changeset 0:fa0693cf076b draft

Uploaded
author nanettec
date Fri, 18 Mar 2016 05:51:39 -0400
parents
children 7fe16841fe35
files qtlmap_15/._.DS_Store qtlmap_15/._readme.txt qtlmap_15/qtlmap7_15nodes.py qtlmap_15/qtlmap7_15nodes.xml qtlmap_15/readme.txt qtlmap_15/test-data/._.DS_Store qtlmap_15/test-data/input/._.DS_Store qtlmap_15/test-data/input/._parameters.txt qtlmap_15/test-data/input/._qtlcart1.inp qtlmap_15/test-data/input/._qtlcart10.inp qtlmap_15/test-data/input/._qtlcart11.inp qtlmap_15/test-data/input/._qtlcart12.inp qtlmap_15/test-data/input/._qtlcart13.inp qtlmap_15/test-data/input/._qtlcart14.inp qtlmap_15/test-data/input/._qtlcart15.inp qtlmap_15/test-data/input/._qtlcart2.inp qtlmap_15/test-data/input/._qtlcart3.inp qtlmap_15/test-data/input/._qtlcart4.inp qtlmap_15/test-data/input/._qtlcart5.inp qtlmap_15/test-data/input/._qtlcart6.inp qtlmap_15/test-data/input/._qtlcart7.inp qtlmap_15/test-data/input/._qtlcart8.inp qtlmap_15/test-data/input/._qtlcart9.inp qtlmap_15/test-data/input/._qtlcart_original.map.txt qtlmap_15/test-data/input/parameters.txt qtlmap_15/test-data/input/qtlcart1.inp qtlmap_15/test-data/input/qtlcart10.inp qtlmap_15/test-data/input/qtlcart11.inp qtlmap_15/test-data/input/qtlcart12.inp qtlmap_15/test-data/input/qtlcart13.inp qtlmap_15/test-data/input/qtlcart14.inp qtlmap_15/test-data/input/qtlcart15.inp qtlmap_15/test-data/input/qtlcart2.inp qtlmap_15/test-data/input/qtlcart3.inp qtlmap_15/test-data/input/qtlcart4.inp qtlmap_15/test-data/input/qtlcart5.inp qtlmap_15/test-data/input/qtlcart6.inp qtlmap_15/test-data/input/qtlcart7.inp qtlmap_15/test-data/input/qtlcart8.inp qtlmap_15/test-data/input/qtlcart9.inp qtlmap_15/test-data/input/qtlcart_original.map.txt qtlmap_15/test-data/output/._qtl_out_1.txt qtlmap_15/test-data/output/._qtl_out_10.txt qtlmap_15/test-data/output/._qtl_out_11.txt qtlmap_15/test-data/output/._qtl_out_12.txt qtlmap_15/test-data/output/._qtl_out_13.txt qtlmap_15/test-data/output/._qtl_out_14.txt qtlmap_15/test-data/output/._qtl_out_15.txt qtlmap_15/test-data/output/._qtl_out_2.txt qtlmap_15/test-data/output/._qtl_out_3.txt qtlmap_15/test-data/output/._qtl_out_4.txt qtlmap_15/test-data/output/._qtl_out_5.txt qtlmap_15/test-data/output/._qtl_out_6.txt qtlmap_15/test-data/output/._qtl_out_7.txt qtlmap_15/test-data/output/._qtl_out_8.txt qtlmap_15/test-data/output/._qtl_out_9.txt qtlmap_15/test-data/output/qtl_out_1.txt qtlmap_15/test-data/output/qtl_out_10.txt qtlmap_15/test-data/output/qtl_out_11.txt qtlmap_15/test-data/output/qtl_out_12.txt qtlmap_15/test-data/output/qtl_out_13.txt qtlmap_15/test-data/output/qtl_out_14.txt qtlmap_15/test-data/output/qtl_out_15.txt qtlmap_15/test-data/output/qtl_out_2.txt qtlmap_15/test-data/output/qtl_out_3.txt qtlmap_15/test-data/output/qtl_out_4.txt qtlmap_15/test-data/output/qtl_out_5.txt qtlmap_15/test-data/output/qtl_out_6.txt qtlmap_15/test-data/output/qtl_out_7.txt qtlmap_15/test-data/output/qtl_out_8.txt qtlmap_15/test-data/output/qtl_out_9.txt
diffstat 71 files changed, 11271 insertions(+), 0 deletions(-) [+]
line wrap: on
line diff
Binary file qtlmap_15/._.DS_Store has changed
Binary file qtlmap_15/._readme.txt has changed
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/qtlmap_15/qtlmap7_15nodes.py	Fri Mar 18 05:51:39 2016 -0400
@@ -0,0 +1,469 @@
+"""
+@summary: MAP and PARSE
+@version 7
+
+"""
+# MAPPER  --> save only QTL output
+
+# Input: qtlcart.inp
+#        qtlcart.map
+#      	 parameters.txt
+
+# Output: QTLs_total.txt
+
+import optparse, sys
+import tempfile
+import re
+
+def stop_err( msg ):
+	sys.stderr.write( "%s\n" % msg )
+	sys.exit()
+    
+def __main__():
+	parser = optparse.OptionParser()
+	parser.add_option("-i", "--input1", default=None, dest="input1", 
+			  help="qtlcart.inp file")
+	parser.add_option("-j", "--input2", default=None, dest="input2", 
+			  help="qtlcart.map file")
+	parser.add_option("-k", "--input3", default=None, dest="input3", 
+			  help="parameters.txt file")
+    
