diff --git a/tools/fastq/fastq_trimmer_by_quality.py b/tools/fastq/fastq_trimmer_by_quality.py
index b6694e8e336..229248fa9fb 100644
--- a/tools/fastq/fastq_trimmer_by_quality.py
+++ b/tools/fastq/fastq_trimmer_by_quality.py
@@ -55,6 +55,12 @@ def main():
     if len ( args ) != 2:
         parser.error( "Need to specify an input file and an output file" )
     
+    if options.window_size < 1:
+        parser.error( 'You must specify a strictly positive window size' )
+    
+    if options.window_step < 1:
+        parser.error( 'You must specify a strictly positive step size' )
+    
     #determine an exhaustive list of window indexes that can be excluded from aggregation
     exclude_window_indexes = []
     last_exclude_indexes = []
@@ -76,7 +82,6 @@ def main():
     
     out = fastqWriter( open( args[1], 'wb' ), format = options.format )
     action = ACTION_METHODS[ options.aggregation_action ]
-    window_step = abs( options.window_step )
     
     num_reads = None
     num_reads_excluded = 0
@@ -93,7 +98,7 @@ def main():
                     if exclude_and_compare( action, quality_list[ lwindow_position:lwindow_position + options.window_size ], options.score_comparison, options.quality_score, exclude_window_indexes ):
                         fastq_read = fastq_read.slice( lwindow_position, None )
                         break
-                    lwindow_position += window_step
+                    lwindow_position += options.window_step
             else:
                 rwindow_position = len( quality_list ) #right position of window
                 while True:
@@ -105,7 +110,7 @@ def main():
                     if exclude_and_compare( action, quality_list[ lwindow_position:rwindow_position ], options.score_comparison, options.quality_score, exclude_window_indexes ):
                         fastq_read = fastq_read.slice( None, rwindow_position )
                         break
-                    rwindow_position -= window_step
+                    rwindow_position -= options.window_step
         if options.keep_zero_length or len( fastq_read ):
             out.write( fastq_read )
         else:
diff --git a/tools/fastq/fastq_trimmer_by_quality.xml b/tools/fastq/fastq_trimmer_by_quality.xml
index e57bb1eba9a..b8196d14810 100644
--- a/tools/fastq/fastq_trimmer_by_quality.xml
+++ b/tools/fastq/fastq_trimmer_by_quality.xml
@@ -94,6 +94,32 @@
       <param name="quality_score" value="1"/>
       <output name="output_file" file="sanger_full_range_original_sanger.fastqsanger" />
     </test>
+    <test>
+      <!-- Trim entire sequences; keep empty reads -->
+      <param name="input_file" value="sanger_full_range_original_sanger.fastqsanger" ftype="fastqsanger" />
+      <param name="keep_zero_length" value="true" />
+      <param name="trim_ends" value="53"/>
+      <param name="window_size" value="1"/>
+      <param name="step_size" value="1"/>
+      <param name="exclude_count" value="0"/>
+      <param name="aggregation_action" value="min"/>
+      <param name="score_comparison" value="&gt;="/>
+      <param name="quality_score" value="999"/>
+      <output name="output_file" file="sanger_full_range_empty_reads.fastqsanger" />
+    </test>
+    <test>
+      <!-- Trim entire sequences; discard empty reads -->
+      <param name="input_file" value="sanger_full_range_original_sanger.fastqsanger" ftype="fastqsanger" />
+      <param name="keep_zero_length"/>
+      <param name="trim_ends" value="53"/>
+      <param name="window_size" value="1"/>
+      <param name="step_size" value="1"/>
+      <param name="exclude_count" value="0"/>
+      <param name="aggregation_action" value="min"/>
+      <param name="score_comparison" value="&gt;="/>
+      <param name="quality_score" value="999"/>
+      <output name="output_file" file="empty_file.dat" />
+    </test>
   </tests>
   <help>
 This tool allows you to trim the ends of reads based upon the aggregate value of quality scores found within a sliding window; a sliding window of size 1 is equivalent to 'simple' trimming of the ends.