c4b0bffb34ea956be81bd62bc1d8cd61e530e5d0
ceisenhart
  Wed Jun 4 16:20:59 2014 -0700
stylistic changes
diff --git src/utils/fastqMottTrim/fastqMottTrim.c src/utils/fastqMottTrim/fastqMottTrim.c
index 93cc23a..48d9628 100644
--- src/utils/fastqMottTrim/fastqMottTrim.c
+++ src/utils/fastqMottTrim/fastqMottTrim.c
@@ -12,40 +12,40 @@
 #include "common.h"
 #include "linefile.h"
 #include "hash.h"
 #include "options.h"
 #include "dystring.h"
 #include "fq.h"
 
 int clMinLength = 30;
 boolean clIsIllumina = FALSE;
 int clCutoff = 3;
 
 void usage()
 /* Explain usage and exit. */
 {
 errAbort(
-  "fastqMottTrim - applies Mott's trimming algorithm to a fastq file\n"
-  " trims the 3 prime end based on cumulative quality \n"
+  "fastqMottTrim - Applies Mott's trimming algorithm to a fastq file.\n"
+  "Trims the 3 prime end based on cumulative quality \n"
   "usage:\n"
   "   fastqMottTrim input.fq output.fq\n"
-  "for paired end use \n"
+  "for paired end use; \n"
   "   fastqMottTrim pair1.fq pair2.fq output1.fq output2.fq \n"
   "options:\n"
-  " -minLength=N the minimum length allowed for a trimmed sequence default 20  \n"
-  " -isIllumina TRUE for illumina, FALSE for Sanger \n"
-  " -cutoff=N  the lowest desired phred score, default 30 \n"
+  " -minLength = int The minimum length allowed for a trimmed sequence, the default is 30\n"
+  " -isIllumina bool TRUE for illumina, FALSE for Sanger. Sanger is the default \n"
+  " -cutoff = int The lowest desired phred score, the default is 3.\n"
   );
 }
 
 /* Command line validation table. */
 static struct optionSpec options[] = {
    {"minLength",OPTION_INT},
    {"isIllumina",OPTION_BOOLEAN},
    {"cutoff",OPTION_INT},
    {NULL,0},
 };
 
 
 boolean  mottTrim(struct fq *input, int minLength, boolean isIllumina, int cutoff)
 /* Applies mott's trimming algorithm to the fastq input. 
  * Trims from the 3 prime end based on 
@@ -103,32 +103,32 @@
         /* For paired data both reads must pass the minimum cutoff length.*/
 	{
 	fqWriteNext(fq, f);
         fqWriteNext(fq2, f2);
 	}
     fqFree(&fq);
     fqFree(&fq2);
     }
 carefulClose(&f);
 carefulClose(&f2);
 }
 
 
 
 void trimSingleFastqFile(char *input, char *output, int minLength, boolean isIllumina, int cutoff )
-/* Goes through fastq sequences in a fastq file; */
-/* Parses, stores, mottTrims,  prints, then frees each fastq sequence. */
+/* Goes through fastq sequences in a fastq file; 
+ * Parses, stores, mottTrims,  prints, then frees each fastq sequence. */
 {
 FILE *f = mustOpen(output, "w");
 struct lineFile *lf = lineFileOpen(input, TRUE);
 struct fq *fq;
 while ((fq = fqReadNext(lf)) != NULL)
     {
     if( mottTrim(fq, minLength, isIllumina, cutoff))
         {
 	fqWriteNext(fq, f);
         }
     fqFree(&fq);
     }
 carefulClose(&f);
 }