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Minimap2 #6698

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gdroc opened this issue Jan 24, 2025 · 2 comments · May be fixed by #6707
Open

Minimap2 #6698

gdroc opened this issue Jan 24, 2025 · 2 comments · May be fixed by #6707

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@gdroc
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gdroc commented Jan 24, 2025

I trying to reproduce the workflow presented in SyRi (https://schneebergerlab.github.io/syri/pipeline.html), but it seems that not all options are implemented (-eqx).
When reviewing the XML file, I noticed that this parameter is only applied to CRAM output (line 167) and is not utilized for BAM output.

minimap2 -ax asm5 --eqx refgenome qrygenome

Would it be possible to update this tool?
Gaetan

@bernt-matthias
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I guess the reason was that =/X CIGAR operators were not supported in samtool/bam/Sam in the past.

I guess we can try to change it.

@gdroc
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gdroc commented Jan 24, 2025

I believe it's relatively simple to fix.
You just need to add this code around line 144:

#if $io_options.eqx:
    --eqx
#end if

Additionally, please remove line 167, as the --eqx option doesn't make sense for Samtools.
Regards
Gaetan

@bgruening bgruening linked a pull request Jan 29, 2025 that will close this issue
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2 participants