Use extending reads to improve consensus for gaps

[a-ludi]

We can use reads that reach into gaps without spanning them to improve sequence of reads that span the same gap, ie. for a read R_a extending contig C_xand a read R_b extending contig C_y and C_z (y != z) add R_a to the pileup of R_b iff x = y or x = z.

[a-ludi]

It is insufficient to have matching contigs as the reads might address different ends of each contig (see issue #12).

[a-ludi]

Fixed with issue #14.