Mapper Options

The following options are in the [Mapper] section of the configuration file. For more detailed information on these options, see DNA Mapping.

Name

Description

Command Line Equivalent

Range

ann-sj-max-indel

Maximum indel length to expect near an annotated splice junction.

--Mapper.ann-sj-max-indel

0 to 63

edit-chain-limit

For edit-mode 1 or 2: Maximum seed chain length in a read to qualify for seed editing.

--Mapper.edit-chain-limit

edit-chain-limit >= 0

edit-mode

0 = No edits, 1 = Chain len test, 2 = Paired chain len test, 3 = Edit all std seeds.

--Mapper.edit-mode

0 to 3

 

edit-read-len

For edit-mode 1 or 2: Read length in which to try edit-seed-num edited seeds.

--Mapper.edit-read-len

edit-read-len > 0

edit-seed-num

For edit-mode 1 or 2: Requested number of seeds per read to allow editing on.

--Mapper.edit-seed-num

edit-seed-num >= 0

enable-map-align

Enable use of BAM input files for mapper/aligner.

--enable-map-align

true/false

map-orientations

0=Normal, 1=No Rev Comp, 2=No Forward (paired end requires Normal).

--Mapper.map-orientations

0 to 2

max-intron-bases

Maximum intron length reported.

--Mapper.max-intron-bases

 

min-intron-bases

Minimum reference deletion length reported as an intron.

--Mapper.min-intron-bases

 

seed-density

Requested density of seeds from reads queried in the hash table

--Mapper.seed-density

0 > seed-density > 1