Adam Kiezun issues

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                                            Adam Kiezun

BAM async compression could use multiple threads

Right now, only 1 thread per file is used. Compression easily has enough work for multiple threads and it would speed up the runtime

can we pass bwa index pointer directly?

I see that the index is passed to the JNI laver via the BWAIndex object. Really though I think only the pointer is actually used. Can it be passed directly...