Modify 'colData' slot of SummarizedExperiment output from summarizeOverlaps().
This now holds the class type and length of 'reads'.


git-svn-id: https://hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/GenomicRanges@76812 bc3139a8-67e5-0310-9ffc-ced21a209358
Allow readGAlignmentPairs() to accept a BamFile as 'file'.


git-svn-id: https://hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/GenomicRanges@76835 bc3139a8-67e5-0310-9ffc-ced21a209358
Merge branch 'local-hedgehog'