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Set conv.em to 1e-4 as documented

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Sam Nicholls 2026-05-19 09:29:48 +01:00
parent 0bd6f118b5
commit 051e60792c
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1 changed files with 4 additions and 1 deletions
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bin/workflow_glue_r/R/bambu.R
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@ -277,7 +277,10 @@ bambu_build_args <- function(args, reads, annotation_obj, discovery, quant) {
if (quant) {
# Chunked quant re-estimates degradation bias per chunk, which changes
# the EM inputs and breaks equivalence with unchunked bambu quant.
bambu_args$opt.em <- list(degradationBias = FALSE)
# Use bambu's documented EM convergence threshold here. The looser
# implemented default (1e-2) leaves small deterministic chunk-vs-global
# quant discrepancies in the split workflow.
bambu_args$opt.em <- list(degradationBias = FALSE, conv = 1e-4)
}
bambu_args