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Targeted CNV calling workflow [WIP]#73

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xiao-chen-xc wants to merge 40 commits intomasterIllumina/ExpansionHunter:masterfrom Parse-CatalogIllumina/ExpansionHunter:Parse-CatalogCopy head branch name to clipboard

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Commits on Oct 11, 2019

• Update catalog parser to accomodate new catalog format

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  24fa5d3

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Commits on Oct 18, 2019

• Add CNV variant specifications and CNV workflow

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• Minor update

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Commits on Oct 21, 2019

• GC-based normalization

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Commits on Oct 22, 2019

• Fix line ending and CNV variable names

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  fbc16ad

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• Update NormalizationRegionAnalyzer

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• Introduce end-of-line normalization

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• Merge develop

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Commits on Oct 30, 2019

• Locus spec improvements (#75)

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• Add new variant catalog examples

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Commits on Nov 4, 2019

• Partially reorganize locus spec handling

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• Temporarily comment out code preventing building

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Commits on Nov 5, 2019

• Clean up loading of graph locus specs

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Commits on Nov 6, 2019

• Add CnvLocusDecoding

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• Update CnvLocusSpec and CnvLocusDecoding

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Commits on Nov 7, 2019

• Update CatalogLoading for CNV

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  9d2cec3

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• Make small tweaks

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  d6c0d9f

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• Fix build process

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  ca9a704

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• Make minor tweaks

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  4c715f3

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• Improve loading process

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  743c486

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• Skip reads not matching start position when extract mates

  

  yqiu

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• update gitignore

  

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  3f67cbf

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• Enable loading of graph variants

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• Complete catalogloading so it compiles

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Commits on Nov 8, 2019

• make cnv workflow work

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• make cnv work for both seeking and streaming

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Commits on Nov 12, 2019

• [WIP] Reorganize locus spec handling (#80)

  

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  4f59404

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• use single mateExtractor and htsFileSeeker

  

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• Enable CNV calling in both seeking and streaming mode

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• Add some test input files

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Commits on Nov 13, 2019

• Simplify read collection (#82)

  

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Commits on Nov 14, 2019

• Merge branch 'Parse-Catalog' into perm-improv

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• resolve conflicts for compliling

  

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• resolve conflicts for compliling

  

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  2ac0d0b

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• fix collectReads parameters

  

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Commits on Nov 15, 2019

• Merge pull request #84 from Illumina/perm-improv

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• Streamline output (#83)

  

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Commits on Nov 22, 2019

• Add mapping quality and read position check for CNV (#85)

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Commits on Dec 2, 2019

• Add paralog workflow (#86)

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Commits on Dec 9, 2019

• Fix clang build (#88)

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