Geraldine Van der Auwera edf5880022 Updated SAMPileup codec and pileup-related docs ... Problem: the codec was written to take in consensus pileups produced with pileup -c option (which consists of 10 or 13 fields per line depending on the variant type) but errored out on the basic pileup format (which only has 6 fields per line). This was inconsistent and confusing to users. Solution: I added a switch in the parsing to recognize and handle both cases more appropriately, and updated related docs. While I was at it I also improved error messages in CheckPileup, which now emits User Error: Bad Input exceptions when reporting mismatches. Which may not be the best thing to do (ultimately they're not really errors, they're just reporting unwelcome results) but it beats emitting Runtime Exceptions. Tested by CheckPileupIntegrationTest which tests both format cases.		2014-01-14 09:14:16 -05:00
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net/sf/samtools	Delete unused FastaSequenceIndexBuilder class and accompanying test	2013-05-01 01:02:01 -04:00
org/broadinstitute/sting	Updated SAMPileup codec and pileup-related docs	2014-01-14 09:14:16 -05:00