Index

Symbols

--acc2tax <acc2tax> sam2lca-analyze command line option sam2lca-update-db command line option --acc2tax_json <acc2tax_json> sam2lca-update-db command line option --bam_out sam2lca-analyze command line option --bam_split_rank <bam_split_rank> sam2lca-analyze command line option --bam_split_read <bam_split_read> sam2lca-analyze command line option --conserved sam2lca-analyze command line option --dbdir <dbdir> sam2lca command line option --distance <distance> sam2lca-analyze command line option --identity <identity> sam2lca-analyze command line option --length <length> sam2lca-analyze command line option --output <output> sam2lca-analyze command line option --process <process> sam2lca-analyze command line option --taxo_merged <taxo_merged> sam2lca-update-db command line option --taxo_names <taxo_names> sam2lca-update-db command line option --taxo_nodes <taxo_nodes> sam2lca-update-db command line option

--taxonomy <taxonomy> sam2lca-analyze command line option sam2lca-update-db command line option --version sam2lca command line option -a sam2lca-analyze command line option sam2lca-update-db command line option -b sam2lca-analyze command line option -c sam2lca-analyze command line option -d sam2lca command line option sam2lca-analyze command line option -i sam2lca-analyze command line option -l sam2lca-analyze command line option -n sam2lca-analyze command line option -o sam2lca-analyze command line option -p sam2lca-analyze command line option -r sam2lca-analyze command line option -t sam2lca-analyze command line option sam2lca-update-db command line option

L

list_available_db() (in module sam2lca.main)

M

module sam2lca.main

S

SAM sam2lca-analyze command line option sam2lca command line option --dbdir <dbdir> --version -d sam2lca() (in module sam2lca.main) sam2lca-analyze command line option --acc2tax <acc2tax> --bam_out --bam_split_rank <bam_split_rank> --bam_split_read <bam_split_read> --conserved --distance <distance> --identity <identity> --length <length> --output <output> --process <process> --taxonomy <taxonomy> -a -b -c -d -i -l -n -o -p -r -t SAM

sam2lca-update-db command line option --acc2tax <acc2tax> --acc2tax_json <acc2tax_json> --taxo_merged <taxo_merged> --taxo_names <taxo_names> --taxo_nodes <taxo_nodes> --taxonomy <taxonomy> -a -t sam2lca.main module

U

update_database() (in module sam2lca.main)