+	parser.add_option("-o", "--output1", default=None, dest="output1", 
+			  help="QTLs_total.txt file")
+	(options, args) = parser.parse_args()
+	
+	try:
+	    open(options.input1, "r").close()
+	except TypeError, e:
+	    stop_err("You need to supply the qtlcart.inp file:\n" + str(e))
+	except IOError, e:
+	    stop_err("Can not open the qtlcart.inp file:\n" + str(e))
+    
+	try:
+	    open(options.input2, "r").close()
+	except TypeError, e:
+	    stop_err("You need to supply the qtlcart.map file:\n" + str(e))
+	except IOError, e:
+	    stop_err("Can not open the qtlcart.map file:\n" + str(e))
+
+	try:
+	    open(options.input3, "r").close()
+	except TypeError, e:
+	    stop_err("You need to supply the parameters.txt file:\n" + str(e))
+	except IOError, e:
+	    stop_err("Can not open the parameters.txt file:\n" + str(e))
+	
+	######################################################################
+	# submit.py
+	######################################################################
+	
+	import subprocess
+	import os
+	
+	# Create temp direcotry
+	tempdir = tempfile.mkdtemp()
+	#print tempdir
+	
+	s = "cp %s %s/parameters.txt" %(options.input3, tempdir)
+	subprocess.call(s, shell=True)
+	paramters_file = open(tempdir+"/parameters.txt", "r")
+	parvalues = []
+	for line in paramters_file:
+		l = line.strip().split("\t")
+		if l[0] == "SRmodel":
+			SRmodel = l[1]
+		if l[0] == "Zmodel":
+			Zmodel = l[1]
+		if l[0] == "threshold":
+			threshold = l[1]
+		if l[0] == "walking_speed":
+			walking_speed = l[1]
+		if l[0] == "window_size":
+			window_size = l[1]
+		if l[0] == "minimum_cM_between_QTL":
+			minimum_cM_between_QTL = l[1]
+	paramters_file.close()		
+
+	# copy INPUT file to the temp directory
+	s = "cp %s %s/qtlcart.inp" %(options.input1, tempdir)
+	subprocess.call(s, shell=True)
+	s = "cp %s %s/qtlcart.map" %(options.input2, tempdir)
+	subprocess.call(s, shell=True)
+	
+        f=open(tempdir+"/qtlcart.inp", "r")
+	ln=f.readlines()
+        f.close()
+        
+        if ln[0] == "NA":
+		f1=open(tempdir+"/QTLs_total_parsed_LOD.txt", "w")
+		f1.write("")
+		f1.close()
+		os.system("mv %s/QTLs_total_parsed_LOD.txt %s" %(tempdir,options.output1))
+		#os.system("mv %s/qtlcart.rc %s" %(tempdir,options.output2))
+        else:
+		instruction = "/cluster1/bin/Rcross -i %s/qtlcart.inp -o %s/qtlcart.cro -A -V" %(tempdir, tempdir)
+		os.system(instruction)
+		
+		instruction = "/cluster1/bin/SRmapqtl -i %s/qtlcart.cro -e %s/SRqtlcart.log -o %s/qtlcart.sr -m %s/qtlcart.map -M %s -t 9999999999 -A -V" %(tempdir, tempdir, tempdir, tempdir, str(SRmodel))
+		os.system(instruction)        
+		
+		instruction = "/cluster1/bin/Zmapqtl -i %s/qtlcart.cro -o %s/qtlcart.z -m %s/qtlcart.map -S %s/qtlcart.sr -M %s -d %s -w %s -t 9999999999 -A -V" %(tempdir, tempdir, tempdir, tempdir, str(Zmodel), str(walking_speed), str(window_size))
+		os.system(instruction)
+		
+		#instruction = "/cluster1/bin/Eqtl -m %s/qtlcart.map -z %s/qtlcart.z -e %s/Eqtlcart.log -o %s/qtlcart.eqt -S %s -A -V" %(tempdir, tempdir, tempdir, tempdir, str(threshold))
+		#os.system(instruction)
+
+		#####################
+		# parse_eqt_file.py
+		#####################
+		
+		infile = open(tempdir+"/qtlcart.z","r")
+		outfile = open(tempdir+"/QTLs_total_parsed.txt","w")
+		
+		outfile.write("trait_name\ttrait_number\teQTL_number\tchr\tpeak_marker\tpeak_position\tpeak_LR\tpeak_LOD\tR2\tTR2\tS\tadditive\tdominance\n")
+		
+		for line in infile:
+			l = line.strip().split()
+			if line.startswith("-trait"):
+				trait_num = l[1]
+				trait_name = l[-1][1:-1]
+				prev_lr_max = float(threshold)
+				decrease = 0
+				#print trait_num
+				#print trait_name
+				#print "---"
+				eqtl_keep = ""
+				eqtl_list = []
+				prev_chromosome = 0
+			try:
+				ans = l[0]
+			except:
+				ans = ""
+			if ans != "":
+				if l[0].startswith(('0', '1', '2', '3', '4', '5', '6', '7', '8', '9')):
+					chromosome = l[0]
+					chr_change = 0
+					if chromosome != prev_chromosome:
+						#print "NEW CHROMOSOME !!!!"
