fd846a7b8acbc8b1a0da31405bb475404dc627e3
ceisenhart
  Wed May 21 16:11:28 2014 -0700
Modified comments, camel cased variables
diff --git src/utils/bamToFastq/bamToFastq.c src/utils/bamToFastq/bamToFastq.c
index 5e46d6c..0fafdf5 100644
--- src/utils/bamToFastq/bamToFastq.c
+++ src/utils/bamToFastq/bamToFastq.c
@@ -1,99 +1,98 @@
 /* bamToFastq - converts a BAM file to Fastq. */
-/* currently working, however some header information is lost */
 #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 */
+/* Holds a single fastq sequence. */
     {
-    struct fastqSeq *next;
+    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 */
+/* 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)
-/* a function for writing a single fastq struct to file */
+/* 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 struct */
+/* 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 */
+/* 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 */
+/* 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;