Packaged testing alpha

This testing alpha comprises two jarfiles;

The mask generator
Usage:

java -jar .CLI-maskFactory-v0.1.1.jar <ancestralAlignment> <maskSpecification> <maskfileOutput>

# e.g.: 

java -jar ../../jarfiles/CLI-maskFactory-v0.1.1.jar HCV_data/sub_053/FP7_05301_0.fasta ./HCV_data/mask_spec2 mask_nwe 

The CLI app
Usage:

java -jar CLI-app-v0.1.4.1.jar <maskFile> <ancestralFile> <output.tdf> <comma,separated,main,alignments>

# e.g.: 
java -jar ../../jarfiles/CLI-app-v0.1.4.1.jar mask_nwe ./HCV_data/sub_053/FP7_05301_0.fasta ./CLI_0.1.4_test_mask_5arg.tdf ./HCV_data/sub_053/FP7_05302_0.3644.fasta,./HCV_data/sub_053/FP7_05303_0.6137.fasta,./HCV_data/sub_053/FP7_05304_0.8438.fasta,./HCV_data/sub_053/FP7_05305_1.3699.fasta,./HCV_data/sub_053/FP7_05306_1.7836.fasta,./HCV_data/sub_053/FP7_05307_3.8986.fasta,./HCV_data/sub_053/FP7_05308_6.8429.fasta,./HCV_data/sub_053/FP7_05309_7.6849.fasta

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Mask files consist of one or more lines representing two comma-separated fields, e.g.:

<aggregated|averaged|floating-point-number>,000001111111

Mask specifications are a more concise format parsed by the CLI mask app to full maskfiles. The rate estimation behaviour is given but only the range of start/end positions to include in the mask, ie:

aggregated,1,22
fixed,*,21
averaged,1,*
0.718678,*,*
aggregated,*,*
averaged,*,*

(here the special character '*' is used to mean 'from start' or 'to end'.)