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/utils/bamToFastq/bamToFastq.c src/utils/bamToFastq/bamToFastq.c
index 0fafdf5..4ea7eaf 100644
--- src/utils/bamToFastq/bamToFastq.c
+++ src/utils/bamToFastq/bamToFastq.c
@@ -1,127 +1,130 @@
 /* bamToFastq - converts a BAM file to Fastq. */
+
+/* Copyright (C) 2014 The Regents of the University of California 
+ * See README in this or parent directory for licensing information. */
 #include "common.h"
 #include "linefile.h"
 #include "hash.h"
 #include "options.h"
 #include "bamFile.h"
 
 void usage()
 /* Explain usage and exit. */
 {
 errAbort(
   "bamToFastq - converts a BAM file to Fastq\n"
   "usage:\n"
   "   bamToFastq input.bam output.fastq\n"
   "options:\n"
   "   "
   );
 }
 
 /* Command line validation table. */
 static struct optionSpec options[] = {
    {NULL, 0},
 };
 
 struct fastqSeq
 /* Holds a single fastq sequence. */
     {
     struct fastqSeq *next; /* Next in sequence. */
     int size;       /* Size of the sequence. */
     char *header;   /* Sequence header, begins with '@' */
     char *del;      /* Fastq deliminator '+' */
     char *dna;      /* DNA sequence */
     unsigned char *quality;  /* DNA quality, in ASCII format, unsigned for bam functions */
     };
 
 void fixQuality(struct fastqSeq *seq)
 /* The bam quality reader returns a format that is not FASTQ. */
 /* This function updates the bam quality to a fastq quality. */
 {
 int size = strlen(seq->dna);
 int i = 0;
 for (i=0; i < size; ++i)
     {
     seq->quality[i] += 33;
     }
 seq->quality[size]='\0';
 }
 
 void fastqWriteNext(struct fastqSeq *input, FILE *f)
 /* Writes a single fastq structure to the target file. */
 {
     fprintf(f,"%s\n",input->header);
     fprintf(f,"%s\n",input->dna);
     fprintf(f,"%s\n",input->del);
     fprintf(f,"%s\n",input->quality);
 }
 
 
 void freeFastqSeq(struct fastqSeq **pInput)
 /* Frees the memory allocated to a fastq structure. */
 {
 struct fastqSeq *input = *pInput;
 if (input != NULL)
     {
     freeMem(input->header);
     freeMem(input->dna);
     freeMem(input->del);
     freeMem(input->quality);
     freez(pInput);
     }
 }
 
 char *concat(char *s1, char *s2)
 /* A simple concatenate function. */
 {
 char *result = needMem(strlen(s1)+strlen(s2) +1);
 strcpy(result,s1);
 strcat(result,s2);
 return result;
 }
 
 samfile_t *samMustOpen(char *fileName, char *mode, void *extraHeader)
 /* Open up samfile or die trying. */
 {
 samfile_t *sf = samopen(fileName, mode, extraHeader);
 if (sf == NULL)
     errnoAbort("Couldn't open %s.\n", fileName);
 return sf;
 }
 
 
 void bamToFastq(char *inBam, char *outFastq)
 /* bamToFastq - converts a BAM file to Fastq. */
 {
 samfile_t *in = samMustOpen(inBam, "rb", NULL);
 /* Open up the BAM input  and a fastq sequence */
 FILE *f = mustOpen(outFastq, "w");
 bam1_t one;
 ZeroVar(&one);	// This seems to be necessary!
 struct fastqSeq seq = {};
 for (;;)
     {
     if (samread(in, &one) < 0)
 	{
 	break;
 	}
     seq.header = concat("@",bam1_qname(&one));
     seq.del = "+";  
     seq.dna = bamGetQuerySequence(&one, TRUE);
     seq.quality = bamGetQueryQuals(&one, TRUE);
     /* enter in the required fastqSeq values */
     fixQuality(&seq); 
     fastqWriteNext(&seq, f);
     /* print the fasqSeq to file */
     }
 samclose(in);
 }
 
 int main(int argc, char *argv[])
 /* Process command line. */
 {
 optionInit(&argc, argv, options);
 if (argc != 3)
     usage();
 bamToFastq(argv[1],argv[2]);
 return 0;
 }