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From: Anthony M. <ant...@ei...> - 2014-04-10 13:00:14
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Morty, This is completely normal. Due to some of the changes we implemented in vcftools (specifically the ability to read in from streams), writing an index file is no longer necessary. -- Anthony Marcketta Bioinformatics Analyst Department of Genetics Albert Einstein College of Medicine Van Etten B01 Bronx, New York 10461 ________________________________________ From: Morty [mor...@fr...] Sent: Wednesday, April 09, 2014 6:40 PM To: vcf...@li... Subject: [Vcftools-help] vcfidx files One of the scientists I support at work requested that I upgrade vcftools from 0.1.10 to 0.1.12a. He has noted an issue that the new version does not seem to generate .vcfidx files. I can reproduce this using one of the files from your examples: vcftools --vcf valid-4.1.vcf --get-INFO ID Using 0.1.10, this generates a .vcfidx file. Using 0.1.12a, this does not generate a .vcfidx file. I looked through the announcements for the releases since 0.1.10 and the vcftools-help mailing list archives, but do not see anything that addresses this directly. Is this difference normal? I did see that you removed --force-write-index in 0.1.12 -- was that because you phased out the index? Or do I have a broken installation? The generated out.INFO file itself is identical. Thanks! - Morty ------------------------------------------------------------------------------ Put Bad Developers to Shame Dominate Development with Jenkins Continuous Integration Continuously Automate Build, Test & Deployment Start a new project now. Try Jenkins in the cloud. http://p.sf.net/sfu/13600_Cloudbees _______________________________________________ Vcftools-help mailing list Vcf...@li... https://lists.sourceforge.net/lists/listinfo/vcftools-help |