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Commits on May 22, 2024

• r133: clearer CMD help for extract

  

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• r132: allow shorter reads

  

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• r131: search for the best count threshold

  

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• r130: option to count inversions differently

  

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• r129: another change for SVision-Pro

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• r128: parse SVision-Pro VCF

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• r127: allow to filter by supporting read count

  

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• r126: added mergeflt

  

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• r125: parse GRIPSS VCF

  

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• r124: output "foldback" INFO

  

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• r123: record >< vs <> reads during merge

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• r122: fixed wrong orientation for inversions

  

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• r121: convert to VCF

  

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• r120: call somatic sv from paired sniffles

  

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• r119: removed the old join

  

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• r116: fixed wrong qoff

  

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• r115: output left and right query positions

  

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• r114: report qoff

  

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• r113: parse numbers like 10k with extract -l

  

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• r112: multi-sample eval

  

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• r111: view for multiple files

  

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• r110: renamed format to view; allow BED filter

  

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• r109: don't check GT by default

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• r108: parse GT

  

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• r107: check SVTYPE during join

  

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• r106: added "join"

  

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• r105: print file names

  

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• r104: allow to ignore FILTER in vcf

  

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• r103: allow confident BED

  

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• r102: optionally check VAF if present

  

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• r101: MATEID wrongly parsed; skip FILTER calls

  

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• fixed wrong VCF breakpoint parsing by Alvin

  

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• r99: added format; check len for BED input

  

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• revert

  

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• r94: added format

  

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