Is there a strong repair mode？

[Trandamere]

Hi:
The software you have developed is excellent.
I would like to know if there are any strong repair options including conventional SJ in the third generation including GTAG,GCAG.
Or remove any code in the software that can be completely fixed without considering the GTAG in PacBio

[Trandamere]

I disabled these lines of code to achieve the goal

def cleanNoncanonical(transcript, refs, maxDist, logInfo):
    """ Iterate over each junction in the provided transcript object. If the 
        junction is noncanonical, attempt to correct it, and record the result.
        Returns a modified transcript object that originates from a copy of the 
        object passed into the function, along with the error log entries. 
    """ 
    logInfo.corrected_NC_SJs = 0
    logInfo.uncorrected_NC_SJs = 0 
    TE_entries = ""

    #if transcript.isCanonical == True:
    #    return transcript, TE_entries

    # Iterate over all junctions and attempt to correct
    for splice_jn_num in range(0,len(transcript.spliceJunctions)):
        junction = transcript.spliceJunctions[splice_jn_num]
        #if junction.isCanonical:
        #    continue
        #else: