Wrong number (/ counter / calculation) in summary statistics of fastq-mcf

[GoogleCodeExporter]

What steps will reproduce the problem?

1. Create a mock fastq file with the following content:
@readname
ATCGATCGATCGATCGATCGATCGATCGATCGATCGATCGATCGATCGATCGATCGATCG
+
############################################################

2. Run fastqc-mcf with default parameters:
# ea-utils.1.1.2-686/fastq-mcf n/a test.fastq 
Command Line: n/a test.fastq
Scale used: 2.2
Phred: 33
Threshold used: 1 out of 1
Files: 1
Total reads: 1
Too short after clip: 1
Trimmed 1 reads by an average of 120.00 bases on quality < 7

What is the expected output? What do you see instead?
Observe that fastqc-mcf says on average 120 bases are clipped, though there are 
only 60 bases inside of the fastq file.

What version of the product are you using? On what operating system?
This happened with some older versions, as well as the most recent 
ea-utils.1.1.2-686 on a Linux machine.

This error occurs regardless of whether or not I am using an adapter file.

Original issue reported on code.google.com by delasmurf on 25 Aug 2014 at 12:29

[GoogleCodeExporter]

I just checked: The problem is still present in the svn at revision 772.

Original comment by delasmurf on 25 Aug 2014 at 12:48

[GoogleCodeExporter]

Fixed in release 773.   Test added... yay.

Original comment by earone...@gmail.com on 25 Aug 2014 at 3:52

• Changed state: Fixed