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Commits on Mar 26, 2013

• The indel stats (IS) annotation splitted into two: IDV and IMF

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Commits on Mar 15, 2013

• mpileup: New HWE, QBD, RPS annotations. Modified VDB (beware: this version of VDB may be broken). Fix in indel calling: Ignore insertions with N's. Output contigs in the VCF header. New sam_header2…

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Commits on Mar 12, 2013

• backup commit

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Commits on Mar 7, 2013

• backup commit

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Commits on Aug 2, 2012

• Use int64_t to prevent count overflow in view -c; on behalf of Joshua Randall: Set y2range in quals2.png plot

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Commits on Jul 3, 2012

• Bug fixes

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Commits on Jul 2, 2012

• Alternative model for multiallelic and rare-variant calling. Proof-of-principle implementation.

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Commits on Jun 27, 2012

• New -p switch for increased sensititivy of indel-calling. Here -m and -F are used per-sample which enables to detect rare indels in low-coverage bams. Experimental.

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Commits on Feb 16, 2012

• bugfix: wrong SP; missing DV in the VCF header

  

  Heng Li

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Commits on Feb 8, 2012

• changes from git

  

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Commits on Aug 17, 2011

• * bugfix in index: large memory when a read pos is 1

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Commits on Jul 7, 2011

• Release samtools-0.1.17

  

  Heng Li

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Commits on Feb 25, 2011

• * change the order of PL/GL according to the latest VCF spec

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Commits on Feb 2, 2011

• * fixed an out-of-boundary bug

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Commits on Dec 15, 2010

• * samtools-0.1.12-12 (r889)

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Commits on Dec 8, 2010

• * samtools-0.1.12-2 (r877)

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Commits on Nov 19, 2010

• * samtools-0.1.10-4 (r840)

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Commits on Nov 18, 2010

• * samtools-0.1.10-4 (r834)

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• fixed a bug in printing MNPs

  

  Heng Li

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• * samtools-0.1.10 (r831)

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Commits on Nov 15, 2010

• * samtools-0.1.9-16 (r822)

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Commits on Nov 10, 2010

• * samtools-0.1.9-8 (r809)

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Commits on Nov 9, 2010

• * samtools-0.1.9-6 (r803)

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• * samtools-0.1.9-5 (r802)

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• * samtools-0.1.9-4 (r801)

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Commits on Nov 8, 2010

• fixed a silly bug in the indel caller

  

  Heng Li

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• * samtools-0.1.9-2 (r797)

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• indel calling is apparently working, but more information needs to be collected

  

  Heng Li

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  917ed8c

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• fixed a few bugs in the indel caller. Probably there are more.

  

  Heng Li

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  53afc90

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• prepare for the indel caller. It is not ready yet.

  

  Heng Li

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Commits on Nov 5, 2010

• Revert to r790. The recent changes are not good...

  

  Heng Li

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• * this revision is UNSTABLE

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• for backup. no effective changes

  

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Commits on Oct 29, 2010

• * samtools-0.1.9-1 (r786)

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• Optionally output "DP", the individual read depth

  

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