Merge master to ah var store 2023-07-18 [DRAFT] #8425

mcovarr · 2023-07-18T19:12:22Z

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…n creating temporary files in GermlineCNVCaller and improved documentation of corresponding utility methods. (#7411)

…ntermittent ArrayIndexOutOfBoundsExceptions (#7417) Resolves #7403

Improved the documentation text for ComposeSTRTableFile and related STRDecimationTable.

* remove calls to filter Numt and low het sites * remove extra max_low_het params * remove inputs from example json

…Allele2 in MAF output (#7422) Added code to populate the Match_Norm_Seq_Allele1 and 2 fields when generating MAF output, plus tests. Fixes #7408

Also add some docs details

* Deal with reblocked hom refs with no PLs in CombineGVCFs and GenotypeGVCFs

…lterAlignmentArtifacts. (#6885) * extracted constants, added docs, added TSV methods and tests * bubbled up ALIGNMENT_TO_BEST_HAPLOTYPE_SW_PARAMETERS * bubbled up ORIGINAL_DEFAULT * bubbled up NEW_SW_PARAMETERS and reverted calculateCigar optimization * bubbled up STANDARD_NGS * exposed parameters through AssemblyBasedCallerArgumentCollection * rebased with some fixups * replaced TSV input of args with explicit args * added integration tests for HC and M2 * addressed review comments

#7471) Modify the new reblocked GT calling behavior a little bit more so annotations are more accurate compared to non-reblocked GVCFs Fix bug due to InbreedingCoeff vs. AS_InbreedingCoeff code duplication

Catch corner case for DP=0/no DP variants Clean up raw annotations for AS_QD

* Added an optional --interval-file-prefix flag to SplitIntervals for adding a prefix to interval filenames * Added an optional --interval-file-num-digits flag to SplitIntervals to configure the number of digits used for interval filenames Resolves #7157

#7464) * gCNV in the CASE mode now fills in all hidden DenoisingModelConfig and CopyNumberCallingConfig arguments from the input model configuration.

… gCNV (#7450) * Exposed number of samples used for estimating denoised copy ratios in gCNV engine to the GermlineCNVCaller.

) * Added bounds checking as a bandaid to indel protein string issue.

* updating org.xerial:sqlite-jdbc:3.20.1 -> 3.36.0.3 * this adds native support for M1 macs

Move to GenomicsDB 1.4.2 release to fix #7012 Resolves #7012

#7105)

Make AlleleFrequencyUtils aware of genes with multiple transcripts, enabling successful operation of FilterFuncotations. Fixes #7504.

* Switch travis variable name from DOCKER_SERVICE_PASS -> DOCKER_SERVICE_TOKEN for clarity * Replace gcloud key * Replace deploy key for travis to authenticate to github

* Set gcloud config directory in travis * This fixes an issue while installing gcloud on travis due to permissions in the root directories

Add a --bypass-feature-reader argument to GenomicsDBImport to allow htslib to be used for VCF reading instead of htsjdk. This reduces memory usage and potentially speeds up the import process. Co-authored-by: nalinigans <[email protected]>

* Add defensive programming and null checks to the annotation code to guard against missing values * Correct inconsistent use of NaNs versus empty values in RankSums. * Add integration tests for GenotypeGVCFs and GnarlyGenotyper to demonstrate the fixes Resolves #7483

Adding a comment explaining why we checkout the entire repo history in travis. This caused some understandable confusion.

…ssembly for HaplotypeCaller and Mutect (#7384)

…esentation (#7103) * fixed bug where Mutect2 ignored germline variants with alternate representation * two little things

Co-authored-by: Derek Caetano-Anollés <[email protected]>

…Field parsing more permissive (#8351)

X_FILTERED_COUNT the number of reads in the locus that pass the FeatureMap filters, regardless of whether the considered base matches the reference or not

…ipeline (#8406)

* Allow LocatableXsvFuncotationFactory to read gzipped files * Add test case

* changedReadNameReadFilter to support multipleReadnames inputs (and consequently .list files)

This release contains important bugfixes, including a fix for #8141 (intermittent failure to properly compress outputs)

- Now will count downloads of all artifacts in github releases instead of just the first one.

