TMAP map4 options
The TMAP map 4 module is based on the BWA fastmap routine, and searches for the maximum exact matches between the reads and reference.
The map4 module is the default for TMAP.
The following options are supported with the TMAP map4 module (all are optional).
|
Option |
Type |
Default |
Description |
|---|---|---|---|
|
Integer |
8 |
The number of bases to increase the seed for each seed increase iteration. -1 to disable. |
|
|
Float |
0.2 |
The fraction of seed positions that are under the maximum. |
|
|
Integer |
-1 |
The minimum seed length to accept hits. -1 to disable |
|
|
Integer |
48 |
The maximum seed length to accept hits. |
|
|
Float |
2.0 |
maximum seed length adjustment coefficient. -1 to disable |
|
|
Integer |
20 |
The maximum interval size to accept a hit. |
|
|
Integer |
3 |
The maximum representative hits for repetitive hits. |
|
|
Integer |
false |
Choose the representative hits randomly. Otherwise uniformly. |
|
|
Boolean |
false |
When seed stepping, try seeding when at least the minimum seed length is present. Otherwise, use the maximum seed length. |
|
|
--min-seq-length |
Integer |
-1 |
The minimum sequence length to examine. -1 to disable. |
|
--max-seq-length |
Integer |
-1 |
The maximum sequence length to examine. -1 to disable |