# HG changeset patch
# User Ilya Sytchev <isytchev@hsph.harvard.edu>
# Date 1381863949 14400
# Node ID d4e99c087688fee7b93ea4eac3e812c134886738
# Parent  64f2784d471fb70111844df6a3a11ded7344dc9c
Changes for compatibility with SPP R package version 1.11.

diff -r 64f2784d471f -r d4e99c087688 run_spp.R
--- a/run_spp.R	Thu Feb 07 23:43:43 2013 -0500
+++ b/run_spp.R	Tue Oct 15 15:05:49 2013 -0400
@@ -859,14 +859,14 @@
 	
 	# Write to narrowPeak file
 	if (!is.na(iparams$output.npeak.file)) {
-		write.narrowpeak.binding(narrow.peaks,iparams$output.npeak.file,margin=round(crosscorr$whs/2),npeaks=iparams$npeak)
+		write.narrowpeak.binding(narrow.peaks,iparams$output.npeak.file,margin=round(crosscorr$whs/2))
 		#system(paste('gzip -f ',iparams$output.npeak.file))
 	}
 	
 	# Compute and write regionPeak file
 	if (!is.na(iparams$output.rpeak.file)) {
 		region.peaks <- add.broad.peak.regions(chip.data,control.data,narrow.peaks,window.size=max(50,round(crosscorr$whs/4)),z.thr=10)
-		write.narrowpeak.binding(region.peaks,iparams$output.rpeak.file,margin=round(crosscorr$whs/2),npeaks=iparams$npeak)
+		write.narrowpeak.binding(region.peaks,iparams$output.rpeak.file,margin=round(crosscorr$whs/2))
 		#system(paste('gzip -f ',iparams$output.rpeak.file))
 	}