Read the coordinates information from a bed file.
This function is designed to read the bed file as ‘chrom’, ‘chromStart’, ‘chromEnd’. The strand information is also stored where available.
In the bed file, the ‘chromStart’ is on the 0-based coordinate system
while ‘chromEnd’ is on the 1-based coordinate system.
For example, the first 100 bases of a chromosome are
defined as ‘chromStart=0’, ‘chromEnd=100’,
and span the bases numbered 0-99.
When it is read into
both the ‘chromStart’ and ‘chromEnd’ are on 1-based coordinate,
‘chromStart=1’ and ‘chromEnd=100’.
When ‘assemblyFn’ is not
NULL, the corresponding
will be added into the returned
GRanges object is returned.
When no strand information is available in the bed file,
all the ranges are assumed to be on the positive strand.
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