Linked sequences#190
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needs qiime2/q2-types#388 |
colinvwood
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stat:blocked
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disclaimer: the |
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One outstanding decision is how we want to restructure the stats table to accommodate these changes. |
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| # combine the merged and unmerged/concatenated feature tables | ||
| if(inp.dirR !='NULL' && retain.unmerged){ |
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do we need inp.dirR guard here
| ### Remove chimeras | ||
| cat("5) Remove chimeras (method = ", chimeraMethod, ")\n", sep="") | ||
| if(chimeraMethod %in% c("pooled", "consensus")) { | ||
| if(chimeraMethod %in% c("pooled", "consensus") && ncol(seqtab) > 0) { |
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is ncol(seqtab) > 0 a necessary guard here?
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| abundance=unmerged.j$abundance, | ||
| stringsAsFactors=FALSE | ||
| ) |
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think about whether we can condense at the sample level instead of below separately. Make sure we still have enough information to create e.g. a number unmerged column in the stats table
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| # combine the merged and unmerged/concatenated feature tables | ||
| if(inp.dirR !='NULL' && retain.unmerged){ |
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this entire block will go away if we do sample level table merging
| # single space-delimited representation | ||
| if(length(unmerged.ids) > 0){ | ||
| unmerged.keep <- intersect(colnames(seqtab.nochim), unmerged.ids) | ||
| if(length(unmerged.keep) > 0){ |
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We need to make sure we ONLY replace the 'N' * 10 that we introduced and not any 'N' * 10s that may have already been present in either the forward or reverse (credit to @Oddant1 for noticing this)
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at the very least we error, but we know what the forward and reverse sequences are, so we can deduce what the artificially introduced 'N' * 10 is and remove only it
Oddant1
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Oddant1
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@colinvwood's comments came from the review. Needed to look it over with him to make sure I knew what the R was doing.
4 participants
Allow
denoise-pairedto rescue and return unmerged sequences