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Increase visibility for SupportedHeaderLines.allHeaderLines #1372

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heuermh opened this issue Jan 24, 2017 · 5 comments
Closed

Increase visibility for SupportedHeaderLines.allHeaderLines #1372

heuermh opened this issue Jan 24, 2017 · 5 comments

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@heuermh
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@heuermh heuermh commented Jan 24, 2017

[INFO] Compiling 6 Scala sources to target/scala-2.10.6/classes...
[ERROR] .../Freebayes.scala:77: object SupportedHeaderLines in package converters
cannot be accessed in package org.bdgenomics.adam.converters
[ERROR] implicit val uFormatter = new VCFOutFormatter(SupportedHeaderLines.allHeaderLines)

In this specific use case I'd like to add Freebayes-specific headers to the ones we already support, something like

val freebayesHeaderLines = Seq( ... )
val headerLines = SupportedHeaderLines.addHeaderLines ++ freebayesHeaderLines
implicit val uFormatter = new VCFOutFormatter(headerLines)
@fnothaft
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@fnothaft fnothaft commented Jan 24, 2017

+1, although perhaps we should do a name change as well? SupportedHeaderLines makes it sound like all other header lines will be lost.

@heuermh
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@heuermh heuermh commented Jan 24, 2017

Ah that's right, we combine those in the input VCF with our supported header lines, so I don't actually need to define freebayes specific header lines. How about rename to VCFHeaderLines?

@fnothaft
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@fnothaft fnothaft commented Jan 24, 2017

That's a little too close to htsjdk.variant.vcf.VCFHeaderLine for me.

@heuermh
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@heuermh heuermh commented Jan 24, 2017

ok, propose away :)

@fnothaft
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@fnothaft fnothaft commented Jan 24, 2017

Perhaps DefaultHeaderLines, since they're what we add by default.

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