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DaehwanKimLab / hisat2

Graph-based alignment (Hierarchical Graph FM index)
GNU General Public License v3.0
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--interleaved Option #174

Open ATpoint opened 6 years ago

ATpoint commented 6 years ago

Would it require a larger efford to implement the --interleaved option for interleaved input fastq files as in bowtie2? Would allow to pipe reads directly from the quality/adapter trimmer into hisat without any intermediate files.

best, Alex

bwlang commented 6 years ago

+1

snagaraj0 commented 4 years ago

Has this been implemented?

bwlang commented 4 years ago

It does not appear to be implemented as of 2.2.0.

@parkchanhee - it looks like you are the one most active maintaining this code... Would a PR implementing this feature be likely to be accepted?

parkchanhee commented 4 years ago

@bwlang Yes, I think it is a good idea to add the feature to HISAT2. We will review it once you make the PR. I think it will be accepted.

bwlang commented 4 years ago

I can't work on this right away... but it's good to know that you would be interested in the PR if someone gets to it before I do.

eboyden commented 3 years ago

+1 for adding this feature