Eric Banks 392b5cbcdf The CachingIndexedFastaSequenceFile now automatically converts IUPAC bases to Ns and errors out on other non-standard bases. ... This way walkers won't see anything except the standard bases plus Ns in the reference. Added option to turn off this feature (to maintain backwards compatibility). As part of this commit I cleaned up the BaseUtils code by adding a Base enum and removing all of the static indexes for each of the bases. This uncovered a bug in the way the DepthOfCoverage walker counts deletions (it was counting Ns instead!) that isn't covered by tests. Fortunately that walker is being deprecated soon...		2013-01-16 10:22:43 -05:00
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net/sf	Updated all JAVA file licenses accordingly	2013-01-10 17:06:41 -05:00
org/broadinstitute	The CachingIndexedFastaSequenceFile now automatically converts IUPAC bases to Ns and errors out on other non-standard bases.	2013-01-16 10:22:43 -05:00