Need a way for users to add VCF header lines #1233

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fnothaft opened this Issue Oct 29, 2016 · 0 comments

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fnothaft commented Oct 29, 2016

I've kinda known this to be a problem for a while, but I was just using a VCF I saved with ADAM that had genotype filters (FT field) in a downstream tool, and I got an exception in the downstream tool because my VCF did not have a ##FILTER=<ID=ID,Description="description"> line in the header. I have a general idea for how to do this; will post next week for discussion when I'm not bandwidth limited. I think this approach would also work for SAM program fields, which would be a plus.

@fnothaft fnothaft added this to the 0.21.0 milestone Nov 11, 2016

@fnothaft fnothaft self-assigned this Nov 11, 2016

fnothaft added a commit to fnothaft/adam that referenced this issue Nov 11, 2016

[ADAM-1233] Expose header lines in Variant-related GenomicRDDs
Resolves #1233. Adds a `headerLines` field to all Variant-related GenomicRDDs.
In the current implementation, this field is populated by the set of all
header lines for all INFO/FORMAT fields that we support. In a future patch, we
will also store the header lines that correspond to fields that do not map to
a specific field in the Variant/Genotype schema, and that are stored in an
attribute map.

fnothaft added a commit to fnothaft/adam that referenced this issue Nov 18, 2016

[ADAM-1233] Expose header lines in Variant-related GenomicRDDs
Resolves #1233. Adds a `headerLines` field to all Variant-related GenomicRDDs.
In the current implementation, this field is populated by the set of all
header lines for all INFO/FORMAT fields that we support. In a future patch, we
will also store the header lines that correspond to fields that do not map to
a specific field in the Variant/Genotype schema, and that are stored in an
attribute map.

@heuermh heuermh closed this in #1260 Nov 18, 2016

heuermh added a commit that referenced this issue Nov 18, 2016

[ADAM-1233] Expose header lines in Variant-related GenomicRDDs
Resolves #1233. Adds a `headerLines` field to all Variant-related GenomicRDDs.
In the current implementation, this field is populated by the set of all
header lines for all INFO/FORMAT fields that we support. In a future patch, we
will also store the header lines that correspond to fields that do not map to
a specific field in the Variant/Genotype schema, and that are stored in an
attribute map.
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