58424e56be
RR counts are represented as offsets from the first count, but that wasn't being done correctly when counts are adjusted on the fly. Also, we were triggering the expensive conversion and writing to binary tags even when we weren't going to write the read to disk. The code has been updated so that unconverted counts are passed to the GATKSAMRecord and it knows how to encode the tag correctly. Also, there are now methods to write to the reduced counts array without forcing the conversion (and methods that do force the conversion). Also: 1. counts are now maintained as ints whenever possible. Only the GATKSAMRecord knows about the internal encoding. 2. as discussed in meetings today, we updated the encoding so that it can now handle a range of values that extends to 255 instead of 127 (and is backwards compatible). 3. tests have been moved from SyntheticReadUnitTest to GATKSAMRecordUnitTest accordingly. |
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