Index

A

Annotate_OTU_Table_Command (class in otu.Annotate_OTU_Table_Command)

Assemble_Command (class in assemble.Assemble_Command)

B

Build_OTU_Table_Command (class in otu.Build_OTU_Table_Command)

C

ChewbaccaCommand (class in classes.ChewbaccaCommand) ChewbaccaProgram (class in classes.ChewbaccaProgram) Clean_Adapters_Command (class in clean.Clean_Adapters_Command) Clean_Deep_Command (class in clean.Clean_Deep_Command)

Clean_Deep_Repair_Command (class in clean.Clean_Deep_Repair_Command) Clean_Quality_Command (class in clean.Clean_Quality_Command) Cluster_Command (class in cluster.Cluster_Command) Convert_Fastq_Fasta_Command (class in util.Convert_Fastq_Fasta_Command)

D

default_program (assemble.Assemble_Command.Assemble_Command attribute) (clean.Clean_Adapters_Command.Clean_Adapters_Command attribute) (clean.Clean_Deep_Command.Clean_Deep_Command attribute) (clean.Clean_Deep_Repair_Command.Clean_Deep_Repair_Command attribute) (clean.Clean_Quality_Command.Clean_Quality_Command attribute) (dereplicate.Dereplicate_Command.Dereplicate_Command attribute) (preclean.Preclean_Command.Preclean_Command attribute)

Dereplicate_Command (class in dereplicate.Dereplicate_Command)

E

execute_command() (classes.ChewbaccaCommand.ChewbaccaCommand method)

execute_program() (classes.ChewbaccaProgram.ChewbaccaProgram method)

G

get_program() (classes.ChewbaccaCommand.ChewbaccaCommand method)

M

Merge_Command (class in util.Merge_Command)

P

Partition_Command (class in util.Partition_Command) Preclean_Command (class in preclean.Preclean_Command)

ProgramRunner (class in classes.ProgramRunner)

Q

Query_OTU_DB_Command (class in otu.Query_OTU_DB_Command)

Query_OTU_Fasta_Command (class in otu.Query_OTU_Fasta_Command)

R

Rename_Command (class in rename.Rename_Command)

run() (classes.ProgramRunner.ProgramRunner method)

U

Ungap_Command (class in util.Ungap_Command)