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Parameters¶
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 |
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