Question: Tabix Perl Api Error?
0
gravatar for Zev.Kronenberg
6.2 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.

http://sourceforge.net/p/samtools/mailman/message/31560407/

Thanks!

EDIT:

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

1103

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

perl tabix samtools • 1.4k views
ADD COMMENTlink modified 6.2 years ago • written 6.2 years ago by Zev.Kronenberg11k
1

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 6.2 years ago by SES8.3k
Please log in to add an answer.

Help
Access

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.
Powered by Biostar version 2.3.0
Traffic: 1052 users visited in the last hour