Re: [Vcftools-help] VCF file can not be read and merged after it was compressed, Why?

[Petr D. <pd...@sa...>]

An easy way to check: 
diff /path/to/the/checkout/Vcf.pm /Users/jianfengmao/programe_files/VCFtools/VCFtools_0.1.3.2/lib//Vcf.pm

The new revision does not contain 'zcat', 'grep zcat /Users/.../Vcf.pm'
should give no output.
Petr


On Tue, 2011-01-04 at 12:13 +0100, Mao Jianfeng wrote:
> Dear Petr,
> 
> Thanks for your reply.
> 
> I do not know if the the file,
> /Users/jianfengmao/programe_files/VCFtools/lib/Vcf.pm, is the new
> revision 403. I do not know how to check it.
> 
> I downloaded the new version of VCFtools from the website, and
> installed it. It works like my older one. It can not work for
> merge-vcf command, the same results.
> 
> I think my VCFtools is not the most updated version. Could you please
> help me on that? I send my Vcf.pm to you.
> 
> In the followed command and returns from the terminal, you could find
> VCFtools has been the updated version, and it works for me by using
> other commands other than merge-vcf.
> 
> 
> abt6-mao-mbp:examples jianfengmao$ vcf-validator merge-test-a.vcf
> abt6-mao-mbp:examples jianfengmao$ bgzip merge-test-a.vcf
> abt6-mao-mbp:examples jianfengmao$ bgzip merge-test-b.vcf
> abt6-mao-mbp:examples jianfengmao$ tabix -p vcf merge-test-a.vcf.gz
> abt6-mao-mbp:examples jianfengmao$ tabix -p vcf merge-test-b.vcf.gz
> abt6-mao-mbp:examples jianfengmao$ merge-vcf merge-test-a.vcf.gz
> merge-test-b.vcf.gz
> zcat: merge-test-a.vcf.gz.Z: No such file or directory
> Error reading VCF file.
> 
>  at /Users/jianfengmao/programe_files/VCFtools/VCFtools_0.1.3.2/lib//Vcf.pm
> line 167
> 	Vcf::throw('Vcf=HASH(0x1008f3188)', 'Error reading VCF file.\x{a}')
> called at /Users/jianfengmao/programe_files/VCFtools/VCFtools_0.1.3.2/lib//Vcf.pm
> line 280
> 	Vcf::next_line('Vcf=HASH(0x1008f3188)') called at
> /Users/jianfengmao/programe_files/VCFtools/VCFtools_0.1.3.2/lib//Vcf.pm
> line 219
> 	Vcf::_open('Vcf=HASH(0x1008f3188)') called at
> /Users/jianfengmao/programe_files/VCFtools/VCFtools_0.1.3.2/lib//Vcf.pm
> line 161
> 	Vcf::new('Vcf', 'file', 'merge-test-a.vcf.gz') called at
> /Users/jianfengmao/programe_files/VCFtools/VCFtools_0.1.3.2/bin/merge-vcf
> line 125
> 	main::init_cols('HASH(0x10082a3a0)', 'Vcf4_0=HASH(0x10082e0e0)')
> called at /Users/jianfengmao/programe_files/VCFtools/VCFtools_0.1.3.2/bin/merge-vcf
> line 219
> 	main::merge_vcf_files('HASH(0x10082a3a0)') called at
> /Users/jianfengmao/programe_files/VCFtools/VCFtools_0.1.3.2/bin/merge-vcf
> line 12
> abt6-mao-mbp:examples jianfengmao$ pwd
> /Users/jianfengmao/programe_files/VCFtools/VCFtools_0.1.3.2/examples
> abt6-mao-mbp:examples jianfengmao$



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