[ensembl-dev] VEP warnings after finish

[Guillermo Marco Puche]

Dear devs,

I'm getting a lot of warnings when annotating a big VCF file. VEP 
annotation seems to write a correctly annotated VCF however I'm getting 
a lot of "TranscriptVariationAllele.pm" warnings. Any idea what could be 
causing this issue?

    2016-10-18 14:53:38 - Writing output
    2016-10-18 14:53:38 - Processed 415372 total variants (26 vars/sec,
    35 vars/sec total)
    2016-10-18 14:53:38 - Finished!
    Use of uninitialized value $cdna_position in pattern match (m//) at
    /share/apps/local/ensembl_api/86/Bio/EnsEMBL/Variation/TranscriptVariationAllele.pm
    line 1901.
    Use of uninitialized value $cdna_coord in concatenation (.) or
    string at
    /share/apps/local/ensembl_api/86/Bio/EnsEMBL/Variation/TranscriptVariationAllele.pm
    line 1933.
    Use of uninitialized value $exon_start_coord in addition (+) at
    /share/apps/local/ensembl_api/86/Bio/EnsEMBL/Variation/TranscriptVariationAllele.pm
    line 703.
    Use of uninitialized value $cdna_position in pattern match (m//) at
    /share/apps/local/ensembl_api/86/Bio/EnsEMBL/Variation/TranscriptVariationAllele.pm
    line 1901.
    Use of uninitialized value $cdna_coord in numeric gt (>) at
    /share/apps/local/ensembl_api/86/Bio/EnsEMBL/Variation/TranscriptVariationAllele.pm
    line 1907.
    Use of uninitialized value $cdna_coord in string eq at
    /share/apps/local/ensembl_api/86/Bio/EnsEMBL/Variation/TranscriptVariationAllele.pm
    line 1913.
    Use of uninitialized value $cdna_coord in pattern match (m//) at
    /share/apps/local/ensembl_api/86/Bio/EnsEMBL/Variation/TranscriptVariationAllele.pm
    line 1921.
    Use of uninitialized value $cdna_coord in numeric ge (>=) at
    /share/apps/local/ensembl_api/86/Bio/EnsEMBL/Variation/TranscriptVariationAllele.pm
    line 1924.


Regards,
Guillermo.

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