Jin Yu - 2012-11-28

A new development version 1.4.2 of Atlas-SNP2 had been submitted to the trunk.

The changes since 1.4.1:

1.Add an option “-w” in Atlas-SNP2 to only evaluate the sites in a given VIP list.
2.Atlas-SNP2 will evaluate the VIP sites of extra-high coverage, regardless of the setting of “maximum coverage”. And these VIP sites will be marked as “high_coverage” in the filter column if they are higher than “maximum coverage”. (In previous version, these sites are skipped)
3.Require the users to set the sequencing platform. The labels are “--Illumina” ,”454_FLX”,”454_XLR”. To make it compatible to previous submission scripts of various users, “-s” for Illumina data will still work.