gatk-3.8/public/java
Mark DePristo 52ef4a3e26 Function to compute whether a VariantContext indel is part of a TandemRepeat
Returns true iff VC is an non-complex indel where every allele represents an expansion or
 contraction of a series of identical bases in the reference.

 The logic of this function is pretty simple.  Take all of the non-null alleles in VC.  For
 each insertion allele of n bases, check if that allele matches the next n reference bases.
 For each deletion allele of n bases, check if this matches the reference bases at n - 2 n,
 as it must necessarily match the first n bases.  If this test returns true for all
 alleles you are a tandem repeat, otherwise you are not.  Note that in this context n is the
 base differences between the ref and alt alleles
2012-04-06 16:07:46 -04:00
..
config Reorganized the codebase beneath top-level public and private directories, 2011-06-28 06:55:19 -04:00
src Function to compute whether a VariantContext indel is part of a TandemRepeat 2012-04-06 16:07:46 -04:00
test Function to compute whether a VariantContext indel is part of a TandemRepeat 2012-04-06 16:07:46 -04:00