remove homopolymere deletion part, rename output files

dna_add.sh

@@ -111,15 +111,15 @@ frag_length=$(get_container_param $container_path "frag_length")
 assembly_type=$(get_container_param $container_path "assembly_type")
 
 source_encoding_script="$project_dir"/source_encoding/source_encoding.py
-source_path="$stored_document_path"/1_fragments.fasta
+source_path="$stored_document_path"/0_encoded_source.fasta
 
 call_function python3 "$source_encoding_script" -i "$document_path" -o "$source_path" -l $frag_length -t "$assembly_type" -c "$container_path" --doc_index $doc_index
 
 
 #----Channel Encoding----#
-
+#TODO channel coding for whole sequence
 channel_encoding_script="$project_dir"/channel_code/encode_from_file.jl 
-channel_path="$stored_document_path"/2_channel.fasta
+channel_path="$stored_document_path"/1_channel.fasta
 
 add_doc_param "$container_path" $doc_index "channel_coding" $channel_coding
 
@@ -131,16 +131,6 @@ else
 fi
 
 
-#----Homopolymere Deletion----#
-
-#h_deletion_script="$project_dir"/synthesis_modules/homoplymere_deletion/homopolymere_deletion.py
-fragments_path="$stored_document_path"/3_final_fragments.fasta
-
-echo "homopolymere deletion not implemented yet; skipping..."
-call_function cp "$channel_path" "$fragments_path"
-
-: 'call_function $h_deletion_script "$channel_path" "$fragments_path" #TODO
-'
 
 echo "Document $(basename $document_path) successfully added to container $(basename $container_path) !"