Commit 79f7f513 authored by Jakob Wirbel's avatar Jakob Wirbel

Add output of make.names(-1) to list of possible names of unclassified reads.

parent de25c122
Pipeline #3109 passed with stage
in 5 minutes and 59 seconds
......@@ -72,7 +72,7 @@ filter.feat <- function(feat, filter.method=abundance, cutoff=0.001, recomp.prop
### postprocessing and output generation
if (rm.unmapped) {
# remove 'unmapped' feature
unm.idx <- rownames(feat) == 'UNMAPPED' | rownames(feat) == 'unmapped' | rownames(feat) == '-1' | rownames(feat) == 'UNCLASSIFIED' | rownames(feat) == 'unclassified' | rownames(feat) == 'UNASSIGNED' | rownames(feat) == 'unassigned'
unm.idx <- rownames(feat) == 'UNMAPPED' | rownames(feat) == 'unmapped' | rownames(feat) == '-1' | rownames(feat) == 'X.1' | rownames(feat) == 'UNCLASSIFIED' | rownames(feat) == 'unclassified' | rownames(feat) == 'UNASSIGNED' | rownames(feat) == 'unassigned'
if (any(unm.idx)) {
feat <- feat[!unm.idx,]
cat('Removed ', sum(unm.idx), ' features corresponding to UNMAPPED reads',
......
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