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Commits on Dec 15, 2021

• fix coverage check

  hdashnow

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• update benchmark for CI

  hdashnow

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• add GitHub Actions CI badge

  hdashnow

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Commits on Dec 3, 2021

• Merge into one job, avoid large upload

  

  lonsbio

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  hdashnow

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• Try artifact solution

  

  lonsbio

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  hdashnow

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• ls to see of test exists

  

  lonsbio

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  hdashnow

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• Diagnose error with paths

  

  lonsbio

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  hdashnow

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• Rename env variable workaround

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  lonsbio

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  hdashnow

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• Testing Github Actions repalcement for Travis

  

  lonsbio

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  hdashnow

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Commits on Nov 23, 2021

• edit to trigger CI

  hdashnow

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Commits on Nov 20, 2021

• update hg19 reference download to UoU chpc

  hdashnow

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Commits on Feb 25, 2021

• Merge pull request #62 from Oshlack/BioAlphabet

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  hdashnow

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Commits on Nov 7, 2020

• remove Bio.Alphabet/generic_dna as this has been removed from BioPython

  hdashnow

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Commits on Apr 25, 2020

• Merge pull request #61 from bharatij/master

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  hdashnow

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Commits on Apr 24, 2020

• added cram option to exome bam pipeline

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  bharatij

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Commits on Jun 2, 2019

• pinning scipy to avoid factorial import error, until statsmodels fixes it #59

  hdashnow

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Commits on Jan 24, 2019

• Merge pull request #52 from wdecoster/master

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  hdashnow

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Commits on Jan 22, 2019

• Adding script to reformat STRs.tsv output

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  wdecoster

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• make CI unit testing command run all tests matching test_*.py

  hdashnow

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• Merge pull request #43 from Oshlack/exome_bam

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  hdashnow

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Commits on Jan 21, 2019

• commend out printing bam filenames

  hdashnow

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• update STRs.benchmark.tsv to use full filename prefix as sample and use rounded values

  hdashnow

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• update diff command in travis to error if different

  hdashnow

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• Put Travis CI and codecov badges on the same line

  hdashnow

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• use mosdepth to calculate coverage over target regions for use in exome pipeline, add .gitignore

  hdashnow

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• first draft of STRetch exome from bam pipeline #42

  hdashnow

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• Merge pull request #49 from Oshlack/short_allele

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  hdashnow

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Commits on Jan 20, 2019

• limit the number of decimal points reported in the final STRetch results

  hdashnow

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Commits on Jan 16, 2019

• test identify_locus with required bed input

  hdashnow

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• Revert "only consider primary alignments"

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  hdashnow

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• basic unit test of parse_arg

  hdashnow

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• test lengths of decoys

  hdashnow

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• only consider primary alignments

  hdashnow

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• write an allele_freq function

  hdashnow

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• basic tests for all functions in decoySTR.py

  hdashnow

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