[Bioc-devel] should genome() be so complicated?/add genome report to GRanges show method

Vincent Carey stvjc at channing.harvard.edu
Mon Sep 8 16:21:06 CEST 2014

For GRanges x, my naive expectation is that genome(x) returns a length-

one tag identifying the genome to which chromosomal coordinates

correspond.  The genome() method seems to have sequence-specific

semantics, which makes sense, but when we identify sequence

with chromosome, it seems too complicated.  Is there a use case for

a GRanges with sequences from several different genomes?

One reason I am inquiring is that I feel it would be nice to have the
GRanges show() method report, prominently, the genome in use (or NA

if unspecified).  This could be accomplished by reporting
unique(genome(x)), and perhaps that would be satisfactory.

after example(genome) :

> seqinfo(txdb)

Seqinfo of length 15

seqnames seqlengths isCircular genome

CH2L       23011544      FALSE    dm3

CH2R       21146708      FALSE    dm3

CH3L       24543557      FALSE    dm3

CH3R       27905053      FALSE    dm3

CH4         1351857      FALSE    dm3

...             ...        ...    ...

CH3LHet     2555491      FALSE    dm3

CH3RHet     2517507      FALSE    dm3

CHXHet       204112      FALSE    dm3

CHYHet       347038      FALSE    dm3

CHUextra   29004656      FALSE    dm3

> genome(seqinfo(txdb))

    CH2L     CH2R     CH3L     CH3R      CH4      CHX      CHU        M

   "dm3"    "dm3"    "dm3"    "dm3"    "dm3"    "dm3"    "dm3"    "dm3"

 CH2LHet  CH2RHet  CH3LHet  CH3RHet   CHXHet   CHYHet CHUextra

   "dm3"    "dm3"    "dm3"    "dm3"    "dm3"    "dm3"    "dm3"

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