Generate bam format alignments using bfast
output_aln
type: mapsource: fq_inputcategory: outputoptional: {}pattern: ./*.aln
output_bam
type: mapsource: fq_inputcategory: outputoptional: {}pattern: ./*.bam
true -> colour space, false -> NT space
Specifies the average mismatch quality
Any extra parameters for the localalign command
Any extra parameters for the match command
Any extra parameters for the postprocess command
Specifies to remove low mapping quality alignments
Specifies to remove low (alignment) scoring alignments
0 - BAF, 1 - SAM
Specifies that paired reads are on opposite strands
Specifies the pairing distance standard deviation to examine when recuing
print program parameters
Specifies the number of threads to use
specifies output timing information
Do ungapped local alignment
Specifies that ungapped pairing rescue should be performed
True value specifies that pairing should not be performed
Display usage summary (help)
0 - consider both strands, 1 - forwards strand only, 2 - reverse strand only