Feature/ximmer coverage#173

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kkobylin wants to merge 23 commits intomasterfrom

feature/ximmer_coverage

Commits on Jan 12, 2023

Init commit
kkobylin
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Commits on Jan 16, 2023

Improve target counts query
kkobylin
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Commits on Jan 18, 2023

Use dataframe in converters
kkobylin
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Commits on Jan 19, 2023

Fix coverage stats in xhmm
kkobylin
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Commits on Jan 20, 2023

Modify converter tests
kkobylin
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Commits on Jan 22, 2023

Add saveAsSparkFormat option, add perBaseCoverage and targetCounts tests
kkobylin
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Add saveAsSparkFormat option, add perBaseCoverage and targetCounts tests
kkobylin
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Merge branch 'feature/ximmer_coverage' of github.com:biodatageeks/sequila into feature/ximmer_coverage
kkobylin
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Add cache on targetCounts result
kkobylin
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Change spark save
kkobylin
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Change mean coverage query
kkobylin
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Commits on Jan 23, 2023

Replace median with percentile_approx function
kkobylin
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Commits on Jan 24, 2023

Remove cache in TargetCounts
kkobylin
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Commits on Jan 25, 2023

Sum coniferCov instead of count all reads to get readsNr
kkobylin
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Commits on Jan 26, 2023

Collect only ones, count reads instead of sum cov
kkobylin
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Commits on Jan 28, 2023

Change readsNr method
kkobylin
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Commits on Jan 29, 2023

Xhmm fix
kkobylin
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Commits on Feb 1, 2023

fix:race condition for local[n] in toCoverage method

mwiewior
authored and
kkobylin
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Add fasta to arguments
kkobylin
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Add log to GngsConverter
kkobylin
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Add log to GngsConverter
kkobylin
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Commits on Feb 4, 2023

Add test script on GCP
kkobylin
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Commits on Feb 19, 2023

Remove time logging and comments
kkobylin
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