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lindenb / jvarkit

Java utilities for Bioinformatics
https://jvarkit.readthedocs.io/
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remove brackets in sequences #49

Closed CNoune closed 8 years ago

CNoune commented 8 years ago

Description

Removal of brackets from the sequences and sequence name in order to streamline pipeline and save storage space with large combinations

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lindenb commented 8 years ago

Hi @CNoune thank you for the PR, but I don't really understand why you changed

if(super.bracket) sequence.append("[");

to

if(super.bracket);

The -b option is disabled by default: https://github.com/lindenb/jvarkit/blob/master/src/main/java/com/github/lindenb/jvarkit/tools/biostar/Biostar175929.xml#L15 , so not using '-b' will hide the bracket.

CNoune commented 8 years ago

Hi Pierre,

I am such a fool. I didn't even notice that when I ran it. I think I am over tired.

Please disregard the change.

Thanks, Chris On 31 Mar 2016 17:07, "Pierre Lindenbaum" notifications@github.com wrote:

Hi @CNoune https://github.com/CNoune thank you for the PR, but I don't really understand why you changed

if(super.bracket) sequence.append("[");

to

if(super.bracket);

The -b option is disabled by default: https://github.com/lindenb/jvarkit/blob/master/src/main/java/com/github/lindenb/jvarkit/tools/biostar/Biostar175929.xml#L15 , so not using '-b' will hide the bracket.

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