52ef4a3e26
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 |
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| .. | ||
| alignment | ||
| commandline | ||
| gatk | ||
| jna | ||
| utils | ||
| BaseTest.java | ||
| MD5DB.java | ||
| MedianUnitTest.java | ||
| StingTextReporter.java | ||
| WalkerTest.java | ||