Update detailed alleles table help option (#116) (#513)

Author: Colelyman

CRISPResso2/args.json

@@ -458,7 +458,7 @@
         },
         "write_detailed_allele_table": {
             "keys": ["--write_detailed_allele_table"],
-            "help": "If set, a detailed allele table will be written including alignment scores for each read sequence.",
+          "help": "R|If set, a detailed allele table will be written with the following columns:\n  - #Reads: the number of reads this allele represents.\n  - Aligned_Sequence: the alignment of the read sequence.\n  - Reference_Sequence: the alignment of the amplicon sequence.\n  - n_inserted: the number of insertions within the quantification window.\n  - n_deleted: the number of deletions within the quantification window.\n  - n_mutated: the number of substitutions within the quantification window.\n  - Reference_Name: the amplicon name to which this allele is assigned.\n  - Read_Status: the bin to which this allele is classified.\n  - Aligned_Reference_Names: if there are multiple amplicons, this lists the amplicon names. The order corresponds to the alignment scores in Aligned_Reference_Scores.\n  - Aligned_Reference_Scores: the alignment score (out of 100) for each amplicon.\n  - ref_positions: this represents the indices in the Aligned_Sequence that map back to the original sequence. Negative values represent places that don't map back to the original reference.\n  - all_insertion_positions: all of the indices where there is an insertion regardless of the quantification window.\n  - all_insertion_left_positions: for all insertions, the left most index (e.g. where each insertion starts).\n  - insertion_positions: the insertion positions within the quantification window.\n  - insertion_coordinates: the start and end indices of the insertions within the quantificaiton window.\n  - insertion_sizes: the size of each insertion within the quantification window.\n  - all_deletion_positions: all of the indices where there is a deletion regardless of the quantification window.\n  - deletion_positions: the indices where there is a deletion within the quantification window.\n  - deletion_coordinates: the start and end indices of the deletions within the quantification window.\n  - deletion_sizes: the size of the deletions within the quantification window.\n  - all_substitution_positions: all of the indices where there is a substitution.\n  - substitution_positions: the indices where there is a substitution within the quantification window.\n  - substitution_values: the nucleotide to which it is substituted within the quantification window.\n  - %%Reads: the percentage of read this allele represents.",
             "action": "store_true",
             "tools": ["Core", "Batch", "Pooled", "WGS"]
         },