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Commits on Sep 18, 2022

• Add INFO/FIXREF annotation, add a new -m swap mode

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Commits on Feb 14, 2022

• New -m flip-all mode and support for arbitrary ids

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Commits on Jun 23, 2021

• Summer 2021 release copyright updates.

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  whitwham

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Commits on May 28, 2020

• Two minor documentation updates

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Commits on Feb 20, 2020

• Use #include <assert.h> in source files that use assert()

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Commits on Sep 25, 2019

• Merge pull request samtools#1083 from daviesrob/bigness

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  pd3

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Commits on Sep 20, 2019

• Fix minor bug

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• Check that a filename has been provided [minor]

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  jmarshall

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Commits on Sep 9, 2019

• Prepare for 64-bit positions

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  daviesrob

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Commits on Aug 13, 2018

• Add new -m ref-alt mode to +fixref

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Commits on Jun 30, 2018

• Fix serious bug in fixref .. -m top and add a test

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Commits on May 23, 2018

• Clean error reporting code and warn if incorrect parameters given. Resolves samtools#801

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Commits on May 25, 2017

• Allow multiallelic sites in the -i, --use-id reference.

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Commits on Apr 5, 2017

• Tidy upsfor C99 / _XOPEN_SOURCE=700 compliance.

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  jkbonfield

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Commits on Mar 14, 2017

• Fix travis failures with CFLAGS="-std=gnu99 -O0"

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• Add new -i, --use-id option to +fixref for swapping ALT/REF by ID

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Commits on Jan 23, 2017

• Minor: fix usage page text

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Commits on Aug 3, 2016

• plugin: new fixref plugin to convert from Illumina TOP to fwd strand (samtools#447)

  mcshane

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