* ReblockGVCFs cleanup for dragen inputs * addressing comments

…var_store_2023_07_18

gatk-bot · 2023-07-18T19:29:49Z

Github actions tests reported job failures from actions build 5591447053
Failures in the following jobs:

Test Type	JDK	Job ID	Logs
cloud	17.0.6+10	5591447053.10	logs
unit	17.0.6+10	5591447053.12	logs
unit	17.0.6+10	5591447053.1	logs

gatk-bot · 2023-07-18T19:41:17Z

Github actions tests reported job failures from actions build 5591508043
Failures in the following jobs:

Test Type	JDK	Job ID	Logs
cloud	17.0.6+10	5591508043.10	logs
unit	17.0.6+10	5591508043.12	logs
unit	17.0.6+10	5591508043.1	logs

gatk-bot · 2023-07-18T22:07:59Z

Github actions tests reported job failures from actions build 5592732341
Failures in the following jobs:

Test Type	JDK	Job ID	Logs
cloud	17.0.6+10	5592732341.10	logs

…ethod

…elds

samuelklee and others added 30 commits August 16, 2021 15:02

Fixed bug resulting from prefix strings of less than 3 characters whe…

0566cab

…n creating temporary files in GermlineCNVCaller and improved documentation of corresponding utility methods. (#7411)

Fix a thread safety issue in CalibrateDragstrModel that could cause i…

55b241b

…ntermittent ArrayIndexOutOfBoundsExceptions (#7417) Resolves #7403

Update annotation args to GATK4 names (#7413)

b912fad

Fix issues with missing documentation for ComposeSTRTableFile. (#7409)

0d5aee7

Improved the documentation text for ComposeSTRTableFile and related STRDecimationTable.

remove calls to filter Numt and low het sites (#7325)

962f1d1

* remove calls to filter Numt and low het sites * remove extra max_low_het params * remove inputs from example json

Funcotator fix for missing Match_Norm_Seq_Allele1 and Match_Norm_Seq_…

f16cc95

…Allele2 in MAF output (#7422) Added code to populate the Match_Norm_Seq_Allele1 and 2 fields when generating MAF output, plus tests. Fixes #7408

ReblockGVCF is now out of beta (#7419)

cafc6ce

Also add some docs details

GenotypeGVCFs update for reblocked GVCFs (#7223)

24a8e02

* Deal with reblocked hom refs with no PLs in CombineGVCFs and GenotypeGVCFs

Improve consistency for heterozygosity annotations on reblocked inputs (

c1f3737

#7471) Modify the new reblocked GT calling behavior a little bit more so annotations are more accurate compared to non-reblocked GVCFs Fix bug due to InbreedingCoeff vs. AS_InbreedingCoeff code duplication

Fix GenotypeGVCFs bug for variants with zero or no INFO DP (#7491)

ec514b7

Catch corner case for DP=0/no DP variants Clean up raw annotations for AS_QD

Update SV clustering classes (#7243)

95852a1

Propagated all hidden arguments in gCNV CASE mode from the given model (

eed998c

#7464) * gCNV in the CASE mode now fills in all hidden DenoisingModelConfig and CopyNumberCallingConfig arguments from the input model configuration.

Exposed number of samples used for estimating denoised copy ratios in…

da3c0cd

… gCNV (#7450) * Exposed number of samples used for estimating denoised copy ratios in gCNV engine to the GermlineCNVCaller.

Added bounds checking as a bandaid to indel protein string issue. (#7513

f085d3f

) * Added bounds checking as a bandaid to indel protein string issue.

Update sqllite library to support M1 Macs (#7519)

db971f0

* updating org.xerial:sqlite-jdbc:3.20.1 -> 3.36.0.3 * this adds native support for M1 macs

CNV wdl tasks now provide BAM index directly as input (#7518)

ff215c3

Move to GenomicsDB 1.4.2 (#7520)

64a47cd

Move to GenomicsDB 1.4.2 release to fix #7012 Resolves #7012

SW implementation is command line argument in FilterAlignmentArtifacts (

f74cf29

#7105)

Allow FilterFuncotations to process multi-transcript genes (#7506)

1766f30

Make AlleleFrequencyUtils aware of genes with multiple transcripts, enabling successful operation of FilterFuncotations. Fixes #7504.

