Structural variant without CHR2

[j-hudecek]

Hi, we're using older version (1.6.17) of vcf2maf and recently it choked on a vcf with line (I zeroed out the exact locus)

13      32900000        NM_000059.3:c.0000-000_*1500000del      G       <DEL>   .       PASS;EXT        "END=34400000;SVTYPE=DEL;SVLEN=1500000;CIPOS=0,1;CIEND=0,1;HOMLEN=1;HOMSEQ=C";ANN=<DEL>|upstream_gene_variant.....

Here are the error messages

Use of implicit split to @_ is deprecated at vcf2maf.pl line 1046.
Use of uninitialized value in concatenation (.) or string at vcf2maf.pl line 289, <GEN0> line 167.
Use of uninitialized value in concatenation (.) or string at vcf2maf.pl line 289, <GEN0> line 167.
Use of uninitialized value in concatenation (.) or string at vcf2maf.pl line 289, <GEN0> line 167.
[fai_fetch] Warning - Reference :- not found in FASTA file, returning empty sequence
Failed to fetch sequence in :-
Use of uninitialized value in join or string at vcf2maf.pl line 291, <GEN0> line 167.
Use of uninitialized value in join or string at vcf2maf.pl line 291, <GEN0> line 167.
Use of uninitialized value in concatenation (.) or string at vcf2maf.pl line 289, <GEN0> line 171.
Use of uninitialized value in concatenation (.) or string at vcf2maf.pl line 289, <GEN0> line 171.
Use of uninitialized value in concatenation (.) or string at vcf2maf.pl line 289, <GEN0> line 171.
[fai_fetch] Warning - Reference :- not found in FASTA file, returning empty sequence
Failed to fetch sequence in :-
Use of uninitialized value in join or string at vcf2maf.pl line 291, <GEN0> line 171.
Use of uninitialized value in join or string at vcf2maf.pl line 291, <GEN0> line 171.
Argument "" isn't numeric in subtraction (-) at vcf2maf.pl line 361, <GEN2> line 167.
Argument "" isn't numeric in subtraction (-) at vcf2maf.pl line 361, <GEN2> line 172.
[fai_fetch] Warning - Reference :-1-1 not found in FASTA file, returning empty sequence
Failed to fetch sequence in :-1-1
[tabix] failed to load the index file.
WARNING: Couldn't retrieve bps around :1 from reference FASTA: Homo_sapiens.GRCh37.75.dna.primary_assembly.fa
WARNING: Couldn't retrieve bps around :1 from reference FASTA: Homo_sapiens.GRCh37.75.dna.primary_assembly.fa
STATUS: Running VEP and writing to: /tmp/tmp.0iCZQthiPu/sample.vep.vcf
WARNING: Chromosome  not found in annotation sources or synonyms on line 24
Argument "946047"" isn't numeric in abs at /mnt/datateamsftp/bin/vcf2maf/VEP/ensembl-vep-release-95.3/Bio/EnsEMBL/IO/Parser/BaseVCF4.pm line 316, <$__ANONIO__> line 173.
Argument "946047"" isn't numeric in abs at /mnt/datateamsftp/bin/vcf2maf/VEP/ensembl-vep-release-95.3/modules/Bio/EnsEMBL/VEP/Parser/VCF.pm line 412, <$__ANONIO__> line 173.
Argument "946047"" isn't numeric in abs at /mnt/datateamsftp/bin/vcf2maf/VEP/ensembl-vep-release-95.3/Bio/EnsEMBL/IO/Parser/BaseVCF4.pm line 316, <$__ANONIO__> line 173.

The first warning seems to point to this code

        # Fetch the REF allele at the second breakpoint using samtools faidx
        my $ref2 = `$samtools faidx $ref_fasta $info{CHR2}:$info{END}-$info{END} | grep -v ^\\>`;

But it seems CHR2 is an optional term in INFO? Is that the problem or am I missing something? The exact line is still there now, btw