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              grep rough audit - static analysis tool
                  v2.8 written by @Wireghoul
=================================[justanotherhacker.com]===
r-bioc-dada2-1.18.0+dfsg/NEWS-5-
r-bioc-dada2-1.18.0+dfsg/NEWS:6:    o The `dada-class$clustering` data.frame includes a new column `$birth_from` which encodes the cluster (ASV) from which the associated cluster (ASV) was divided (or "born").
r-bioc-dada2-1.18.0+dfsg/NEWS-7-
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r-bioc-dada2-1.18.0+dfsg/NEWS-13-
r-bioc-dada2-1.18.0+dfsg/NEWS:14:    o A rare error in how the `dada-class$clustering$birth_pval` was calculated has been fixed.
r-bioc-dada2-1.18.0+dfsg/NEWS-15-
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r-bioc-dada2-1.18.0+dfsg/inst/doc/dada2-intro.Rmd-85-
r-bioc-dada2-1.18.0+dfsg/inst/doc/dada2-intro.Rmd:86:Dereplication is a common step in almost all modern ASV inference (or OTU picking) pipelines, but a unique feature of `derepFastq` is that it maintains a summary of the quality information for each dereplicated sequence in `$quals`.
r-bioc-dada2-1.18.0+dfsg/inst/doc/dada2-intro.Rmd-87-
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r-bioc-dada2-1.18.0+dfsg/inst/doc/dada2-intro.Rmd-109-
r-bioc-dada2-1.18.0+dfsg/inst/doc/dada2-intro.Rmd:110:The `dada(...)` algorithm inferred `r nrow(dadaF1$clustering)` sequence variants from the forward reads.
r-bioc-dada2-1.18.0+dfsg/inst/doc/dada2-intro.Rmd-111-
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r-bioc-dada2-1.18.0+dfsg/inst/doc/dada2-intro.Rmd-118-
r-bioc-dada2-1.18.0+dfsg/inst/doc/dada2-intro.Rmd:119:The `mergePairs(...)` function returns a `data.frame` corresponding to each successfully merged unique sequence. The `$forward` and `$reverse` columns record which forward and reverse sequence contributed to that merged sequence.  
r-bioc-dada2-1.18.0+dfsg/inst/doc/dada2-intro.Rmd-120-
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r-bioc-dada2-1.18.0+dfsg/vignettes/dada2-intro.Rmd-85-
r-bioc-dada2-1.18.0+dfsg/vignettes/dada2-intro.Rmd:86:Dereplication is a common step in almost all modern ASV inference (or OTU picking) pipelines, but a unique feature of `derepFastq` is that it maintains a summary of the quality information for each dereplicated sequence in `$quals`.
r-bioc-dada2-1.18.0+dfsg/vignettes/dada2-intro.Rmd-87-
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r-bioc-dada2-1.18.0+dfsg/vignettes/dada2-intro.Rmd-109-
r-bioc-dada2-1.18.0+dfsg/vignettes/dada2-intro.Rmd:110:The `dada(...)` algorithm inferred `r nrow(dadaF1$clustering)` sequence variants from the forward reads.
r-bioc-dada2-1.18.0+dfsg/vignettes/dada2-intro.Rmd-111-
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r-bioc-dada2-1.18.0+dfsg/vignettes/dada2-intro.Rmd-118-
r-bioc-dada2-1.18.0+dfsg/vignettes/dada2-intro.Rmd:119:The `mergePairs(...)` function returns a `data.frame` corresponding to each successfully merged unique sequence. The `$forward` and `$reverse` columns record which forward and reverse sequence contributed to that merged sequence.  
r-bioc-dada2-1.18.0+dfsg/vignettes/dada2-intro.Rmd-120-