trouble reading from STDIN about cutadapt HOT 5 CLOSED

From [email protected] on March 09, 2011 11:44:52

cutadapt 0.9 on linux.

from cutadapt.

From [email protected] on March 10, 2011 07:23:27

Hello,

thanks for your report. I could reproduce your problem: This is a bug or rather a missing feature.

The problem is that cutadapt reads the first few lines from the input file in order to autodetect whether it is in FASTA or FASTQ format. It then closes the file and re-opens it and starts from the beginning. When reading from standard input, those lines that have been read are just gone and re-opening standard input also does not work.

I have removed the feature for now and updated the documentation, but I'll leave this issue open as an enhancement request.

Labels: -Type-Defect Type-Enhancement

from cutadapt.

From [email protected] on March 13, 2011 15:31:00

hello,

thank you for the explanation. i modified the code for my needs.
also i believe there is a mixup between 'r' and 'w' in cutadapt line 104.

really helpful tool so far, thanks for the great work!

from cutadapt.

From [email protected] on March 14, 2011 00:36:56

You're right, the comment in line 104 was incorrect. Great to hear cutadapt is helpful!

from cutadapt.

From [email protected] on March 16, 2011 04:09:54

This should be fixed in cutadapt 0.9.2.

Status: Fixed

from cutadapt.