ah - use new GT encoding #6822
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ah - use new GT encoding #6822
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…ample metadata tsv
meganshand
reviewed
Sep 15, 2020
| if (columns == null) { | ||
| columns = line; | ||
| } else { | ||
| values = line; |
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Is there only one line in the metrics file? If so, can you put in a check for that?
| @@ -30,67 +36,39 @@ public String getColumnValue(VariantContext variant, ProbeInfo probeInfo, String | |||
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| // This where the validation step (required vs not) lives -- fail if there is missing data for a required field | |||
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Should this comment be deleted too?
meganshand
approved these changes
Sep 16, 2020
kcibul
approved these changes
Sep 16, 2020
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| public static String getGTString(final VariantContext variant) { |
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I'm so surprised this code doesn't exist anywhere? the VCFWriter must be doing (largely) the same thing?
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yes, but it is very embedded in the actual writing of the output and in htsjdk which for some reason i think it's more difficult for us to modify to make it modular.
| gt = RawArrayTsvCreator.GT_encoding.AA; | ||
| } else if (allele.basesMatch(probeInfo.alleleB)) { | ||
| gt = RawArrayTsvCreator.GT_encoding.BB; | ||
| if (alleleIndexes.size() == 2) { |
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what if it's not two? should we throw an exception?
| } | ||
| return gt.getValue(); | ||
| return gt == RawArrayTsvCreator.value_to_drop ? "null" : gt.getValue(); |
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do you mean the string null or an actual null?
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yes, the actual string "null". the tsv needs some value and the bq import will convert it to an actual null in the db. added to the comment to explain
meganshand
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* change GTs to single character, drop hom ref, add sample metrics to sample metadata tsv
kcibul
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Jan 29, 2021
* change GTs to single character, drop hom ref, add sample metrics to sample metadata tsv
kcibul
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Jan 29, 2021
* change GTs to single character, drop hom ref, add sample metrics to sample metadata tsv
kcibul
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Feb 1, 2021
* change GTs to single character, drop hom ref, add sample metrics to sample metadata tsv
kcibul
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Feb 1, 2021
* change GTs to single character, drop hom ref, add sample metrics to sample metadata tsv
Marianie-Simeon
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Feb 16, 2021
* change GTs to single character, drop hom ref, add sample metrics to sample metadata tsv
Marianie-Simeon
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Feb 16, 2021
* change GTs to single character, drop hom ref, add sample metrics to sample metadata tsv
kcibul
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Mar 9, 2021
* change GTs to single character, drop hom ref, add sample metrics to sample metadata tsv
kcibul
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Mar 9, 2021
* change GTs to single character, drop hom ref, add sample metrics to sample metadata tsv
mmorgantaylor
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Apr 6, 2021
* change GTs to single character, drop hom ref, add sample metrics to sample metadata tsv
mmorgantaylor
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Apr 6, 2021
* change GTs to single character, drop hom ref, add sample metrics to sample metadata tsv
mmorgantaylor
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Apr 6, 2021
* change GTs to single character, drop hom ref, add sample metrics to sample metadata tsv
mmorgantaylor
pushed a commit
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Apr 6, 2021
* change GTs to single character, drop hom ref, add sample metrics to sample metadata tsv
This was referenced Mar 17, 2023
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change GTs to single character, drop hom ref, add sample metrics to sample metadata tsv