[Vcftools-help] (no subject)

[carol w. <wh...@ya...>]

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