+						chr_change = 1
+						prev_chromosome = l[0]
+					if chr_change == 1 and eqtl_keep != "":
+						eqtl_list.append(eqtl_keep)
+						#print "APPEND PREV"
+						eqtl_keep = ""
+						decrease = 0
+						prev_lr_max = float(threshold)
+						
+					if float(l[3]) > float(threshold):
+						#print line
+						if float(l[3]) > prev_lr_max:
+							eqtl_keep = line.strip()
+							prev_lr_max = float(l[3])
+							decrease = 0
+							#print "KEEP"
+						else:
+							decrease += 1
+							if decrease == 1:
+								eqtl_list.append(eqtl_keep)
+								#print "APPEND PREV"
+								eqtl_keep = ""
+								prev_lr_max = float(l[3])
+							else:
+								prev_lr_max = float(l[3])
+					else:
+						decrease += 1
+						if decrease == 1 and eqtl_keep != "":
+							eqtl_list.append(eqtl_keep)
+							#print "APPEND PREV"
+							eqtl_keep = ""
+						decrease = 0
+						prev_lr_max = float(threshold)
+					#print decrease
+					
+			if line.startswith("-e"):
+				if eqtl_keep != "":
+					eqtl_list.append(eqtl_keep)
+					#print "APPEND PREV"
+					eqtl_keep = ""
+					decrease = 0
+					prev_lr_max = float(threshold)	
+				#print "########"
+				count = 0
+				for eqtl in eqtl_list:
+					e = eqtl.split()
+					#print e
+					count += 1
+					index = str(count)
+					chrom = str(e[0])
+					marker = str(e[1])
+					pos = str(e[2])
+					lr = str(e[3])
+					lod = str(0.217*float(e[3]))
+					additive = str(e[6])
+					dominance = str(e[8])
+					r2 = str(e[4])
+					tr2 = str(e[5])
+					s = str(e[7])
+					outfile.write(trait_name+"\t"+trait_num+"\t"+index+"\t"+chrom+"\t"+marker+"\t"+pos+"\t"+lr+"\t"+lod+"\t"+r2+"\t"+tr2+"\t"+s+"\t"+additive+"\t"+dominance+"\n")
+				#print len(eqtl_list)
+		infile.close()
+		outfile.close()
+		
+		#########################
+		# calc_LOD_intervals.py
+		#########################
+		outfile = open(tempdir+"/QTLs_total_parsed_LOD.txt","w")
+		eqtfile = open(tempdir+"/QTLs_total_parsed.txt","r")
+		
+		eQTL_dict = {}
+		eQTL_id = 0
+		for line in eqtfile:
+		    l = line.strip().split("\t")
+		    if (l[0] != "trait_name"):
+			eQTL_id += 1
+			eQTL_dict[eQTL_id] = [l[0],l[3],l[4],l[5],l[7]]
+		eqtfile.close()
+		#print eQTL_dict
+		
+		for i in range(1,len(eQTL_dict)+1):
+		    ans = []
+		    
+		    eqt_eQTL = eQTL_dict[i][0]
+		    eqt_c = eQTL_dict[i][1]
+		    eqt_m = eQTL_dict[i][2]
+		    eqt_pos = eQTL_dict[i][3]
+		    eqt_lod = eQTL_dict[i][4]
+		    
+		    z_eQTL = ""
+		    z_id = 0
+		    z_dict = {}
+		    peak_id = 0
+		    
+		    zfile = open(tempdir+"/qtlcart.z","r")
+		    for line in zfile:
+			if line.startswith("-trait"):
+			    l = line.strip().split("[")
+			    z_eQTL = l[1][:-1]
+			    #print "z_eQTL = "+z_eQTL
+			    #print "eqt_eQTL = "+eqt_eQTL
+			if (eqt_eQTL == z_eQTL) and (line.strip().startswith(eqt_c)):
+			    if str(line.strip().split()[0]) == str(eqt_c):
+				l = line.strip().split()
+				z_id += 1
+				z_c = l[0]
+				z_m = l[1]
+				z_pos = l[2]
+				z_lod = float(l[3])*0.217
