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wwood / CoverM

Read coverage calculator for metagenomics
GNU General Public License v3.0
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Include secondary in filter mode #152

Open natalia-rodilla opened 1 year ago

natalia-rodilla commented 1 year ago

Dear developers, Thank you very much for this tool. I am using the filter mode on the alignments of metatranscriptomics reads to a database of MAGs. I would like to keep all those alignments with a high identity, regardless of them being primary or secondary. From the description in the documentation (and my experience), only primary alignments are considered. However, there is also the option "--exclude-supplementary", which seems strange to me because they are always excluded even when it is not set. This made me wonder if there was a way to make the filter mode consider all alignments. Would this be possible? Best regards, Natalia

wwood commented 1 year ago

Hi,

No problem.

You are right for the currently released version. However, if you install the version by git clone'ing the current main branch, then you the options for this are changed.

Let me know if that doesn't solve it. ben