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broadinstitute / gatk-protected

Obsolete/Legacy GATK repository -- go to https://github.com/broadinstitute/gatk instead
BSD 3-Clause "New" or "Revised" License
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Implement Circular Binary Segmentation algorithm #9

Closed vruano closed 9 years ago

vruano commented 9 years ago

We need to have a Circular Binary Segmentation algorithm implementation in Java. The algorithm is described here: Olshen, A. B., Venkatraman, E. S., Lucito, R., and Wigler, M. (2004). Circular binary segmentation for the analysis of array-based dna copy number data. Biostatistics, 5:557–72.

and speed improvements described here: Venkatraman, E. S. and Olshen, A. B. (2007). A faster circular binary segmentation algorithm for the analysis of array cgh data. Bioinformatics, 23:657–63.

The R implementation is in the DNACopy package: http://bioconductor.wustl.edu/bioc/vignettes/DNAcopy/inst/doc/DNAcopy.pdf

The requirement is to take data from the R package and implement the algorithm to produce results equivalent to those from R (there may be small differences due to random number generation).

vruano commented 9 years ago

Imported twice thus duplicated in #10