Adding arg to VariantFiltration to write your own description in Header #8831
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@droazen could you please suggest a reviewer? |
droazen
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May 15, 2024
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Looks good to me @meganshand -- just one minor comment on naming
| @@ -114,6 +114,7 @@ public final class VariantFiltration extends VariantWalker { | |||
| public static final String CLUSTER_WINDOW_SIZE_LONG_NAME = "cluster-window-size"; | |||
| public static final String MASK_EXTENSION_LONG_NAME = "mask-extension"; | |||
| public static final String MASK_NAME_LONG_NAME = "mask-name"; | |||
| public static final String MASK_DESCRIPTION_LONG_NAME = "mask-desc"; | |||
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I might spell out mask-description for this argument name, since the other mask arguments don't have abbreviations
mcovarr
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Jul 1, 2024
…in VCF header (#8831) Added a --mask-description argument to VariantFiltration to write a custom description for the mask filter in the VCF header
mcovarr
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Jul 10, 2024
…in VCF header (#8831) Added a --mask-description argument to VariantFiltration to write a custom description for the mask filter in the VCF header
mcovarr
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Jul 15, 2024
…in VCF header (#8831) Added a --mask-description argument to VariantFiltration to write a custom description for the mask filter in the VCF header
mcovarr
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Jul 19, 2024
…in VCF header (#8831) Added a --mask-description argument to VariantFiltration to write a custom description for the mask filter in the VCF header
mcovarr
pushed a commit
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Jul 19, 2024
…in VCF header (#8831) Added a --mask-description argument to VariantFiltration to write a custom description for the mask filter in the VCF header
mcovarr
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Jul 22, 2024
…in VCF header (#8831) Added a --mask-description argument to VariantFiltration to write a custom description for the mask filter in the VCF header
mcovarr
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Jul 23, 2024
…in VCF header (#8831) Added a --mask-description argument to VariantFiltration to write a custom description for the mask filter in the VCF header
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This allows the user to write their own description in the FILTER line in the header. Currently a user can define an interval list to filter with and name that filter, but the description line is always "Doesn't overlap a user-input mask" or "Overlaps a user-input mask", whereas it might be more useful to let the user provide a more detailed description (for example, "Outside of sequencing target intervals").