Use Plink encoding for chromsome names in BIM format output
Merge pull request #7 from keithj/devel

In Plink BIM output, the chromosomes were not encoded as integers
Added the option to export SNP metadata from the Beadpool Manifest as JSON.
Merged Plink format-related code into one file.
Added writing of gender field.
Added supoort for writing un-normalized intensity data to SIM files

Added support for converting SIM data to GenoSNP input format
SIM default is now raw, rather than normalized

Added normalize keyword arguments where necessary

Updated CLI to enable selection of normalization
Bumped version
Merge pull request #8 from keithj/devel

New feature (raw intensities) and some extra Plink support
Bump up heap space for large manifests
Fixed bug where application did not exit with an appropriate error code on file errors

Removed export of GenoSNP annotation (these data have been added to the JSON SNP metadata)
Bumped version for removal of a CLI option
Merge pull request #9 from keithj/devel

Removal of a GenoSNP-related CLI option
Changed JSON export of SNP metadata to use event-driven writing.

Reduced dynamic space size request for building.

Disabled saving the dynamic space size in the image (enables setting by CLI).
Merge pull request #10 from keithj/devel

Reduction in memory use when exporting SNP JSON
Fixed a bug in converting SIM to GenoSNP format where partial datasets are requested (start argument is used). The seek step to skip samples was missing.

Added method to skip intensities of some number of samples by seeking.
Fixed a bug in converting SIM to GenoSNP format where partial datasets are requested (start argument is used). The seek step to skip samples was missing.

Added method to skip intensities of some number of samples by seeking.
Merge branch 'devel' of github.com:keithj/genotype-call into devel
Fixed severe bug causeing haeap exhaustion when throwing an illegal
argument error for mismatched SIM and manifest files. The large
manifest object was being prett-printed, using all memory in string
creation.

Removed the manifest condition slot as it's not strictly required.
Fixed bug in test data where the generated GTC files contained extra X and Y intensities (vectors were 2x expected length). The file offsets in the header were still correct, so data later in the file were still valid and found correctly (hence tests passed).