StoreTagInSequence #

Insert a tag’s string value into a read sequence at the position defined by another location tag.

[[step]]
    action = "StoreTagInSequence"
    in_value_label    = "mytag"    # location or string tag to insert
    in_position_label = "mytag2"   # location tag defining where to insert
    anchor = "Start"               # "Start"/"left" or "End"/"right" or 'replace'
    on_lost = "Complain" # Ignore|Complain

Parameters #

Parameter	Type	Required	Description
`in_value_label`	location or string tag	yes	Tag whose sequence is inserted into the read
`in_position_label`	location tag	yes	Tag that defines the insertion position
`anchor`	`"Start"` / `"left"` / `"End"` / `"right"` / `"Replace"`	yes	Whether to insert before the leftmost position (`Start`), after the rightmost end (`End`) of the position tag, or replace the tag from start..end (single location tags or same length tags only)

How it works #

in_position_label is a location tag pointing to a region (or multiple regions) in a read. The insertion point is derived from the anchor:

Start / left — insert before the leftmost start coordinate across all regions.
End / right — insert after the rightmost start + len coordinate across all regions. -
** Replace — replace the position’s tag sequence.

The bytes inserted come from in_value_label:

If it is a location tag, its sequences are joined (without spacer) and used.
If it is a string tag, the string value is used directly.

Quality scores for the inserted bases are taken from the in_value if available, otherwise set to ~ (Phred+33 = Q93, maximum Sanger quality).

For replace, the positon tag must be a single consecutive location, or have the same length as replacement strings (individually for each read). Otherwise, a run-time failure will be issued.

Location tag adjustment #

Location tag’s are tracked through all edits, though

Behaviour when tags are missing #

If in_value_label is Missing or produces an empty sequence, or if in_position_label carries no location information, the read is left unchanged and no error is raised.

Behaviour when the location is no longer available #

If reads have been manipulated in away that this tag’s bases are (even partially lost), the on_lost handling comes to pass. By default, a run-time error is raised. Set it to ‘Ignore’ to instead leave the reads unchanged.

Example #

Given read1 = AAACCCGGG (quality IIIIIIIII), with:

val_tag extracting bases 0–2 (AAA, location [0,3])
pos_tag extracting bases 3–5 (CCC, location [3,3])

# ignore_in_test
[[step]]
    action = "StoreTagInSequence"
    in_value_label    = "val_tag"
    in_position_label = "pos_tag"
    anchor = "Start"

Result: AAA inserted before position 3 → AAAAAACCCGGG (quality III~~~IIIIII).

With anchor = "End":

Result: AAA inserted after position 6 → AAACCCAAAGGG (quality IIIIII~~~III).