Set chromap to not shift reads by default
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@JoseEspinosa is already working on this.
Since Sep 27, 2024.
enhancement
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Description
Description of feature
The parameters used by chromap are the ones suggested for ATAC-seq in their documentation, see here. This includes the --Tn5-shift; thus, the shift is applied by default, unlike the rest of the aligners. As the --shift_reads parameter has been implemented now, it would make sense to not shift reads by default and only use the --Tn5-shift chromap parameter when the --shift_reads is set.
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