AuxBF/TranslateIMGTJ.bf doesn't translate

[sdwfrost]

HyPhy is clearly reading in the sequences, but is not translating in the correct frame. This was also an issue in the macaque alignments.

$ HYPHYMP AuxBF/TranslateIMGTJ.bf

AuxBF/IMGT J-region nucleotide sequences:homo_sapiens/ighj_edit.fas     
[WARNING] Sequence J00256|IGHJ1*01|Homo sapiens|F|J-REGION|723..774|52 nt|1| | | | |52+0=52| | | appears to have premature stop codons or is empty and will be skipped
[WARNING] Sequence J00256|IGHJ2*01|Homo sapiens|F|J-REGION|932..984|53 nt|2| | | | |53+0=53| | | appears to have premature stop codons or is empty and will be skipped
[WARNING] Sequence J00256|IGHJ3*01|Homo sapiens|F|J-REGION|1537..1586|50 nt|2| | | | |50+0=50| | | appears to have premature stop codons or is empty and will be skipped
[WARNING] Sequence X86355|IGHJ3*02|Homo sapiens|F|J-REGION|1107..1156|50 nt|2| | | | |50+0=50| | | appears to have premature stop codons or is empty and will be skipped
[WARNING] Sequence J00256|IGHJ4*01|Homo sapiens|F|J-REGION|1912..1959|48 nt|3| | | | |48+0=48| | | appears to have premature stop codons or is empty and will be skipped
[WARNING] Sequence X86355|IGHJ4*02|Homo sapiens|F|J-REGION|1480..1527|48 nt|3| | | | |48+0=48| | | appears to have premature stop codons or is empty and will be skipped
[WARNING] Sequence M25625|IGHJ4*03|Homo sapiens|F|J-REGION|446..493|48 nt|3| | | | |48+0=48| | | appears to have premature stop codons or is empty and will be skipped
[WARNING] Sequence J00256|IGHJ5*01|Homo sapiens|F|J-REGION|2354..2404|51 nt|3| | | | |51+0=51| | | appears to have premature stop codons or is empty and will be skipped
[WARNING] Sequence X86355|IGHJ5*02|Homo sapiens|F|J-REGION|1878..1928|51 nt|3| | | | |51+0=51| | | appears to have premature stop codons or is empty and will be skipped
[WARNING] Sequence J00256|IGHJ6*01|Homo sapiens|F|J-REGION|2947..3009|63 nt|3| | | | |63+0=63| | | appears to have premature stop codons or is empty and will be skipped
[WARNING] Sequence X86355|IGHJ6*02|Homo sapiens|F|J-REGION|2482..2543|62 nt|3| | | | |62+0=62| | | appears to have premature stop codons or is empty and will be skipped
[WARNING] Sequence X86356|IGHJ6*03|Homo sapiens|F|J-REGION|2482..2543|62 nt|3| | | | |62+0=62| | | appears to have premature stop codons or is empty and will be skipped
[WARNING] Sequence AJ879487|IGHJ6*04|Homo sapiens|F|J-REGION|39..101|63 nt|3| | | | |63+0=63| | | appears to have premature stop codons or is empty and will be skipped
Error:
No fully annotated sequences found in call to assert(

Function call stack
1 : Assert 'Abs(sequences)>0'
-------
Segmentation fault

[spond]

Hi Simon,

Please push a test file to the test directory.

Sergei

[spond]

Resolved with c44844a5c35123b21955954d7ada9996882b100e