I'm playing with the package org.broadinstitute.gatk.tools.walkers.annotator and I wonder if I can write the following custom variant annotator:
I've got a set of tabix-ed files in a directory (one txt.bgz per chromosome) and I want to peek the information from those files.
- Can I specify an external resource like a directory for
-T VariantAnnotator
? If no, can I add something like a java annotation to specify a new cmd-line argument in my CustomAnnotation.java ? (I don't want to modify VariantAnnotator.java )
class CustomAnnotation extends InfoFieldAnnotation {
@Argument(fullName = "mydir", shortName = "mydir", doc="My directory of tabix files", required=true)
File dir;
}
Parallelism : if my CustomAnnotation open some tabix files, should I care about parallelism ? (e.g: open the tabix file for each thread )
there is a
initialize
method in VariantAnnotatorAnnotation but nodispose
?
Thanks !
Pierre