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...