Rotating travis secrets part 1 and 2 (#7521)

8230258

* Switch travis variable name from DOCKER_SERVICE_PASS -> DOCKER_SERVICE_TOKEN for clarity * Replace gcloud key * Replace deploy key for travis to authenticate to github

Set gcloud config directory in travis (#7525)

60ef1ab

* Set gcloud config directory in travis * This fixes an issue while installing gcloud on travis due to permissions in the root directories

Adding comment to .travis.yml about the checkout depth (#7421)

b8669c9

Adding a comment explaining why we checkout the entire repo history in travis. This caused some understandable confusion.

Added a debug option to output a side-vcf with variants detected by a…

29d5649

…ssembly for HaplotypeCaller and Mutect (#7384)

fixed bug where Mutect2 ignored germline variants with alternate repr…

39a379f

…esentation (#7103) * fixed bug where Mutect2 ignored germline variants with alternate representation * two little things

MarkDuplicatesSpark documentation tweak (#7191) (#7535)

f3df0b3

Co-authored-by: Derek Caetano-Anollés <[email protected]>

genotype-germline-sites not called experimental (#7533)

f638603

jamesemery and others added 16 commits June 28, 2023 10:01

Fixed support for newer Gencode GTF versions by making the GencodeGTF…

01e45a2

…Field parsing more permissive (#8351)

Free up space on github actions runners for all jobs. (#8386)

3b95e6b

Pinning joblib to v1.1.1. for python env (#8391)

2b9d54d

Additional annotation in FeatureMap (#8347)

c068947

X_FILTERED_COUNT the number of reads in the locus that pass the FeatureMap filters, regardless of whether the considered base matches the reference or not

created variable for user to specify java heap size in picard in MT p…

66e35bb

…ipeline (#8406)

Allow LocatableXsvFuncotationFactory to read gzipped files (#8363)

810326c

* Allow LocatableXsvFuncotationFactory to read gzipped files * Add test case

Changed ReadNameReadFilter to support mulitple readname inputs (#8405)

a959ceb

* changedReadNameReadFilter to support multipleReadnames inputs (and consequently .list files)

Update the Intel GKL to the latest release, 0.8.11 (#8409)

9216207

This release contains important bugfixes, including a fix for #8141 (intermittent failure to properly compress outputs)

change runtime attrs to args in MT pipeline (#8413)

e0090de

Add support for breakend replacement alleles in SVCluster (#8408)

d79823f

Fixed bug in download metrics script. (#8418)

1529aa1

- Now will count downloads of all artifacts in github releases instead of just the first one.

Made runtime attrs to args in MT pipeline (#8417)

8b7a3f6

ReblockGVCFs cleanup (#8411)

248dd79

* ReblockGVCFs cleanup for dragen inputs * addressing comments

Add haploid support to GnarlyGenotyper (#7750)

7d900f5

Merge remote-tracking branch 'origin/master' into merge_master_to_ah_…

19f3803

…var_store_2023_07_18

merge fixes

e36f5f3

mcovarr changed the base branch from master to ah_var_store July 18, 2023 19:12

mcovarr added 7 commits July 18, 2023 18:26

Fix reference reference

566ce60

Annotation adjustments for ExtractTool

d0d1f81

Call new ReferenceConfidenceVariantContextMerger#mergeWithRemapping m…

a5e33f7

…ethod

Java 17 for most spots, Java 8 remains for Hail

74a2b69

Dockstore

88c6543

Adapt for Avro 1.11 behavior of throwing on get()s of non-existent fi…

9dfd910

…elds

Update GATK Docker image to get required Java 17 JRE

1b657c2

mcovarr force-pushed the merge_master_to_ah_var_store_2023_07_18 branch from 48e5e00 to 1b657c2 Compare July 18, 2023 23:19

mcovarr closed this Jul 21, 2023

mcovarr deleted the merge_master_to_ah_var_store_2023_07_18 branch September 1, 2023 12:32

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Merge master to ah var store 2023-07-18 [DRAFT] #8425

Merge master to ah var store 2023-07-18 [DRAFT] #8425

mcovarr commented Jul 18, 2023

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gatk-bot commented Jul 18, 2023

Merge master to ah var store 2023-07-18 [DRAFT] #8425

Merge master to ah var store 2023-07-18 [DRAFT] #8425

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