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lindenb / jvarkit

Java utilities for Bioinformatics
https://jvarkit.readthedocs.io/
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vcf2mongo.xslt missing #132

Closed darked89 closed 5 years ago

darked89 commented 5 years ago

Hello,

I have compiled vcf2.xml.jar, but to use the following command to insert it it into mongodb:

java -jar vcf2.xml.jar < file.vcf | xsltproc vcf2mongo.xslt - | mongo

I cannot find vcf2mongo.xslt anywhere neither inside the jvarkit directory tree nor by googling it.

Is this an obsolete/unsupported vcf->mongodb route, or one can obtain the vcf2mongo.xslt file?

Many thanks for your help

Darek Kedra

lindenb commented 5 years ago

I haven't used vcf2xml for years but the vcf2mongo.xsl is in the doc : https://github.com/lindenb/jvarkit/blob/95c9069a5029319d7baa69dfa9c1d11772f0895c/docs/Vcf2Xml.md#example-2-inserting-into-mongodb just copy + paste the code in a text file ' vcf2mongo.xslt'.

darked89 commented 5 years ago

Thank you very much.

The example works fine with openjdk version "12.0.1", mongodb 4.0.11 & mongodb-compass 1.18 on Linux Manjaro. I have to play with vcf2mongo.xsl to get few versions of it compatible with VCFs types I have.

Best,

Darek Kedra