def best_blat_al(onequery_psltable, get_translocations = False):
    index1, index2, max_trans_score = -1,-1,-500000
    qsize = onequery_psltable[0][10]
    scores = [int(match) + (int(repmatch)>>1) - int(mismatch) - int(qgapbases) - int(tgapbases) for [match, mismatch, repmatch, ncount, qgapcount, qgapbases, tgapcount, tgapbases, strand, qname, qsize, qstart, qend, tname, tsize, tstart, tend, blockcount, blocksizes, qstarts, qends] in onequery_psltable]
    max_score = max(scores)
    print(max_score)
    max_ind = scores.index(max_score)
    is_good = max_score >= 0.95*qsize
    #bug in the translocations part
    if get_translocations & not is_good:
        ind_product = [[ind1, ind2] for ind1 in range(0,len(scores)) for ind2 in range(0, len(scores)) if ind1<ind2]
        ran = range(-2, 10,)
        qstart1 = onequery_psltable[ind1][11]
        qend1 = onequery_psltable[ind1][12]        
        qstart2 = onequery_psltable[ind2][11]
        qend2 = onequery_psltable[ind2][12]
        if ((qend2 > qend1) & (qstart2 > qstart1) & (qstart2 - qend1 in ran)) | ((qend1 > qend2) & (qstart1 > qstart2) & (qstart1 - qend2 in ran)):
            if (scores[ind1] + scores[ind2] > max_trans_score):
                index1, index2, max_trans_score = ind1, ind2, scores[ind1]+scores[ind2]
        if max_trans_score>max_score:
            print("Translocation detected")
            print(max_trans_score)
            return [onequery_psltable[index1], onequery_psltable[index2]]
        else:
            return[onequery_psltable[max_ind]]
    else:
        return [onequery_psltable[max_ind]]
        
                
                        
                
#best blat alignment for multiple queries
def best_blat_alignment(psltable, writefile = ""):
    psldata = psltable[1:]
    best_alignment = []
    best_alignment.append(psldata[0])
    #print(psltable)
    q_names = set([pslrow[9] for pslrow in psldata])
    print(q_names)
    for q_name in q_names: