Question: inconsistent default of file suffix
gravatar for TimothéeFlutre
2.1 years ago by
TimothéeFlutre70 wrote:

By default, the bgzip function in the Rsamtools package appends ".bgz" to the file name. However, the filterVcf function in the VariantAnnotation package appends ".gz" (see here for Bioc 3.2).

Can you use ".bgz" by default in all functions (or at least in filterVcf)?

ps: this a minor thing, but I thought it can still be useful to fix it for the next release as it can be deconcerting for new users

ADD COMMENTlink modified 2.1 years ago by Valerie Obenchain ♦♦ 6.4k • written 2.1 years ago by TimothéeFlutre70
gravatar for Valerie Obenchain
2.1 years ago by
Valerie Obenchain ♦♦ 6.4k
United States
Valerie Obenchain ♦♦ 6.4k wrote:

Thanks for noticing this. The extension has been changed to .bgz in VariantAnnotation 1.17.7.


ADD COMMENTlink written 2.1 years ago by Valerie Obenchain ♦♦ 6.4k
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