Question: Tabix Perl Api Error?
gravatar for Zev.Kronenberg
7.2 years ago by
United States
Zev.Kronenberg11k wrote:

I love Tabix and have rolled it into a software library. Most of the data we are working with are de-novo assemblies that have more than 1000 seqids...

I found something that is worrying me:

$tabix->getnames() only returns 1000 seqids ???

I wrote to the mailing list, but thought I would ask here as well.



cat my.vcf | grep -v "#" | awk '{print $1}' | sort | uniq -c | wc


So I know I have more than 1000 seqids in the file...

perl tabix samtools • 1.5k views
ADD COMMENTlink modified 7.2 years ago • written 7.2 years ago by Zev.Kronenberg11k

Are you sure it's not an issue with line endings or format? It sounds simple, but that always throws off line/sequence counts.

ADD REPLYlink written 7.2 years ago by SES8.4k
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