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Commits on Oct 23, 2024

• v2.4.6

  

  Peter Audano

  committed
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• Fixed errors in VCF output.

  

  Peter Audano

  committed
  c38ff5a

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Commits on Oct 21, 2024

• v2.4.5

  

  Peter Audano

  committed
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• v2.4.4 Fixed bugs in VCF output.

  

  Peter Audano

  committed
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Commits on Oct 9, 2024

• v2.4.3

  

  Peter Audano

  committed
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• v2.4.2

  

  Peter Audano

  committed
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• v2.4.1.3 - Added "no_link_qry" configuration parameter.

  

  Peter Audano

  committed
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Commits on Sep 16, 2024

• Version 2.4.1.2

  

  Peter Audano

  committed
  2177afb

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• Variants failing PAV QC are retained and output in the VCF with a descriptive FILTER.

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  Peter Audano

  committed
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Commits on Sep 13, 2024

• Reverting to VCFs in working directory (future versions may write to a vcf directory).

  

  Peter Audano

  committed
  8cf0c48

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• Integrating VCF changes.

  

  Peter Audano

  committed
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Commits on Sep 10, 2024

• Merge branch 'main' into 202404

  

  Peter Audano

  committed
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• SV-Pop module version.

  

  Peter Audano

  committed
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• v2.4.1.1

  

  Peter Audano

  committed
  c96f4b5

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• Fixed dependencies in containers and default VCF rule.

  

  Peter Audano

  committed
  cad0f58

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Commits on Jul 22, 2024

• Version 2.4.1

  

  Peter Audano

  committed
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Commits on Jul 18, 2024

• Updated CHANGES.md and profile resources.

  

  Peter Audano

  committed
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Commits on Jun 20, 2024

• SV-Pop updates.

  

  Peter Audano

  committed
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Commits on May 1, 2024

• Adjusted latency wait.

  

  Peter Audano

  committed
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Commits on Apr 23, 2024

• Avoid copying contig FASTA to temp (symlink if possible).

  

  Peter Audano

  committed
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• Updated SV-Pop dep (fix regex warnings for Python 3.12)

  

  Peter Audano

  committed
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Commits on Apr 22, 2024

• Implemented inversion core-only filtering.

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  Peter Audano

  committed
  1f7b9c9

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• Do not reindex input FASTAs that are already indexed.

  

  Peter Audano

  committed
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Commits on Apr 18, 2024

• Minor fixes for hap merging and figures.

  

  Peter Audano

  committed
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Commits on Mar 24, 2024

• Update svpop submodule.

  

  Peter Audano

  committed
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Commits on Mar 23, 2024

• SV-Pop track updates.

  

  Peter Audano

  committed
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Commits on Mar 11, 2024

• Updated build.

  

  Peter Audano

  committed
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Commits on Feb 23, 2024

• Updated container build.

  

  Peter Audano

  committed
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• Updated through BED merging (VCF needs some updates and testing).

  

  Peter Audano

  committed
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Commits on Feb 16, 2024

• Support for multiple haplotypes and call filtering implemented through haplotype merging.

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  Peter Audano

  committed
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Commits on Feb 9, 2024

• Pulled minor change from SV-Pop.

  

  Peter Audano

  committed
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Commits on Feb 8, 2024

• Simplifying alignment tables.

  

  Peter Audano

  committed
  3f7ea48

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• Adjusted rule imports to eliminate IDE warnings.

  

  Peter Audano

  committed
  4f6e280

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Commits on Feb 7, 2024

• Assembly configuration allows an arbitrary number of named haplotypes.

  

  Peter Audano

  committed
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Commits on Jan 30, 2024

• Added pavlib.align.strip_cigar()

  

  Peter Audano

  committed
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