Beta 3 build posted

[Christopher Chang]

Beta 3 is now posted.  In addition to bugfixes, this includes:

* --meta-analysis.

* basic filters for VCF genotype calls (--vcf-min-gq, --vcf-min-gp).

* clean import of single-chromosome Oxford-format files (--oxford-single-chr).

* allelic scoring for dosage data.

* --set-test (PLINK 1.07's gene-based test).

* --list-duplicate-vars, which identifies pairs of variants with identical position and allele codes.

* more conformant VCF output.  ALT column is now '.' when it isn't present in the immediate dataset.  REF alleles are flagged as "possibly swapped with ALT" unless the user asserts (with --real-ref-alleles) that they are correct.

* --epistasis.  The quantitative trait linear regression has been heavily optimized, and can be more than two orders of magnitude faster than PLINK 1.07 on large datasets.