Delete a lot of unused VCF constants #6361

davidbenjamin · 2020-01-08T18:45:02Z

Closes #5678.

@ldgauthier I was addressing #5678 and decided to continue cleaning house. Do you object to any of these? They are all unused.

ldgauthier

These are all fine to delete since nothing calculates them, but some of them are good annotations that may return if I get a chance.

ldgauthier · 2020-01-08T19:15:43Z

src/main/java/org/broadinstitute/hellbender/utils/variant/GATKVCFConstants.java

    public static final String ORIGINAL_DP_KEY =                    "DP_Orig"; //SelectVariants
-    public static final String DOWNSAMPLED_KEY =                    "DS";


I have a branch where I hook this up so it actually works. It's pretty handy for debugging some types of things. If you want to delete it now in the case that I never merge that branch, that's fair.

I'll leave this in.

ldgauthier · 2020-01-08T19:17:14Z

src/main/java/org/broadinstitute/hellbender/utils/variant/GATKVCFConstants.java

@@ -26,60 +26,42 @@
    public static final String AS_RAW_RMS_MAPPING_QUALITY_KEY =     "AS_RAW_MQ";
    public static final String AS_CULPRIT_KEY =                     "AS_culprit";
    public static final String AS_VQS_LOD_KEY =                     "AS_VQSLOD";
-    public static final String ALLELE_BALANCE_HET_KEY =             "ABHet";
-    public static final String ALLELE_BALANCE_HOM_KEY =             "ABHom";


These would be useful, but there's no code to generate them. You can delete them, but they're not bad annotations.

ldgauthier · 2020-01-08T19:17:55Z

src/main/java/org/broadinstitute/hellbender/utils/variant/GATKVCFConstants.java

    public static final String GQ_MEAN_KEY =                        "GQ_MEAN";
    public static final String GQ_STDEV_KEY =                       "GQ_STDDEV";
    public static final String HAPLOTYPE_SCORE_KEY =                "HaplotypeScore";
    public static final String HI_CONF_DENOVO_KEY =                 "hiConfDeNovo";
-    public static final String HOMOPOLYMER_RUN_KEY =                "HRun";


The TandemRepeat annotation will annotate repeat unit length one, right?

Yes, it does, so this is safe.

ldgauthier · 2020-01-08T19:19:30Z

src/main/java/org/broadinstitute/hellbender/utils/variant/GATKVCFConstants.java

    public static final String MAP_QUAL_RANK_SUM_KEY =              "MQRankSum";
    public static final String RAW_MAP_QUAL_RANK_SUM_KEY =          "RAW_MQRankSum";
    public static final String AS_MAP_QUAL_RANK_SUM_KEY =           "AS_MQRankSum";
    public static final String AS_RAW_MAP_QUAL_RANK_SUM_KEY =       "AS_RAW_MQRankSum";
-    public static final String MENDEL_VIOLATION_LR_KEY =            "MVLR";


Was this from PhaseByTransmission? Alas, even after the entire duration of Laurent's postdoc, we still never got that code into GATK4.

gatk-bot · 2020-01-08T19:25:22Z

Travis reported job failures from build 28535
Failures in the following jobs:

Test Type	JDK	Job ID	Logs
variantcalling	openjdk8	28535.4	logs
integration	openjdk11	28535.12	logs
integration	oraclejdk8	28535.11	logs
integration	openjdk8	28535.2	logs

gatk-bot · 2020-01-09T17:55:19Z

Travis reported job failures from build 28547
Failures in the following jobs:

Test Type	JDK	Job ID	Logs
integration	oraclejdk8	28547.11	logs
variantcalling	openjdk8	28547.4	logs
integration	openjdk11	28547.12	logs
integration	openjdk8	28547.2	logs

gatk-bot · 2020-01-09T19:57:16Z

Travis reported job failures from build 28552
Failures in the following jobs:

Test Type	JDK	Job ID	Logs
integration	oraclejdk8	28552.11	logs
variantcalling	openjdk8	28552.4	logs
integration	openjdk11	28552.12	logs
integration	openjdk8	28552.2	logs

gatk-bot · 2020-01-09T19:57:41Z

Travis reported job failures from build 28550
Failures in the following jobs:

Test Type	JDK	Job ID	Logs
variantcalling	openjdk8	28550.4	logs
integration	oraclejdk8	28550.11	logs
integration	openjdk11	28550.12	logs
unit	openjdk8	28550.3	logs
integration	openjdk8	28550.2	logs

gatk-bot · 2020-01-09T20:01:07Z

Travis reported job failures from build 28553
Failures in the following jobs:

Test Type	JDK	Job ID	Logs
variantcalling	openjdk8	28553.4	logs
integration	oraclejdk8	28553.11	logs
integration	openjdk11	28553.12	logs
integration	openjdk8	28553.2	logs

gatk-bot · 2020-01-09T21:12:08Z

Travis reported job failures from build 28559
Failures in the following jobs:

Test Type	JDK	Job ID	Logs
variantcalling	openjdk8	28559.4	logs

gatk-bot · 2020-01-10T08:26:00Z

Travis reported job failures from build 28569
Failures in the following jobs:

Test Type	JDK	Job ID	Logs
variantcalling	openjdk8	28569.4	logs

davidbenjamin added 22 commits January 8, 2020 13:15

got rid of unused DS INFO field

fc772c4

Likewise for Hrun

c13e494

likewise for ABHet and ABHom

d174e96

likewise for BaseCounts

d669c7c

likewise for Dels

6d3f483

likewise for GC

383ebb7

likewise for HW

491da43

likewise for IDP

b8893bf

duplicated variable

17b7bf9

likewise for LowMQ

b7ac30a

likewise for LMLPSAC and MLPSAF

b20db44

likewise for MVLRF

c85f7da

likewise for OND

f1ccc8e

likewise for OriginalChr and OriginalStart

a73a48f

likewise for PhasingInconsistent

252f6aa

likewise for REFDEPTH

35f1229

likewise for TDT

5c4cedc

likewise for VariantType

0282ad3

likewise for APL

5db0a7f

likewise for HP

ac5fba9

likewise for LL

360be4c

likewise for ZL

dfb31ed

davidbenjamin requested a review from ldgauthier January 8, 2020 18:45

davidbenjamin assigned ldgauthier Jan 8, 2020

ldgauthier approved these changes Jan 8, 2020

View reviewed changes

review

898d5d9

davidbenjamin changed the title ~~Db ds annotation~~ Delete a lot of unused VF constants Jan 9, 2020

davidbenjamin force-pushed the db_ds_annotation branch from cfbcf60 to fb4ac13 Compare January 9, 2020 19:18

test

3da3b1d

davidbenjamin force-pushed the db_ds_annotation branch from fb4ac13 to 3da3b1d Compare January 9, 2020 19:21

davidbenjamin changed the title ~~Delete a lot of unused VF constants~~ Delete a lot of unused VCF constants Jan 9, 2020

index changed test files

d5149e7

more test update

21601a3

ditto

1e0118b

davidbenjamin merged commit 65f5772 into master Jan 10, 2020

davidbenjamin deleted the db_ds_annotation branch January 10, 2020 14:55

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Delete a lot of unused VCF constants #6361

Delete a lot of unused VCF constants #6361

davidbenjamin commented Jan 8, 2020

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gatk-bot commented Jan 10, 2020

		public static final String ORIGINAL_DP_KEY = "DP_Orig"; //SelectVariants
		public static final String DOWNSAMPLED_KEY = "DS";

Delete a lot of unused VCF constants #6361

Delete a lot of unused VCF constants #6361

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