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FelixKrueger / SNPsplit

Allele-specific alignment sorting
http://felixkrueger.github.io/SNPsplit/
GNU General Public License v3.0
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single end mode not working #66

Closed rberrens closed 1 year ago

rberrens commented 1 year ago

When I try to run SNPsplit in single end mode it gives me the following error: SNPsplit --single_end --snp_file Unknown option: single_end Please respecify command line options

If I add nothing to autodetect it says: Testing if input file 'Aligned.out.bam' looks like a Bisulfite-Seq file Unable to detect library type automatically, please specify whether the file is single- or paired-end manually

If I run the same forcing it to be paired SNPsplit is running.

FelixKrueger commented 1 year ago

Hi Rebecca,

The option --single_end has been added very recently: https://github.com/FelixKrueger/SNPsplit/blob/master/CHANGELOG.md#v050dev. If you do:

git clone git@github.com:FelixKrueger/SNPsplit.git

it should start working.

rberrens commented 1 year ago

thank you Felix!