Updating program names from earlier versions

The names of the programs of CLC Assembly Cell have changed since version 3.2.2 and earlier.

A mapping of the new program names to the old program names is contained in the distribution in a file called clc_name_changes.txt.

For Linux and Mac users, a script has been included as an example of how you could update the Assembly Cell program names in existing scripts you have. The script is called change_clc_names.sh. If you plan to use the script without changes, please read through it first, to make sure that it will do what you need.

Below is a listing of the old names followed by the new names for the CLC Assembly Cell programs:

assembly_info            -->  clc_mapping_info
assembly_table           -->  clc_mapping_table
castosam                 -->  clc_cas_to_sam
change_assembly_files    -->  clc_change_cas_paths
clc_assembly_viewer      -->  clc_mapping_viewer
clc_novo_assemble        -->  clc_assembler
clc_ref_assemble_long    -->  clc_mapper_legacy
clc_ref_assemble         -->  clc_mapper
filter_matches           -->  clc_filter_matches
find_variations          -->  clc_find_variations
host_info                -->  clc_host_info
join_assemblies          -->  clc_join_mappings
join_pairs               -->  clc_overlap_reads
quality_trim             -->  clc_quality_trim
remove_duplicates        -->  clc_remove_duplicates
samtocas                 -->  clc_sam_to_cas
sequence_info            -->  clc_sequence_info
simulate_reads           -->  clc_simulate_reads
sort_pairs               -->  clc_sort_pairs
split_sequences          -->  clc_split_reads
sub_assembly             -->  clc_submapping
tofasta                  -->  clc_convert_sequences
unassembled_reads        -->  clc_unmapped_reads
unpaired_reads           -->  clc_unpaired_reads