zlib and gzip

[Thomas van Gurp]

Dear Developers,

First of, thanks for creating this script. It does exactly what is needed and does so very fast. I have one request.

To save space I normally work with gzip in both input and output files. Would it be possible to add an option for bzip2/gzip in both input and output file? Also, I would like to specify the names of all output files instead of pear deciding for me. Third, would it be possible to read from a pipe/stdin?

Kind regards,

Thomas

[Alexandros Stamatakis]

Dear Thomas,

Are you using the latest PEAR-version from github?

It implements gzip parsing.

Alexis

--
Alexandros (Alexis) Stamatakis

Research Group Leader, Heidelberg Institute for Theoretical Studies
Full Professor, Dept. of Informatics, Karlsruhe Institute of Technology
Adjunct Professor, Dept. of Ecology and Evolutionary Biology, University
of Arizona at Tucson

www.exelixis-lab.org

[Qiyun Zhu]

Dear developer,

I tried the latest GitHub release as of today and it did not seem to parse gzip files.

What I did:
pear -f forward.fastq.gz -r reverse.fastq.gz -o peared.fastq

And it said:
[ERROR] - Cannot determine the file type of SRR1204963.fastq.gz. Ensure it is a BZIP2 compressed FASTQ file or plain FASTQ.

Is there anything I missed? Thanks!

Qiyun

[Tomas Flouri]

Hello Qiyun,

I must admit this is my mistake. I commited the gzip implementation only locally and not on github. I'll push it later in the evening together with a --no-trim option.

Tomas

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[Tomas Flouri]

Hello Qiyun,

in the bin folder on GitHub, you will find the file

pear-0.9.5-bin-64

which is a statically compiled binary that can read both bz2 and gz files.

I haven't yet updated the source code on GitHub, and hence you will get no gzip (zlib) support when compiling from source code.
I'll update the source code in a couple of days when I finish with some new features in pear.

Cheers,
tomas

On 12/09/2014 10:44 PM, Qiyun Zhu wrote:

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[Qiyun Zhu]

Dear Tomas,

I appreciate your quick response and fix. I have tested the latest binary on my 64-bit Ubuntu 14.04 machine, and it worked! Thank you very much!

Best,
Qiyun