[Bioc-devel] Fwd: readGAlignmentsFromBam function

Michael Lawrence lawrence.michael at gene.com
Thu Feb 19 22:15:41 CET 2015

---------- Forwarded message ----------
From: "Karolis Uziela" <karolis.uziela at scilifelab.se>
Date: Feb 19, 2015 9:22 AM
Subject: readGAlignmentsFromBam function
To: "Michael Lawrence" <lawrence.michael at gene.com>
Cc: "bioconductor at r-project.org" <bioconductor at r-project.org>


I have looked at R check results for the devel version of Bioconductor and
I noticed that the package I developed ("prebs") gives this warning:

Warning: 'readGAlignmentsFromBam' is deprecated.

What is the new function that should be used instead of
readGAlignmentsFromBam (GenomicAlignments package)? Do the changes
affect readGAlignmentPairs function, too?



Karolis Uziela

PhD student
Science for Life Laboratory
Box 1031
17121 Solna, Sweden
Mob. +46 729 120 395

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