Module: Bio

Defined in:

lib/bio/maf/parser.rb,
lib/bio/maf/maf.rb,
lib/bio/maf/index.rb,
lib/bio/maf/struct.rb,
lib/bio/ucsc/ucsc_bin.rb,
lib/bio/ucsc/genomic-interval-bin.rb

Overview

UCSCBin

Author

MISHIMA, Hiroyuki

Copyright

MISHIMA, Hiroyuki, 2010-2011

License

The Ruby licence (Ryby's / GPLv2 dual)

Original program in C by Jim Kent, 2002 See also http://genomewiki.ucsc.edu/index.php/Bin_indexing_system; a paper Kent, et. al. Genome Research 2002.12:996-1006; and src/lib/binRange.c in the kent source tree.

Bio::Ucsc::UcscBin -

1. convert between 0-based half-open interval and 1-based full-close intervals.
2. Calculate Bin number from genomic physical position according to UCSC's Bin Indexing System.

Defined Under Namespace

Modules: MAF, Ucsc Classes: GenomicInterval