Problem

yassai_identifier(c(V="TRAV14N-3", J="TRAJ16", dna="GCAACTTCAAGTGGCCAGAAGCTGGTT", pep="ATSSGQKLV"))
# takes ages

yassai_identifier(c(V="TRAV14N-3", J="TRAJ16", dna="GCAGCAACCGCAACTTCAAGTGGCCAGAAGCTGGTT", pep="AATATSSGQKLV"))
## [1] "aTa.2A14N3A16L12"
# returns immediately.

Troubleshooting

The problematic clonotype comes from read GWYEMNS10GHZUF.

@GWYEMNS10GHZUF
gactAACTGGTACACAGCAGGTTCTGGGTTCTGGATGTGCAGGTACACCTTTAATATGGTCCCCTGGCCAAAAACCAGCTTCTGGCCACTTGAAGTTGCACAGAAGTAGGTGGCTGAGTCTCCAGGCTGAGAGTCTTTGATGTGCAAGGAGAGATTTTTCTCCCTTTTATTGAAGAAGATTGTGAATCGTCCATCTTCCTTTTTATCGGACACTGAACGTATGGCTATCAGGAGAGCAGGGCCTTCCCCAGGGAACTGCTGGTACCATGGGAAGTAGTCAAAAGCACTGTTCTCAtaactagcagttcagaattgcggtctctccttccccagactgtcagagattggagtcgtgggagacaaggcacacaggggataggngngnnnnnnnnnnnnn
+
FFF::;;FFFFFFFFIIIIHFFFHF666=<FFGGDDDFFHFDIIIIIIIHHHIIIHFFFD54449662200001335>>AAABDFDDDFDDDFFFFFFFFFFFFFFFFFCCCCCFFFFFFFFFFFFDDBBBBB==110?@@@@@>4455BBA??3357;F4:::;;==D88?AA<;:==BAAAA==??AAB@AAA=>>>222//02A8898BDDFFFDDFFFFFF666:DBAAAABB:::???DD;;;;D?????DDBA?<<<><<<<000444<8993222233393...:663322<9233776899:;;963326755551111,,,,3313335333799.....23322666726;;;66772222,,,,47400!,!,!!!!!!!!!!!!!

Here is the alignment made by clonotypeR

GWYEMNS10GHZUF  16  TRAV14N-3   105 17  49S17M1I29M1I201M99S    *   0   0   NNNNNNNNNNNNNCNCNCCTATCCCCTGTGTGCCTTGTCTCCCACGACTCCAATCTCTGACAGTCTGGGGAAGGAGAGACCGCAATTCTGAACTGCTAGTTATGAGAACAGTGCTTTTGACTACTTCCCATGGTACCAGCAGTTCCCTGGGGAAGGCCCTGCTCTCCTGATAGCCATACGTTCAGTGTCCGATAAAAAGGAAGATGGACGATTCACAATCTTCTTCAATAAAAGGGAGAAAAATCTCTCCTTGCACATCAAAGACTCTCAGCCTGGAGACTCAGCCACCTACTTCTGTGCAACTTCAAGTGGCCAGAAGCTGGTTTTTGGCCAGGGGACCATATTAAAGGTGTACCTGCACATCCAGAACCCAGAACCTGCTGTGTACCAGTTAGTC   !!!!!!!!!!!!!,!,!00474,,,,22227766;;;62766622332.....9973335333133,,,,111155557623369;;:9986773329<223366:...3933322223998<444000<<<<><<<?ABDD?????D;;;;DD???:::BBAAAABD:666FFFFFFDDFFFDDB8988A20//222>>>=AAA@BAA??==AAAAB==:;<AA?88D==;;:::4F;7533??ABB5544>@@@@@?011==BBBBBDDFFFFFFFFFFFFCCCCCFFFFFFFFFFFFFFFFFDDDFDDDFDBAAA>>53310000226694445DFFFHIIIHHHIIIIIIIDFHFFDDDGGFF<=666FHFFFHIIIIFFFFFFFF;;::FFF AS:i:233    XS:i:218    XF:i:3  XE:i:4  XN:i:0

The problem was that the V segment was completely digested in favor of the J segment.

           351                                            400
GWYEMNS10GHZUF CTGTGCAACTTCAAGTGGCCAGAAGCTGGTTTTTGGCCAGGGGACCATAT
TRAJ16         ~~~~GCAACTTCAAGTGGCCAGAAGCTGGTTTTTGGCCAGGGGACCATAT
TRAV14N-3      CTGTGCAGC...AAGTG~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~

           401                                            450
GWYEMNS10GHZUF TAAAGGTGTACCTGCACATCCAGAACCCAGAACCTGCTGTGTACCAGTTA
TRAJ16         TAAAGGTGTACCTGC~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
TRAV14N-3      ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~

This triggered an infinite loop when calling is.germline().

Done in 42ab98729c5c77462b5929b00ee973074ae4c1c7.

Now the function should return as in the following example.

yassai_identifier(c(V="TRAV14N-3", J="TRAJ16", dna="GCAACTTCAAGTGGCCAGAAGCTGGTT", pep="ATSSGQKLV"))
## [1] "a.A14N3A16L9"