updated ALT readme due to recent changes
updated directory name
r939: fixed a memory leak (issue #35)
r940: fixed a bug - missing primary hit
r941: set a min length for 3rd-round seeding
r942: ignore ALT hits when counting n_sub for ...

non-ALT hits. Counting leads to underestimated mapQ.
r943: change the default -y to 20, but ...

for GRCh38 ALT, this is not enough. We need -y at least 40 to get high accuracy
because a locus at chr19 has 35 copies.
Merge branch 'dev' into mem