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Commits on May 13, 2021

• Replace ShortRead::nFilter calls

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  benjjneb

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Commits on May 3, 2021

• PacBioErrfun error rates at Q93 sum to exactly 1

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  benjjneb

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Commits on Apr 13, 2021

• Include 16S tax testing file in package

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  benjjneb

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Commits on Dec 7, 2020

• Added code to process new RDP trainset 18 into DADA2 format

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  benjjneb

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Commits on Nov 1, 2020

• Fix documentation error

  mikemc

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Commits on Aug 10, 2020

• Fix derepFastq bug introduced in last commit

  benjjneb

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• Remove handle.zerolen from derepFastq arguments

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Commits on Aug 8, 2020

• Add new function for digesting Silva releases into assignTaxonomy format

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Commits on Aug 7, 2020

• Remove deprecated C_assign_taxonomy

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  benjjneb

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Commits on Jul 16, 2020

• derepFastq now handles zero-length reads in the input

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  benjjneb

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Commits on Jul 13, 2020

• Fix plotQualityProfile scaling when n < rc

  claraqin

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Commits on May 18, 2020

• removePrimers messaging improvements

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  benjjneb

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Commits on Apr 8, 2020

• assignTaxonomy gracefully handles short sequences

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Commits on Apr 7, 2020

• Removed class(x)=="YYY" calls from dada.R

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  benjjneb

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• Removed class(x) == "YYY" calls from multisample.R

  benjjneb

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• Removed class(x) == "YYY" calls from removeBimeraDenovo

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Commits on Mar 9, 2020

• Change class(a) == "x" to is(a, "x")

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Commits on Mar 7, 2020

• Fix paren error

  benjjneb

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• Fix NOTE

  benjjneb

  committed
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• Merge pull request benjjneb#971 from ycl6/master

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  benjjneb

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• Fixing NOTEs

  benjjneb

  committed
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Commits on Mar 6, 2020

• Better integer vector checking in getUniques

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  benjjneb

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• Fix double "y" scale warning for plotQualityProfile()

  ycl6

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Commits on Feb 3, 2020

• nchar instead of length to correctly check string length

  wbazant

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• More text in mergeSequenceTables error messages

  wbazant

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Commits on Jan 31, 2020

• mergeSequenceTables says what's wrong when stopping

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Commits on Jan 27, 2020

• Fix read length plotting in aggregate mode

  fanli-gcb

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Commits on Nov 16, 2019

• Fix for regex in getSRR

  benjjneb

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Commits on Oct 23, 2019

• Directories can now be provided in place of lists of fastq file paths to core dada2 functions

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  benjjneb

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Commits on Oct 22, 2019

• Added parseFastqDirectory function

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  benjjneb

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• Added DETECT_SINGLETONS dadaOpt

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Commits on Oct 21, 2019

• Indels can now be allowed when using removePrimers

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  benjjneb

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Commits on Oct 20, 2019

• Better error messaging when error-estimation fails

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Commits on Oct 17, 2019

• Added deletion of PDict and garbage collection to assignSpecies

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  benjjneb

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Commits on Oct 16, 2019

• Add tryRC option to mergeSequenceTables

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  benjjneb

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