Segfault running snp2h5 about wasp HOT 4 CLOSED

Hi Nick. Thanks for letting us know about this problem. Recently I have been testing using just one input file so I didn't notice the problem. I have committed some changes that should fix the issue. Please pull the changes and give it a try again.

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Looks like the new code fixed the bug! Thanks. I'll let you know if I find any more. ;)

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Hi,
I'm use snp2h5 to convert vcf to h5. I find there is an problem in the latest version.
I use version (v 0.2 & v 0.2.1). The error happened.
...................................................................................................................
long alleles will be truncated to 100bp
writing SNP index to: snp_index.h5
chromosome: C2, length: 52886895bp
reading from file chr_vcf/C2.vcf
counting lines in file
total lines: 0
reading VCF header
ERROR: expected last line in header to start with #CHROM
....................................................................................................................

I check the vcf file, and
....................................................................................................................
grep "#CHR" chr_vcf/C2.vcf
#CHROM POS ID REF ALT QUAL FILTER INFO FORMAT SRR3203096
.....................................................................................................................
However, I use the old version (v 01 ), it is fine.

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Hi ZhengYaa

I believe that this issue was fixed on the master branch after version 0.2.1. Can you try to checkout the master rather than v0.2.1? (I should make a version 0.2.2 that includes the latest changes).

You might also try adding sample names to your header line if you have more than one sample in the VCF, since it looks like you only have one 'SRR3203096'.

Hope this helps,

Graham

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