Re: [Vcftools-help] (no subject)

[Laura C. <la...@eb...>]

Do your other vcf files come out without warnings when running vcf-validate

Laura

On Wednesday, 6 November 2013, carol white wrote:

> Hi,
> when I installed vcftools, I got many warnings (see below for some of
> them). Then, when I wanted to merge vcf files, I wrongly got the following
> message on the column name whereas there is already column name in each vcf
> file file.
>
> Perhaps, I should reinstall vcftools?
> --------------------------------------------------
> vcftools_0.1.11/bin/vcf-merge *.gz > merge.vcf
>
> Using column name 'S1' for file1.vcf.gz:S1
> Using column name 'S2' for file1.vcf.gz:S2
>
> and all other gz file
>
> Broken VCF header, no column names?
>  at vcftools_0.1.11/perl//Vcf.pm line 177
> Vcf::throw('Vcf4_1=HASH(0x7fdfcb251f98)', 'Broken VCF header, no column
> names?') called at vcftools_0.1.11/perl//Vcf.pm line 869
> VcfReader::_read_column_names('Vcf4_1=HASH(0x7fdfcb251f98)') called at
> vcftools_0.1.11/perl//Vcf.pm line 604
> VcfReader::parse_header('Vcf4_1=HASH(0x7fdfcb251f98)') called at
> vcftools_0.1.11/bin/vcf-merge line 181
> main::init_cols('HASH(0x7fdfcb034ca8)', 'Vcf4_1=HASH(0x7fdfcb032c58)')
> called at vcftools_0.1.11/bin/vcf-merge line 277
> main::merge_vcf_files('HASH(0x7fdfcb034ca8)') called at
> vcftools_0.1.11/bin/vcf-merge line 12
>
>
> ---------------------------------------------------
> make
> g++ -c -O2 -D_FILE_OFFSET_BITS=64  vcftools.cpp -o vcftools.o
> g++ -MM -O2 -D_FILE_OFFSET_BITS=64  vcftools.cpp > vcftools.d
> g++ -c -O2 -D_FILE_OFFSET_BITS=64  bcf_file.cpp -o bcf_file.o
> bcf_file.cpp:474:2: warning: delete called on 'entry' that is abstract but
> has non-virtual destructor [-Wdelete-non-virtual-dtor]
>         delete e;
>         ^
> bcf_file.cpp:541:2: warning: delete called on 'entry' that is abstract but
> has non-virtual destructor [-Wdelete-non-virtual-dtor]
>         delete e;
>         ^
> 2 warnings generated.
> g++ -MM -O2 -D_FILE_OFFSET_BITS=64  bcf_file.cpp > bcf_file.d
> g++ -c -O2 -D_FILE_OFFSET_BITS=64  vcf_file.cpp -o vcf_file.o
> vcf_file.cpp:25:13: warning: initialization of pointer of type 'gzFile'
> (aka 'void *') to null from a constant boolean expression
> [-Wbool-conversion]
>         gzvcf_in = false;
>                    ^~~~~
> vcf_file.cpp:315:2: warning: delete called on 'entry' that is abstract but
> has non-virtual destructor [-Wdelete-non-virtual-dtor]
>         delete e;
>         ^
> vcf_file.cpp:394:2: warning: delete called on 'entry' that is abstract but
> has non-virtual destructor [-Wdelete-non-virtual-dtor]
>         delete e;
>         ^
> 3 warnings generated.
> g++ -MM -O2 -D_FILE_OFFSET_BITS=64  vcf_file.cpp > vcf_file.d
> g++ -c -O2 -D_FILE_OFFSET_BITS=64  variant_file.cpp -o variant_file.o
> g++ -MM -O2 -D_FILE_OFFSET_BITS=64  variant_file.cpp > variant_file.d
> g++ -c -O2 -D_FILE_OFFSET_BITS=64  bcf_entry.cpp -o bcf_entry.o
> g++ -MM -O2 -D_FILE_OFFSET_BITS=64  bcf_entry.cpp > bcf_entry.d
> g++ -c -O2 -D_FILE_OFFSET_BITS=64  vcf_entry.cpp -o vcf_entry.o
> g++ -MM -O2 -D_FILE_OFFSET_BITS=64  vcf_entry.cpp > vcf_entry.d
> g++ -c -O2 -D_FILE_OFFSET_BITS=64  entry.cpp -o entry.o
> g++ -MM -O2 -D_FILE_OFFSET_BITS=64  entry.cpp > entry.d
> g++ -c -O2 -D_FILE_OFFSET_BITS=64  entry_setters.cpp -o entry_setters.o
> g++ -MM -O2 -D_FILE_OFFSET_BITS=64  entry_setters.cpp > entry_setters.d
> g++ -c -O2 -D_FILE_OFFSET_BITS=64  entry_getters.cpp -o entry_getters.o
> g++ -MM -O2 -D_FILE_OFFSET_BITS=64  entry_getters.cpp > entry_getters.d
> g++ -c -O2 -D_FILE_OFFSET_BITS=64  vcf_entry_setters.cpp -o
> vcf_entry_setters.o
> g++ -MM -O2 -D_FILE_OFFSET_BITS=64  vcf_entry_setters.cpp >
> vcf_entry_setters.d
> g++ -c -O2 -D_FILE_OFFSET_BITS=64  bcf_entry_setters.cpp -o
> bcf_entry_setters.o
> g++ -MM -O2 -D_FILE_OFFSET_BITS=64  bcf_entry_setters.cpp >
> bcf_entry_setters.d
> g++ -c -O2 -D_FILE_OFFSET_BITS=64  variant_file_filters.cpp -o
> variant_file_filters.o
> variant_file_filters.cpp:35:2: warning: delete called on 'entry' that is
> abstract but has non-virtual destructor [-Wdelete-non-virtual-dtor]
>         delete e;
>         ^
> variant_file_filters.cpp:1341:2: warning: delete called on 'entry' that is
> abstract but has non-virtual destructor [-Wdelete-non-virtual-dtor]
>         delete e;
>         ^
> 18 warnings generated.
> g++ -MM -O2 -D_FILE_OFFSET_BITS=64  variant_file_filters.cpp >
> variant_file_filters.d
> g++ -c -O2 -D_FILE_OFFSET_BITS=64  variant_file_output.cpp -o
> variant_file_output.o
> variant_file_output.cpp:148:2: warning: delete called on 'entry' that is
> abstract but has non-virtual destructor [-Wdelete-non-virtual-dtor]
>         delete e;
>         ^
> variant_file_output.cpp:278:2: warning: delete called on 'entry' that is
> abstract but has non-virtual destructor [-Wdelete-non-virtual-dtor]
>         delete e;
>         ^
> v
>