TMAP map2 Options
This page describes the parameters for the TMAP map2 module. The map2 module implements BWA-long / BWASW reads mapping.
Options supported with the TMAP map2 module (all are optional):
|
Option |
Type |
Default |
Description |
|---|---|---|---|
|
--max-seed-hits |
INT |
1024 |
The maximum number of hits returned by a seed |
|
--length-coef |
FLOAT |
5.5 |
The coefficient of length-threshold adjustment |
|
--max-seed-intv |
INT |
6 |
The maximum seeding interval size |
|
--z-best |
INT |
1 |
The maximum number of top-scoring nodes to keep on each iteration |
|
--seeds-rev |
INT |
5 |
The number of seeds to trigger reverse alignment |
|
--narrow-rmdup |
INT |
false |
Remove duplicates for narrow SA hits |
|
--max-chain-gap |
INT |
10000 |
The maximum gap size during chaining |
|
--min-seq-length |
INT |
-1 |
The minimum sequence length to examine (-1 to disable) |
|
--max-seq-length |
INT |
-1 |
The maximum sequence length to examine (-1 to disable) |