FlowFeatureMapper speed improvements

[dror27]

1. Allow for using separate threads for reading / processing / writing (max 3)
2. Use NM SAM tag instead of edit distance
3. Perform likelihood scoring on trimmed read

Additional changes include:

1. CachingIndexedFastaSequenceFile is enhanced to be thread safe and allow for adjusting its cache size. The change involved synchronizing the main query method (getSubsequenceAt) and deriving the cache size from a settable variable rather than from a constant.