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changed pre.py params to work with single gvcf #113

Merged
merged 1 commit into from
Mar 1, 2021
Merged

changed pre.py params to work with single gvcf #113

merged 1 commit into from
Mar 1, 2021

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hguturu
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@hguturu hguturu commented Feb 27, 2020

Closes #106

pre.py was crashing since it was expecting two args convert_gvcf_truth and convert_gvcf_query but referencing convert_gvcf since running pre.py directly only has one input. Updated the code and the documentation to use a single arg convert_gvcf_to_vcf.

@johanneskoester
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Can we get this merged and released, or another kind of fix for this issue? Fixing this would also have a high priority for the GIAB project.

@johanneskoester johanneskoester mentioned this pull request Mar 1, 2021
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dskola
dskola approved these changes Mar 1, 2021
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Looks good to me.

@dskola dskola merged commit 214ec68 into Illumina:master Mar 1, 2021
@hguturu hguturu mentioned this pull request Mar 1, 2021
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@hguturu hguturu deleted the hg-fix-pre-convert-gvcf branch March 1, 2021 18:36
@johanneskoester
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@dskola, could you also release a new version?

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dskola commented Mar 2, 2021

Done!

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Thank you!

@nate-d-olson
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I tried running the hap.py command after this update, hap.py {TRUTH}.vcf.gz {QUERY}.vcf.gz -f {TRUTH REGIONS}.bed -r {REF}.fa --engine=vcfeval --stratification {STRATIFICATIONS}.tsv -o {OUTDIR}, using the updated bioconda package and the snakemake/snakemake docker container and get the following error. Which I think is due to changes made as part of this update.

2021-03-03 16:37:26,577 WARNING  No reference file found at default locations. You can set the environment variable 'HGREF' or 'HG19' to point to a suitable Fasta file.
Hap.py 
2021-03-03 16:37:26,700 ERROR    'Namespace' object has no attribute 'convert_gvcf_truth'
2021-03-03 16:37:26,700 ERROR    Traceback (most recent call last):
2021-03-03 16:37:26,701 ERROR      File "/opt/conda/envs/happy/bin/hap.py", line 529, in <module>
2021-03-03 16:37:26,701 ERROR        main()
2021-03-03 16:37:26,701 ERROR      File "/opt/conda/envs/happy/bin/hap.py", line 286, in main
2021-03-03 16:37:26,701 ERROR        if args.convert_gvcf_truth:
2021-03-03 16:37:26,701 ERROR    AttributeError: 'Namespace' object has no attribute 'convert_gvcf_truth'

@hguturu
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hguturu commented Mar 9, 2021

I think this can be resolved if references to args.convert_gvcf_truth in hap.py are replaced by args.convert_gvcf_to_vcf. Since the parameters used by pre.py have been changed.

@nate-d-olson nate-d-olson mentioned this pull request Mar 12, 2021
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Thanks! I submitted a pull request.

nicholas-owen pushed a commit to nicholas-owen/hap.py that referenced this pull request Mar 17, 2022
Remove tag (Illumina#113)
6542350 
* Documentation updates for 0.3.12 release (Illumina#110)

* Update RELEASES.md (Illumina#87)

* Updated RELASES.md and normalization.md (Illumina#109)

* Merge doc changes from dev (Illumina#112)

* Update RELEASES.md (Illumina#87)

* Updated RELASES.md and normalization.md (Illumina#109)

* Update more docs (Illumina#111)

* Update happy.md

* Cleaned up normalisation.md

* Update happy.md

* Created a new section for working with genome VCFs
  * Added description of --filter-nonref
  * Updated description of --convert-gvcf-xxxx options
  * Added note toward beginning of document calling attention to genome VCF section
* Fixed broken links in TOC
* Fixed inconsistent case in headings
nicholas-owen pushed a commit to nicholas-owen/hap.py that referenced this pull request Mar 17, 2022
Merge all (Illumina#116)
eb9d746 
* fix bold GFM rendering

Without a space between the *** and the : , Github won't render *** as bold.

* typos?

