From af9ef485cdc814541da57f8ad43899bb0d7e44c6 Mon Sep 17 00:00:00 2001 From: sol Date: Wed, 27 May 2015 09:10:48 -0400 Subject: [PATCH] this corrects a bug in the 'compare' command when the results from the 'assemble' step are located in different directories. --- IsoSCM/src/executable/IsoSCM.java | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/IsoSCM/src/executable/IsoSCM.java b/IsoSCM/src/executable/IsoSCM.java index e9f1299..8b37c9c 100644 --- a/IsoSCM/src/executable/IsoSCM.java +++ b/IsoSCM/src/executable/IsoSCM.java @@ -595,7 +595,7 @@ else if(jc.getParsedCommand().equals("compare")){ Strandedness s1=Strandedness.valueOf(assemblyConfiguration1.strandedness); Strandedness s2=Strandedness.valueOf(assemblyConfiguration2.strandedness); File spliced_exon_gtf1 = FileUtils.getFile(assemblyConfiguration1.dir,"tmp",assemblyConfiguration1.base+".exon"+(s1==Strandedness.unstranded?".trimmed":"")+".gtf"); - File spliced_exon_gtf2 = FileUtils.getFile(assemblyConfiguration1.dir,"tmp",assemblyConfiguration2.base+".exon"+(s2==Strandedness.unstranded?".trimmed":"")+".gtf"); + File spliced_exon_gtf2 = FileUtils.getFile(assemblyConfiguration2.dir,"tmp",assemblyConfiguration2.base+".exon"+(s2==Strandedness.unstranded?".trimmed":"")+".gtf"); File table = FileUtils.getFile(compare.dir,Util.sprintf("%s.txt",compare.base)); File gtf = FileUtils.getFile(compare.dir,Util.sprintf("%s.gtf",compare.base));