Improved Safe Flow Decomposition Algorithms for RNA Assembly

Compile

mkdir build
cd build
cmake ..
cmake --build .

Running Algorithms

./build/[ALGORITHM_NAME] [INPUT_FILE] [STORE_BOOL] [PRINT_BOOL]

Running Tests

• All Tests

cd build
ctest

• For particular algorithm

cd build
ctest -R [ALGORITHM_NAME] 

• For particular dataset

cd build
ctest -R [DATASET_NAME] 

Algorithms

[ALGORITHM_NAME] ([ALGORITHM_NAME_AS_MENTIONED_IN_PAPER])

• RawRep (RawRep_o)
• RawRepT (RawRep)
• ConRep (ConRep_o)
• ConRepT (ConRep)
• OptRaw (OptRawRep)
• OptCon (OptConRep)
• OptConH (OptConRep^#)
• OptRep (OptRep)
• OptRepH (OptRep^#)

Datasets

• Reference-Sim
  • refsim
• Catfish
  • human
  • mouse
  • salmon
  • zebrafish
  • simulation
• Randomly Generated
  • Uniform Random
  • Power Law
  • Improved Random