Miscellaneous VCF fixes #1247

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fnothaft commented Nov 7, 2016

Fixes #1202, #1226, #1232, supersedes #1205.

var sort: Boolean = false
+ @Args4jOption(required = false,
+ name = "-sort_lexicographically_on_save",
+ usage = "Sort the VCF output by lexicographic order. Conflicts with -sort_on_save.")

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heuermh Nov 7, 2016

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Is there any possibility of a third sort method? If so, maybe separate -sort_on_save and -sort_by [method] arguments would be preferrable

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Is there any possibility of a third sort method? If so, maybe separate -sort_on_save and -sort_by [method] arguments would be preferrable

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fnothaft Nov 7, 2016

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I can't think of one...

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fnothaft Nov 7, 2016

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I can't think of one...

+ * @param asSingleFile If true, saves the output as a single file by merging
+ * the sharded output after completing the write to HDFS. If false, the
+ * output of this call will be written as shards, where each shard has a
+ * valid VCF header. Default is false.
*/
def saveAsVcf(filePath: String,

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heuermh Nov 7, 2016

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too many boolean parameters here

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heuermh Nov 7, 2016

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too many boolean parameters here

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I kinda agree. I think it would probably make sense to break this out as is done with AlignmentRecords and have sortByXYZ functions.

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fnothaft Nov 7, 2016

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I kinda agree. I think it would probably make sense to break this out as is done with AlignmentRecords and have sortByXYZ functions.

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@heuermh

heuermh Nov 7, 2016

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+1

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jpdna and others added some commits Oct 11, 2016

[ADAM-1226] Properly export strand bias components.
Resolves #1226. Adds logic to
`org.bdgenomics.adam.converters.VariantContextConverter` that checks for a
4 element array in the `strandBiasComponents` field. If this is present, this
is exported as the "SB" VCF field.
[ADAM-1232] Default to contig order sort when saving sorted VCF.
Resolves #1232. Adds ability to select between lexicographic and contig index
sort order when saving a sorted VCF file.
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heuermh approved these changes Nov 8, 2016

@heuermh heuermh merged commit 480c23e into bigdatagenomics:master Nov 8, 2016

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Thank you, @fnothaft

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heuermh commented Nov 8, 2016

Thank you, @fnothaft

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