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Custom GFA tags
Anton Korobeynikov edited this page Jul 31, 2022
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Bandage-NG supports a handful custom GFA tags that could be utilized to change to visual representation of nodes and edges as well as provide additional metadata.
The following tags could be used to specify depth of a node. Note that they are processed in the order and the one listed earlier always "wins". If a tag is present, but of wrong type (e.g. string where integer is expected or float for integer value, then the value will be silently ignored).
| Tag name | Expected type | Description |
|---|---|---|
DP (aka "Depth") |
Float | Average node depth |
KC (aka "Kmer Count") |
Integer | K-mer count, node depth is calculated as KC / length
|
RC (aka "Read Count") |
Integer | Read count, node depth is calculated as RC / length
|
FC (aka "Fragment Count") |
Integer | Fragment count, node depth is calculated as FC / length
|
| Tag name | Expected type | Description |
|---|---|---|
LB (aka "Label") |
String | Custom label for a node |
L2 (aka "Label for second node") |
String | Custom label for reverse-complementary node |
| Tag name | Expected type | Description |
|---|---|---|
CB (aka "Color") |
String | Custom color for a node / edge |
C2 (aka "Color for second node / edge") |
String | Custom color for reverse-complementary node / edge |
WD (aka "Edge width") |
Float or Integer | Custom width for an edge |
PS (aka "Pen style") |
Integer | Pen style used to draw edge (see Qt docs for information of meaning of values) |
Any color supported by QColor is accepted. Note that if edge width is overridden, then pen style should be explicitly specified for jump links.
| Tag name | Expected type | Description |
|---|---|---|
LN (aka "Node length") |
Integer | Node length if node sequence is omitted |