[Bioc-devel] BSgenome changes

[Leonard Goldstein]

Dear Bioc team,

I'm following up on this recent GitHub issue
<https://github.com/ldg21/SGSeq/issues/5>. Please see the issue for more
details and code examples.

It looks like changes in Bioc devel result in two copies of the
mitochondrial chromosome for BSgenome.Hsapiens.UCSC.hg19 -- one named chrM
like in previous package versions (length 16571) and one named chrMT
(length 16569).

When using seqlevelsStyle() to change chromosome names from UCSC to NCBI
format, this results in new behavior -- in the past chrM was simply renamed
MT, now the different sequence chrMT is used. Is this intended?

Leonard

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