Commit fb90d825 authored by bow's avatar bow
Browse files

Ensure TopHat keeps index contig order when aligning

parent 6ffdacf9
......@@ -361,11 +361,11 @@ class Mapping(val root: Configurable) extends QScript with SummaryQScript with S
tophat.R1 = tophat.R1 :+ R1
if (R2 != null && R2.getPath != "") tophat.R2 = tophat.R2 :+ R2
tophat.output_dir = new File(outputDir, "tophat_out")
// always output BAM
tophat.no_convert_bam = false
tophat.deps = deps
// always output BAM
tophat.no_convert_bam = false
// and always keep input ordering
tophat.keep_fasta_order = true
add(tophat)
val sortSam = new SortSam(this)
......
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