HiC.scala
    In buildInteractionGraph, an interaction is added only if
    the read is the first read of the pair.  This prevents double
    counting the number of reads in the interaction.

    Implemented and minimally test HiC.printMatrix.

    Fixed InteractionGraph.printMatrix to print the matrix between two
    different chromosomes to work properly.  When printing the
    interaction (r, s) where r is in chrA and s in chrB, needed to check
    that s was on chrB (i.e.; within the interval [startB, endB].

HiCTests.scala
    Wrote tests for printMatrix.  Not thorough.

new file:   testdata/test1.sam