Commit 1f67096f authored by Pierre Marijon's avatar Pierre Marijon

Add definition for containment and internal match

parent e2771a83
......@@ -30,6 +30,36 @@ optional arguments:
Remove all internal match (default: False)
## Definition
This definition are inspired by [Miniasm](
### Containment
A: ------------>
B: ---->
Read B are contained in read A (the container) if length of B are minus than length A and begin of B upper than begin of A and end of B minus than end of A.
### Internal match
overhang A
A: ----------- -------->
\ mapping /
/ \
B: ------ ------------------->
overhang B
Overhang is the sum of minus length for each read around match zone.
If ratio overhang by mapping length is upper than 0.8 (hard coded actualy) this overlap are an internal match.
## Usage as python module
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