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Gh1325 eva igv - #1360

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kebarr wants to merge 39 commits into

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GH1325-EVA-IGV

Open

Gh1325 eva igv#1360
kebarr wants to merge 39 commits into
masterfrom
GH1325-EVA-IGV

Commits on Sep 25, 2026
- Claude suggestions for pulling VCFs from zarr datasets
  
  Katie Barr
  authored and
  Katie Barr
  committed
  3be6e9c
Commits on Sep 28, 2026
- claude suggestions for BAM-replacement, not really possible for data in zarr datasets
  
  Katie Barr
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  Katie Barr
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  73f547f
- don't allow None for sample_sets or sample_query in to_vcf
  
  Katie Barr
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  Katie Barr
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  b2651bc
- remove optional from sample_Sets and sample_query
  
  Katie Barr
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  Katie Barr
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  837260d
- claude fixes for tests making sample_sets and sample_Wuery non-optional
  
  Katie Barr
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  Katie Barr
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  8d0d336
- updated doctring re sample_sets and sample_query
  
  Katie Barr
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  Katie Barr
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  a302a13
- claude draft input validation
  
  Katie Barr
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  Katie Barr
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  bc181ea
- updated docstring to specify only one sample can be used- can revisit later if usage expands beyond IGV
  
  Katie Barr
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  Katie Barr
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  317c2b0
Commits on Sep 29, 2026
- claude suggested changes to batch call rather than separate for each chunk
  
  Katie Barr
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  Katie Barr
  committed
  cf3e6b6
- removed the numpy array that is edited through a loop- i.e. not a vectorised implementation, noticed in diff igv.ipynb had changed due to me running it previously, restored to original state and ad…
  
  Katie Barr
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  Katie Barr
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  50d620e
- fix field order to hopefully enable analysis of outputs from bcftools
  
  Katie Barr
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  Katie Barr
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  6802977
- more format fixing
  
  Katie Barr
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  Katie Barr
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  6428c98
- more twiddling with header due to bcftools warning, still looking into agreement with reference VCF
  
  Katie Barr
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  Katie Barr
  committed
  b7ec7c7
- Claude draft to output only heterozygous sites in VCF
  
  Katie Barr
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  Katie Barr
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  aeab100
Commits on Sep 30, 2026
- Claude draft of bug fix with removing homozygous sites
  
  Katie Barr
  authored and
  Katie Barr
  committed
  050415a
- still trying to get to_vcf correct Claude thinks its something to to with compression despite me testing on uncompressed outputs, so I am unconvinced
  
  Katie Barr
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  Katie Barr
  committed
  8e4b62e
- removing Claudes allele remapping to see if that improves results
  
  Katie Barr
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  Katie Barr
  committed
  417ddb7
- claudes last attempt, problems persisted, going to revert to a better version and figure out removing homozygous sites
  
  Katie Barr
  authored and
  Katie Barr
  committed
  b4876a6
- removed leftover bits from to_vcf_cnv
  
  Katie Barr
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  Katie Barr
  committed
  67f4ed6
- try simple if statement to exclude homozygous sites
  
  Katie Barr
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  Katie Barr
  committed
  5aabdfd
- fixed indentation to only output heterozygous sites
  
  Katie Barr
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  Katie Barr
  committed
  b23e4b6
Commits on Oct 1, 2026
- reverted igv to original version and removed to_coverage as bam urls will be fine
  
  Katie Barr
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  Katie Barr
  committed
  4203d04
- removed OrderedDict
  
  Katie Barr
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  Katie Barr
  committed
  c22b1b5
- trying pysam so bgzf compression can be used so index needed for IGV can be made alognside VCF
  
  Katie Barr
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  Katie Barr
  committed
  f2e074f
- wired through to IGV, checked with notebook
  
  Katie Barr
  authored and
  Katie Barr
  committed
  e126912
Commits on Oct 5, 2026
- fixed type annotaitons and moved homozygous check
  
  Katie Barr
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  Katie Barr
  committed
  04f6c83
- removed the to_vcf_cnf draft for now
  
  Katie Barr
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  Katie Barr
  committed
  b9db52d
- getting ready for PR, removing unused functions that were drafter previously and their related tests
  
  Katie Barr
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  Katie Barr
  committed
  03f8fb3
- make site_masks=None default, updated doctring
  
  Katie Barr
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  Katie Barr
  committed
  f96236f
- merged newest changes from master
  
  Katie Barr
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  Katie Barr
  committed
  209411a
Commits on Oct 6, 2026
- remove pysam as with it, either Windows install of malariagen_data won't work at all, or IGV-related funcitonality will not be available to Windows users
  
  Katie Barr
  authored and
  Katie Barr
  committed
  b018131
- slight changes after running pytest with coverage
  
  Katie Barr
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  Katie Barr
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  ba281e1
- added some extra tests
  
  Katie Barr
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  Katie Barr
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  96f0590
- ran pre-commit run --all-files
  
  Katie Barr
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  Katie Barr
  committed
  a18921d
- think i fixed tests failing under CI
  
  Katie Barr
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  Katie Barr
  committed
  a0cf6b8
Commits on Oct 7, 2026
- limit region size to ensure it will load in IGV
  
  Katie Barr
  authored and
  Katie Barr
  committed
  4e20404
- fixed vcf paths for jupyter lab
  
  Katie Barr
  authored and
  Katie Barr
  committed
  98ad89a
- shown 5bp region with SNPs, and same region with original VCF, plus some extra explanatio in notebookn
  
  Katie Barr
  authored and
  Katie Barr
  committed
  debaed8
Commits on Oct 13, 2026
- hopefully restored notebooks to previous state and commented nbstripout from my pre commit hooks to make sure it doesn't alter them
  
  Katie Barr
  authored and
  Katie Barr
  committed
  5791196

Commits

Commits on Sep 25, 2026

Commits on Sep 28, 2026

Commits on Sep 29, 2026

Commits on Sep 30, 2026

Commits on Oct 1, 2026

Commits on Oct 5, 2026

Commits on Oct 6, 2026

Commits on Oct 7, 2026

Commits on Oct 13, 2026