biopython/biopython — pull request #328 by vincentdavis (2014-05-17 03:30:53+00:00)
Title: TODO's -use_index and -soft_masking options

Fixed based on blastn manual

```
-use_index
Use MegaBLAST database index
Default = `false'
```
and
```
-soft_masking
Apply filtering locations as soft masks
Default = `true'
```