* Clarify that INFO.VQSLOD is required for --roc

* Update read me with GCC/G++ 4.9.2+ requirement

See Illumina#66

* Remove regex dependency + fix test error with gcc 7.3

* Fix Docker build

* Update rtg-tools to work with new Java

* Updated RELASES.md and normalization.md (Illumina#109)

* Documentation updates for 0.3.12 release (Illumina#110)

* Update RELEASES.md (Illumina#87)

* Updated RELASES.md and normalization.md (Illumina#109)

* Update more docs (Illumina#111)

* Update happy.md

* Cleaned up normalisation.md

* Update happy.md

* Created a new section for working with genome VCFs
  * Added description of --filter-nonref
  * Updated description of --convert-gvcf-xxxx options
  * Added note toward beginning of document calling attention to genome VCF section
* Fixed broken links in TOC
* Fixed inconsistent case in headings

* Merge doc changes from dev (Illumina#112)

* Update RELEASES.md (Illumina#87)

* Updated RELASES.md and normalization.md (Illumina#109)

* Update more docs (Illumina#111)

* Update happy.md

* Cleaned up normalisation.md

* Update happy.md

* Created a new section for working with genome VCFs
  * Added description of --filter-nonref
  * Updated description of --convert-gvcf-xxxx options
  * Added note toward beginning of document calling attention to genome VCF section
* Fixed broken links in TOC
* Fixed inconsistent case in headings

* Remove tag (Illumina#113)

* Documentation updates for 0.3.12 release (Illumina#110)

* Update RELEASES.md (Illumina#87)

* Updated RELASES.md and normalization.md (Illumina#109)

* Merge doc changes from dev (Illumina#112)

* Update RELEASES.md (Illumina#87)

* Updated RELASES.md and normalization.md (Illumina#109)

* Update more docs (Illumina#111)

* Update happy.md

* Cleaned up normalisation.md

* Update happy.md

* Created a new section for working with genome VCFs
  * Added description of --filter-nonref
  * Updated description of --convert-gvcf-xxxx options
  * Added note toward beginning of document calling attention to genome VCF section
* Fixed broken links in TOC
* Fixed inconsistent case in headings

* Resolved merge conflict

* Remove seemingly-unused ENV command

* Restore ENV DEBIAN_FRONTEND=noninteractive
nicholas-owen pushed a commit to nicholas-owen/hap.py that referenced this pull request Mar 17, 2022
Dev (Illumina#117)
ef84473 
* Updated RELASES.md and normalization.md (Illumina#109)

* Update more docs (Illumina#111)

* Update happy.md

* Cleaned up normalisation.md

* Update happy.md

* Created a new section for working with genome VCFs
  * Added description of --filter-nonref
  * Updated description of --convert-gvcf-xxxx options
  * Added note toward beginning of document calling attention to genome VCF section
* Fixed broken links in TOC
* Fixed inconsistent case in headings

* Remove tag (Illumina#113)

* Documentation updates for 0.3.12 release (Illumina#110)

* Update RELEASES.md (Illumina#87)

* Updated RELASES.md and normalization.md (Illumina#109)

* Merge doc changes from dev (Illumina#112)

* Update RELEASES.md (Illumina#87)

* Updated RELASES.md and normalization.md (Illumina#109)

* Update more docs (Illumina#111)

* Update happy.md

* Cleaned up normalisation.md

* Update happy.md

* Created a new section for working with genome VCFs
  * Added description of --filter-nonref
  * Updated description of --convert-gvcf-xxxx options
  * Added note toward beginning of document calling attention to genome VCF section
* Fixed broken links in TOC
* Fixed inconsistent case in headings

* Clean merge (Illumina#115)

* fix bold GFM rendering

Without a space between the *** and the : , Github won't render *** as bold.

* typos?

* Clarify that INFO.VQSLOD is required for --roc

* Update read me with GCC/G++ 4.9.2+ requirement

See Illumina#66

* Remove regex dependency + fix test error with gcc 7.3

* Fix Docker build

* Update rtg-tools to work with new Java

* Documentation updates for 0.3.12 release (Illumina#110)

* Update RELEASES.md (Illumina#87)

* Updated RELASES.md and normalization.md (Illumina#109)

* Merge doc changes from dev (Illumina#112)

* Update RELEASES.md (Illumina#87)

* Updated RELASES.md and normalization.md (Illumina#109)

* Update more docs (Illumina#111)

* Update happy.md

* Cleaned up normalisation.md

* Update happy.md

* Created a new section for working with genome VCFs
  * Added description of --filter-nonref
  * Updated description of --convert-gvcf-xxxx options
  * Added note toward beginning of document calling attention to genome VCF section
* Fixed broken links in TOC
* Fixed inconsistent case in headings

* Resolved merge conflict

* Remove seemingly-unused ENV command

* Restore ENV DEBIAN_FRONTEND=noninteractive
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AttributeError when running pre.py directly
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@hguturu @johanneskoester @dskola @nate-d-olson