Float extraSearchDistance parameter.  Change gap extend probability
Merge branch 'MAPQ-matei' of https://github.com/amplab/snap into MAPQ-matei
Fix bug in MultiInputReadSupplier
Minor tweaks used for un-committed utility programs
Silly tools that should be deleted before the beta
Merge branch 'MAPQ-matei' of https://github.com/amplab/snap into MAPQ-matei