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Commits on Dec 14, 2025

• correct custom path handling

  mikolmogorov

  committed
  80afc86

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Commits on Dec 13, 2025

• fix for samples with low coverage with no clear local minima

  mikolmogorov

  committed
  3ddeba0

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Commits on Dec 9, 2025

• fixed peak finding for diploid genomes with no CNAs

  mikolmogorov

  committed
  14f2192

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Commits on Dec 3, 2025

• don't require .fai for reference

  mikolmogorov

  committed
  89b11d6

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Commits on Dec 2, 2025

• Update __version__.py

  tahashmi

  authored
  60c7c44

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Commits on Nov 18, 2025

• moving plots

  mikolmogorov

  committed
  ecbb0ce

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• utils dir moved

  mikolmogorov

  committed
  3ec5f37

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• loh file, utils transfer completed

  mikolmogorov

  committed
  f525a21

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• more utils moving

  mikolmogorov

  committed
  59edbc7

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Commits on Nov 17, 2025

• more utils functions moved to separate modules

  mikolmogorov

  committed
  fb157ef

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Commits on Nov 15, 2025

• cna folder refactoring

  mikolmogorov

  committed
  9eecc20

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Commits on Nov 14, 2025

• utils refactoring: coverage functions

  mikolmogorov

  committed
  ee14294

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Commits on Nov 13, 2025

• imports on top

  mikolmogorov

  committed
  1f54260

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• hapcorrect path changed

  mikolmogorov

  committed
  9b0e8c0

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Commits on Nov 12, 2025

• manual update

  mikolmogorov

  committed
  946ed53

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• command line options restructure

  mikolmogorov

  committed
  0e48850

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• generate_vcf moved

  mikolmogorov

  committed
  f5ca748

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• deleted/commented out unused functions

  mikolmogorov

  committed
  1148c54

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• some uncalled functions and unused imports removed

  mikolmogorov

  committed
  8acb537

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• removed duplication, extras renamed to breakpoints

  mikolmogorov

  committed
  6e387b3

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• new folder for vcf and bam functions

  mikolmogorov

  committed
  1bb87bf

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• some annotations + deleted unused functions

  mikolmogorov

  committed
  e2e08e2

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Commits on Nov 11, 2025

• merging vcf processing tools

  mikolmogorov

  committed
  38c6573

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• bam import fix

  mikolmogorov

  committed
  f2199eb

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• Merge branch 'main' into refactoring

  mikolmogorov

  committed
  7427fd4

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• removed duplicated process_bam

  mikolmogorov

  committed
  e54751f

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• removed duplicated phase_correction

  mikolmogorov

  committed
  ecbe779

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• deleted duplicated hapcorrect/extras.py

  mikolmogorov

  committed
  b125bbc

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• deleted duplicated smoothing.y

  mikolmogorov

  committed
  d4e214b

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Commits on Nov 4, 2025

• small update in command

  tahashmi

  committed
  43c3197

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Commits on Oct 24, 2025

• always generate loh_segments

  mikolmogorov

  committed
  73f4b50

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Commits on Oct 23, 2025

• more strict breakpoint coverage

  mikolmogorov

  committed
  bcd9eed

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Commits on Oct 17, 2025

• ad hoc fix for missing SVLEN

  mikolmogorov

  committed
  65f5735

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• don't recompute correlation every time, add normal coverage to lost haplotypes

  mikolmogorov

  committed
  5306161

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• lowering SV support threshold

  mikolmogorov

  committed
  5427a1c

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