added --max-ppsize for xcor

chipseq.py

@@ -148,6 +148,7 @@ def get_default_param_dict(): # this is not ordered
             "subsample_xcor"    : { "_order_" : 1, "_default_" : "15M", "_help_" : "Number of reads to be subsampled for cross corr. analysis only." },
             "speak_xcor"        : { "_order_" : 2, "_default_" : -1, "_help_" : "Set user-defined cross-corr. peak strandshift (-speak= in run_spp.R). Use -1 to disable." },
             "extra_param_xcor"  : { "_order_" : 3, "_default_" : "", "_help_" : "Set extra parameters for run_spp.R" },
+            "max_ppsize_xcor"    : { "_order_" : 4, "_default_" : "", "_help_" : "R stack size (R parameter --max-ppsize=; between 5000 and 5000000) for cross-corr. analysis."  },
         },
 
         "callpeak" : { "_order_" : 4, "_group_desc_" : "Peak-calling settings. spp and macs2 are stable for calling peaks and IDR analysis on called peaks. peakseq and gem are currently in BETA test.",

modules/callpeak_macs2_chipseq.bds

@@ -95,7 +95,7 @@ string[] macs2_chipseq_npeak_and_signal( string tag, string ctl_tag, string frag
 		sys macs2 callpeak -t $tag $ctl -f BED -n $peak_o_dir/$prefix_basename -g $gensz -p $pval_thresh_macs2 --nomodel --shift $shift_macs2 $extsize_param --keep-dup $keep_dup_macs2 -B --SPMR $extra_param_macs2
 
 		//# Sort by Col8 in descending order and replace long peak names in Column 4 with Peak_<peakRank>
-		sys sort -k 8gr,8gr "$prefix"_peaks.narrowPeak | awk 'BEGIN{OFS="\t"}{$4="Peak_"NR ; print $0}' > $npeakfile.tmp
+		sys sort -k 8gr,8gr "$prefix"_peaks.narrowPeak | awk 'BEGIN{OFS="\t"}{$4="Peak_"NR; if ($2<0) $2=0; if ($3<0) $3=0; print $0}' > $npeakfile.tmp
 		sys head -n $cap_num_peak_macs2 $npeakfile.tmp | gzip -nc > $npeakfile
 		sys rm -f $npeakfile.tmp
 

modules/postalign_xcor.bds

@@ -8,6 +8,7 @@ include "module_template.bds"
 help == postalign bed/tagalign settings
 fraglen0	 := false 	help (LEGACY PARAM) Set predefined fragment length as zero for cross corr. analysis (add -speak=0 to run_spp.R).
 speak_xcor 	 := -1		help Set user-defined cross-corr. peak strandshift (-speak= in run_spp.R). Use -1 to disable (default: -1).
+max_ppsize_xcor	 := ""		help R stack size (R parameter --max-ppsize=; between 5000 and 5000000) for cross corr. analysis.
 extra_param_xcor := ""		help Set extra parameters for run_spp.R (cross-corr. analysis only).
 mem_xcor	 := "15G"	help Max. memory for cross-corr. analysis (default: 15G).
 
@@ -22,6 +23,7 @@ void init_postalign_xcor() {
 	speak_xcor	= get_conf_val_int( speak_xcor,		["speak_xcor"] )
 	extra_param_xcor= get_conf_val( extra_param_xcor,	["extra_param_xcor"] )
 	mem_xcor	= get_conf_val( mem_xcor,		["mem_xcor"] )
+	max_ppsize_xcor = get_conf_val( max_ppsize_xcor, 	["max_ppsize_xcor"] )
 
 	// backward compatibility
 	if ( speak_xcor == -1 && fraglen0 ) speak_xcor = 0
@@ -31,6 +33,7 @@ void init_postalign_xcor() {
 	print( "User-defined cross-corr. peak strandshift\t: $speak_xcor\n")
 	print( "Extra parameters for cross-corr. analysis\t: $extra_param_xcor\n")
 	print( "Max. memory for cross-corr. analysis\t\t: $mem_xcor\n")
+	print( "Stack size for cross-corr. analysis\t\t:$max_ppsize_xcor\n")
 }
 
 string subsample_tag_PE_for_xcor( string tag, int nlines, bool non_mito, string o_dir, string group ) {
@@ -86,6 +89,7 @@ string[] xcor( string tag, string o_dir, string group, int nth_xcor ) {
 	xcor_score 	:= "$prefix.cc.qc"
 	xcor_plot 	:= "$prefix.cc.plot.pdf"	
         param_speak     := speak_xcor > -1 ? "-speak=$speak_xcor" : ""
+        extra_param 	:= max_ppsize_xcor ? "--max-ppsize=$max_ppsize_xcor " : ""
 
 	in 	:= [ tag ]
 	out 	:= [ xcor_score, xcor_plot ]
@@ -106,7 +110,7 @@ string[] xcor( string tag, string o_dir, string group, int nth_xcor ) {
 
 		//# CCSCORE FILE format
 		//# Filename <tab> numReads <tab> estFragLen <tab> correstFragLen <tab> PhantomPeak <tab> corrphantomPeak <tab> argmincorr <tab> mincorr <tab> phantomPeakCoef <tab> relPhantomPeakCoef <tab> QualityTag
-		sys Rscript ${RUN_SPP} -rf \
+		sys Rscript $extra_param ${RUN_SPP} -rf \
 			-c=$tag -p=$nth_xcor \
 			-filtchr=chrM -savp=$xcor_plot -out=$xcor_score $param_speak $extra_param_xcor
 		sys sed -r 's/,[^\t]+//g' $xcor_score > $xcor_score.tmp