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Isoform Enumeration
| input: A CG G = (V, E), and a set of mapped single-end or paired-end reads R |
| output: A set of isoforms T |
| begin |
| Enumeration: |
| T ← ∅ |
for with indeg(vj) = 0 do
|
| Enumerate all possible maximal paths P that begin at vj and end at some vk with outdeg(vk) = 0 |
| T ← T ∪ P |
| Filtration: |
for do
|
Let 
|
| T ← (T\{t}) ∪ {t′} |
| Condensation: |
for do
|
Let 
|
for do
|
Let 
|
if then
|
| T ← (T\{t}) |
