fixed bug where optional arguments should have been required arguments

README.md

@@ -94,7 +94,7 @@ truncation of sequences with Ns.
     sickle se -f input_file.fastq -t illumina -o trimmed_output_file.fastq -q 33 -l 40
     sickle se -f input_file.fastq -t illumina -o trimmed_output_file.fastq -x -n
     sickle se -t sanger -g -f input_file.fastq -o trimmed_output_file.fastq.gz
-    sickle se --fastq-file=input_file.fastq --qual-type=sanger --output-file=trimmed_output_file.fastq
+    sickle se --fastq-file input_file.fastq --qual-type sanger --output-file trimmed_output_file.fastq
 
 ### Sickle Paired End (`sickle pe`)
 
@@ -136,6 +136,6 @@ enable truncation of sequences with Ns.
 
     sickle pe -c combo.fastq -t sanger -M combo_trimmed_all.fastq
 
-    sickle pe --pe-file1=input_file1.fastq --pe-file2=input_file2.fastq --qual-type=sanger \
-    --output-pe1=trimmed_output_file1.fastq --output-pe2=trimmed_output_file2.fastq \
-    --output-single=trimmed_singles_file.fastq
+    sickle pe --pe-file1 input_file1.fastq --pe-file2 input_file2.fastq --qual-type sanger \
+    --output-pe1 trimmed_output_file1.fastq --output-pe2 trimmed_output_file2.fastq \
+    --output-single trimmed_singles_file.fastq

src/trim_paired.c

@@ -18,20 +18,20 @@ int paired_length_threshold = 20;
 
 static struct option paired_long_options[] = {
     {"qual-type", required_argument, 0, 't'},
-    {"pe-file1", optional_argument, 0, 'f'},
-    {"pe-file2", optional_argument, 0, 'r'},
-    {"pe-combo", optional_argument, 0, 'c'},
-    {"output-pe1", optional_argument, 0, 'o'},
-    {"output-pe2", optional_argument, 0, 'p'},
-    {"output-single", optional_argument, 0, 's'},
-    {"output-combo", optional_argument, 0, 'm'},
-    {"qual-threshold", optional_argument, 0, 'q'},
-    {"length-threshold", optional_argument, 0, 'l'},
-    {"no-fiveprime", optional_argument, 0, 'x'},
-    {"truncate-n", optional_argument, 0, 'n'},
-    {"gzip-output", optional_argument, 0, 'g'},
-    {"output-combo-all", optional_argument, 0, 'M'},
-    {"quiet", optional_argument, 0, 'z'},
+    {"pe-file1", required_argument, 0, 'f'},
+    {"pe-file2", required_argument, 0, 'r'},
+    {"pe-combo", required_argument, 0, 'c'},
+    {"output-pe1", required_argument, 0, 'o'},
+    {"output-pe2", required_argument, 0, 'p'},
+    {"output-single", required_argument, 0, 's'},
+    {"output-combo", required_argument, 0, 'm'},
+    {"qual-threshold", required_argument, 0, 'q'},
+    {"length-threshold", required_argument, 0, 'l'},
+    {"no-fiveprime", no_argument, 0, 'x'},
+    {"truncate-n", no_argument, 0, 'n'},
+    {"gzip-output", no_argument, 0, 'g'},
+    {"output-combo-all", required_argument, 0, 'M'},
+    {"quiet", no_argument, 0, 'z'},
     {GETOPT_HELP_OPTION_DECL},
     {GETOPT_VERSION_OPTION_DECL},
     {NULL, 0, NULL, 0}
@@ -45,8 +45,6 @@ void paired_usage (int status, char *msg) {
     fprintf(stderr, "Usage: %s pe [options] -c <interleaved input file> -t <quality type> -m <interleaved trimmed paired-end output> -s <trimmed singles file>\n\n\
 If you have one file with interleaved reads as input and you want ONLY one interleaved file as output:\n\
 Usage: %s pe [options] -c <interleaved input file> -t <quality type> -M <interleaved trimmed output>\n\n", PROGRAM_NAME, PROGRAM_NAME);
-    fprintf(stderr, "Finally, if you are using the long-style options, make sure to use an equals sign (=) with the option:\n\
-Usage: %s pe [options] --pe-file1=<paired-end forward fastq file> --pe-file2=<paired-end reverse fastq file> --qual-type=<quality type> --output-pe1=<trimmed PE forward file> --output-pe2=<trimmed PE reverse file> --output-single=<trimmed singles file>\n\n", PROGRAM_NAME);
     fprintf(stderr, "Options:\n\
 Paired-end separated reads\n\
 --------------------------\n\

src/trim_single.c

@@ -19,12 +19,12 @@ static struct option single_long_options[] = {
     {"fastq-file", required_argument, 0, 'f'},
     {"output-file", required_argument, 0, 'o'},
     {"qual-type", required_argument, 0, 't'},
-    {"qual-threshold", optional_argument, 0, 'q'},
-    {"length-threshold", optional_argument, 0, 'l'},
-    {"no-fiveprime", optional_argument, 0, 'x'},
-    {"discard-n", optional_argument, 0, 'n'},
-    {"gzip-output", optional_argument, 0, 'g'},
-    {"quiet", optional_argument, 0, 'z'},
+    {"qual-threshold", required_argument, 0, 'q'},
+    {"length-threshold", required_argument, 0, 'l'},
+    {"no-fiveprime", no_argument, 0, 'x'},
+    {"discard-n", no_argument, 0, 'n'},
+    {"gzip-output", no_argument, 0, 'g'},
+    {"quiet", no_argument, 0, 'z'},
     {GETOPT_HELP_OPTION_DECL},
     {GETOPT_VERSION_OPTION_DECL},
     {NULL, 0, NULL, 0}
@@ -34,13 +34,10 @@ void single_usage(int status, char *msg) {
 
     fprintf(stderr, "\nUsage: %s se [options] -f <fastq sequence file> -t <quality type> -o <trimmed fastq file>\n\
 \n\
-If you are using the long-style options, make sure to use an equals sign (=) with the option:\n\
-Usage: sickle se [options] --fastq-file=<fastq sequence file> --qual-type=<quality type> --output-file=<trimmed fastq file>\n\n", PROGRAM_NAME);
-
-fprintf(stderr, "Options:\n\
+Options:\n\
 -f, --fastq-file, Input fastq file (required)\n\
 -t, --qual-type, Type of quality values (solexa (CASAVA < 1.3), illumina (CASAVA 1.3 to 1.7), sanger (which is CASAVA >= 1.8)) (required)\n\
--o, --output-file, Output trimmed fastq file (required)\n");
+-o, --output-file, Output trimmed fastq file (required)\n", PROGRAM_NAME);
 
     fprintf(stderr, "-q, --qual-threshold, Threshold for trimming based on average quality in a window. Default 20.\n\
 -l, --length-threshold, Threshold to keep a read based on length after trimming. Default 20.\n\