Center for Integrative Bioinformatics Vienna
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The following table contains all parameters used by the MASon libraries. These parameters have to be provided by the class that implements the IConfig interface. All mandatory parameters have to be set before the CreateAlignment (see Documentation) is called!

Parameter Description Type Used by Mandatory
qry_max_len Length of the longest read int all yes
corridor Length of the corridor (k) int all yes
score_match Score for a match float all yes
score_mismatch Score for a mismatch float all yes
score_gap_read Score for adding a gap to a read float all yes
score_gap_ref Score for adding a gap to the reference float all yes
ocl_threads Number of threads used for execution. int OpenCL (CPU), SSE no
block_multiplier A factor that influences the batch size int OpenCL (CPU, GPU), CUDA no

Printable version of: http://www.cibiv.at/software/ngm/mason/Parameters.shtml

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