diff --git a/GFA1.md b/GFA1.md index 2ab9b3d..7041551 100644 --- a/GFA1.md +++ b/GFA1.md @@ -132,19 +132,31 @@ The Overlap field is optional and can be `*`, meaning that the CIGAR string is n # `C` Containment line -A containment line represents an overlap between two segments where one is contained in the other. +A containment line represents an overlap between two segments where one (the `Contained` segment) +is contained in the other (the `Container` segment). The `Pos` field stores the leftmost +position of the contained segment in the container segment in its forward orientation +(i.e. before this is oriented according to the `ContainerOrient` sign). + +## Example + +The following line describes the containment of segment 2 in the reverse complement of segment 1, +starting at position 110 of segment 1 (in its forward orientation). +``` +C 1 - 2 + 110 100M +``` + ## Required fields -| Column | Field | Type | Regexp | Description -|--------|--------------|-----------|--------------------------|------------ -| 1 | `RecordType` | Character | `C` | Record type -| 2 | `From` | String | `[!-)+-<>-~][!-~]*` | Name of From segment -| 3 | `FromOrient` | String | `+\|-` | Orientation of From segment -| 4 | `To` | String | `[!-)+-<>-~][!-~]*` | Name of To segment -| 5 | `ToOrient` | String | `+\|-` | Orientation of To segment -| 6 | `Pos` | Integer | `[0-9]*` | 0-based start of contained segment -| 7 | `Overlap` | String | `\*\|([0-9]+[MIDNSHPX=])+`| CIGAR string describing overlap +| Column | Field | Type | Regexp | Description +|--------|-------------------|-----------|--------------------------|------------ +| 1 | `RecordType` | Character | `C` | Record type +| 2 | `Container` | String | `[!-)+-<>-~][!-~]*` | Name of container segment +| 3 | `ContainerOrient` | String | `+|-` | Orientation of container segment +| 4 | `Contained` | String | `[!-)+-<>-~][!-~]*` | Name of contained segment +| 5 | `ContainedOrient` | String | `+|-` | Orientation of contained segment +| 6 | `Pos` | Integer | `[0-9]*` | 0-based start of contained segment +| 7 | `Overlap` | String | `\*|([0-9]+[MIDNSHPX=])+`| CIGAR string describing overlap ## Optional fields