToFa.c
@@ -1,152 +1,152 @@
 /* Copyright (C) 2011 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. */
 
 #include <stdio.h>
 #include <stdlib.h>
 #include <string.h>
 #include <math.h>
 
 
 
 #include "common.h"
 #include "linefile.h"
 #include "nib.h"
 #include "jksql.h"
 #include "coordConv.h"
 #include "fa.h"
 #include "genoFind.h"
 #include "psl.h"
 #include "portable.h"
 #include "hdb.h"
 #include "dbDb.h"
 
 
 
 #ifndef DNASEQ_H
     #include "dnaseq.h"
 #endif
 
 #ifndef DNAUTIL_H
     #include "dnautil.h"
 #endif
 
 #ifndef NIB_H
     #include "nib.h"
 #endif
 
 
 
 
 
 unsigned int flipNegStrand( char strand, unsigned int start, unsigned int size )
 {
    if( strand == '-' )
        return( size - start );
    else
        return( start );
 }
 
 void printFa( unsigned char *FA, unsigned int maxFa )
 {
     unsigned int i;
     for( i=0; i<maxFa; i++ )
         printf("%c", FA[i] );
     printf("\n");
 }
 
 
 void initFa( unsigned char *FA, unsigned int maxFa )
 {
     unsigned int i;
     for( i=0; i<maxFa; i++ )
         FA[i] = '-';
 }
 
 void writeFa( unsigned char *FA, unsigned int maxFa, unsigned int theStart, unsigned int size, 
         char *qSeq )
 {
     unsigned int i;
 
 
     if( theStart+size-1 >= maxFa || theStart < 0 )
     {
         fprintf( stderr, "maxFa(%d) is too short for [%d,%d]\n", 
                 maxFa, theStart, theStart+size-1);
         exit(1);
     }
     
     for( i=theStart; i<theStart+size; i++ )
             FA[i] = qSeq[i-theStart];
 }
 
 
 int main( int argc, char **argv )
 {
     unsigned int maxFa;
     unsigned char *FA;
     unsigned int i;
     unsigned int blockNum;
     unsigned int size;
 
     unsigned int ts, qs;
     
     
     struct dnaSeq *seq1;
     struct dnaSeq *seq2;
     struct dnaSeq *tSeq;
     struct dnaSeq *qSeq;
 
     struct dnaSeq *tSeqAll;
 
     struct psl *p;
 
 
     if( argc != 4 && argc != 5 )
     {
         printf( "Usage: pslToFa input.psl master.nib slave.nib [maxFa]\n" );
         exit(1);
     }
 
     tSeqAll = nibLoadAll( argv[2] );
 
     if( argc == 5 )
         maxFa = atoi(argv[5]);
     else
         maxFa = strlen(tSeqAll->dna);    //1877426 + 1 for zoo2
 
     FA = malloc( sizeof( unsigned char ) * ( maxFa + 1 ) );
     initFa(FA, maxFa);
 
 
     p = pslLoadAll(argv[1]);
     while( p )
     {
         qSeq = nibLoadPart( argv[3], p->qStart, p->qEnd - p->qStart );
         tSeq = nibLoadPart( argv[2], p->tStart, p->tEnd - p->tStart );
 
         for( i=0; i<p->blockCount; i++ )
         {
             size = p->blockSizes[i];
             qs = flipNegStrand( p->strand[0], p->qStarts[i], p->qSize);
             ts = flipNegStrand( p->strand[1], p->tStarts[i], p->tSize);
 
             seq1 = nibLoadPart( argv[2], ts, size );   /*master*/
             seq2 = nibLoadPart( argv[3], qs, size );   /*slave*/
 
             writeFa( FA, maxFa, ts, size, seq2->dna );
         }
 
         p = p->next;
     }
 
     if( strlen(tSeqAll->dna) != maxFa )
     {
         printf("Sequence sizes must match!!! (strlen(tSeqAll->dna) = %d, maxFa = %d)\n",  
                 strlen(tSeqAll->dna), maxFa );
     }
     printFa(tSeqAll->dna, maxFa );
     printFa(FA, maxFa );
     return(0);
 }