Illumina SNP validator and meta-data extractor

[Martin Svensson]

The data files should be validated automatically and some data such as number of spot should be extracted for display in the GUI.

[Nicklas Nordborg]

This is for the array design. A BPM file is opened by BeadStudio? and then saved in csv format. The start of that file looks like:

[Heading]
Descriptor File Name(s),HumanCNV370v1_C.bpm
Assay Format,Infinium
SNP Count,370404
[Assay]
IlmnID,Name,IlmnStrand,SNP,AddressA_ID,AlleleA_ProbeSeq,AddressB_ID,AlleleB_ProbeSeq,Chr,MapInfo,Ploidy,Species,CustomerStrand,IlmnStrand,IllumicodeSeq,TopGenomicSeq
rs10000010-126_B_F_IFB1153208421:0,rs10000010,Bot,[T/C],900010475,,0,,4,21227772,2,Homo sapiens,BOT,Bot,,

The "SNP Count" value can be extracted and stored in the array design. No features are imported into the database.

[Martin Svensson]

(In [590]) References #93 You can now validate and extract meta-data from SNP-manifest files. The validator class and metadata extractor class is now being set when creating manifest data file-type in the installation plug-in.

[Martin Svensson]

(In [591]) References #93 Correct some comments and removed debug-code

[Martin Svensson]

(In [620]) Fixes #93 Added some more javadoc and improved the code format in a few places.