This refactorization separates flair's six main programs.
Align, correct, collapse, and quantify can still be called from flair(.py) as before but are now separate functions.
correct-range has been removed
diffExp and diffSplice are now flair_diffExp and flair_diffSplice.
Align, correct and collapse now use functions instead of calling flair helper programs using subprocess. I have
added pipettor to run pipes (e.g. minimap2 to sam filtering) because its error capture is a lot better.
I left the original subprocess statements commented out for debugging purposes. These should be removed soon because it makes the code messy.
tqdm no longer outputs status messages, they tended to drown out actual errors from the code.
All helper programs can still be called separately from the command line, nearly all with the exact same arguments. The exception is match_counts.py, which now needs named input arguments instead of four(!) input parameters in a particular order.
Not all helper programs have been sanitized yet, there are still some remaining subprocess calls.
This refactorization separates flair's six main programs.
Align, correct and collapse now use functions instead of calling flair helper programs using subprocess. I have added pipettor to run pipes (e.g. minimap2 to sam filtering) because its error capture is a lot better.
I left the original subprocess statements commented out for debugging purposes. These should be removed soon because it makes the code messy.
tqdm no longer outputs status messages, they tended to drown out actual errors from the code.
All helper programs can still be called separately from the command line, nearly all with the exact same arguments. The exception is match_counts.py, which now needs named input arguments instead of four(!) input parameters in a particular order.
Not all helper programs have been sanitized yet, there are still some remaining subprocess calls.