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'

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 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 set to ~ (Phred+33 = Q93, maximum Sanger quality).

For replace, the tag must be a single consecutive location. Otherwise, a runtime failure will be issued.

Location tag adjustment #

After insertion, all location tags on the same segment are updated:

Locations after the insertion are shifted forward by the number of inserted bases.
Locations that straddle the insertion (start before, end after) have their coordinate information removed (sequence data is preserved).
Locations before the insertion point are unchanged.

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.

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).