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Added functions/parameters and global variable corresponding to...

audric Cologne requested to merge kissplice_rmRD into master

Added functions/parameters and global variable corresponding to redundancy/low-complexity removal. Updated kissreads to interpret "I" character either as Insertion or Deletion. Added parameters for controlling number of mismatchs on reads during alignment step for SNP (default 0). KNOWN ISSUES: kissreads won't be able to align reads overlapping multiple indels, which can lead to under-quantification of events. Kissreads must be changed to allow gap-alignment.

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