PairHMM : don't pass base indel qualities to native code

[akiezun]

we don't use indel base qualities anymore in GATK, so this code is creating and passing 2 arrays that are always filled with DEFAULT_INSERTION_DELETION_QUAL=45 for every read. This must be expensive. If the number is needed for the PairHMM, then just pass 45.

@eitanbanks wdyt? are the indel quals needed in the pairhmm?

[droazen]

Assigning to @gspowley to determine whether this is still an issue.

[gspowley]

It would help performance if we used constants instead of arrays in PairHMM. I'll investigate.

[magicDGS]

But what if indel qualities are set somehow but an user? Will the PairHMM code still consider them if they are not constant, either in the native or pure-java implementation?