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Added minimal Cram file support through the HTS adapter.
Currently only supports the reference fasta listed in the Cram
file header.
Added fast paired-end option and paired-end start point options
to script bam2wig. Temporary files now written to a temporary
subdirectory, which can be specified. Extreme depth can now be
handled properly by using 32 bit integers instead of 16. Splice
segments can now be fractionally counted.
Brought back and updated old script correlate_position_data to
identify positional shifts in nucleosome or ChIP signal peaks.
Added new SeqFeature methods to duplicate objects and delete
subfeatures.
Added option to format result numbers in script get_datasets.
Fix numerous small bugs in scripts data2gff, data2fasta,
get_intersecting_features, get_relative_data, and more