+				z_dict[z_id] = [z_c, z_m, z_pos, z_lod]
+				if float(eqt_pos) == float(z_pos):
+				    peak_id = z_id
+		    zfile.close()
+		    
+		    lod1 = float(eqt_lod)-1
+		    lod2 = float(eqt_lod)-2
+		    
+		    # lod1_L calculation
+		    #print "==== lod1_L"
+		    subtract = 1
+		    left_id = peak_id-1
+		    if left_id != 0:
+			#print "peak_id-subtract "+ str(peak_id-subtract)
+			#print "left_id "+str(left_id)
+			while (z_dict[peak_id-subtract][3] > lod1) and (left_id > 1):
+			    subtract += 1
+			    left_id = peak_id-subtract
+		
+			s1 = float(z_dict[left_id][2])  # small position
+			s2 = float(z_dict[left_id][3])  # small lod
+			l1 = float(z_dict[left_id+1][2])    # large position
+			l2 = float(z_dict[left_id+1][3])    #  large lod
+			
+			if (l2-s2) != 0:
+				lod1_L_pos = round(((lod1-s2)*(l1-s1)/(l2-s2))+s1,4)
+			else:
+				lod1_L_pos = round(((lod1-s2)*(l1-s1)/(0.00001))+s1,4)
+			lod1_L_m = z_dict[left_id][1]
+			if lod1_L_pos < 0:
+			    lod1_L_pos = z_dict[1][2]
+			    lod1_L_m = z_dict[1][1]
+			if ((lod1_L_pos >= s1) and (lod1_L_pos <= l1)):
+			    pass
+			else:
+			    lod1_L_pos = z_dict[1][2]
+			    lod1_L_m = z_dict[1][1]    
+		    else:
+			lod1_L_pos = z_dict[1][2]
+			lod1_L_m = z_dict[1][1]
+		    ans.append(lod1_L_m)
+		    ans.append(lod1_L_pos)
+		    
+		    # lod1_R calculation
+		    #print "==== lod1_R"
+		    add = 1
+		    right_id = peak_id+1
+		    if right_id <= max(z_dict.keys()):
+			while (z_dict[peak_id+add][3] > lod1) and (right_id < max(z_dict.keys())):
+			    add += 1
+			    right_id = peak_id+add
+			    
+			s1 = float(z_dict[right_id-1][2])  # small position
+			s2 = float(z_dict[right_id-1][3])  # small lod
+			l1 = float(z_dict[right_id][2])    # large position
+			l2 = float(z_dict[right_id][3])    #  large lod
+
+			if (l2-s2) != 0:
+				lod1_R_pos = round(((lod1-s2)*(l1-s1)/(l2-s2))+s1,4)
+			else:
+				lod1_R_pos = round(((lod1-s2)*(l1-s1)/(0.00001))+s1,4)
+			lod1_R_m = z_dict[right_id-1][1]
+
+			if lod1_R_pos > float(z_dict[max(z_dict.keys())][2]):
+			    lod1_pos = z_dict[1][2]
+			    #lod1_m = z_dict[2][1]
+			    #lod1_R_pos = z_dict[max(z_dict.keys())][2]
+			    lod1_R_m = z_dict[max(z_dict.keys())][1]
+			if ((lod1_R_pos >= s1) and (lod1_R_pos <= l1)):
+			    pass
+			else:
+			    lod1_R_pos = z_dict[max(z_dict.keys())][2]
+			    lod1_R_m = z_dict[max(z_dict.keys())][1]
+		    else:
+			lod1_R_pos = z_dict[max(z_dict.keys())][2]
+			lod1_R_m = z_dict[max(z_dict.keys())][1]
+
+		    ans.append(lod1_R_m)
+		    ans.append(lod1_R_pos)
+		    
+		    # lod2_L calculation
+		    #print "==== lod2_L"
+		    subtract = 1
+		    left_id = peak_id-1
+		    if left_id != 0 :
+			while (z_dict[peak_id-subtract][3] > lod2) and (left_id > 1):
+			    subtract += 1
+			    left_id = peak_id-subtract
+			
+			s1 = float(z_dict[left_id][2])  # small position
+			s2 = float(z_dict[left_id][3])  # small lod
+			l1 = float(z_dict[left_id+1][2])    # large position
+			l2 = float(z_dict[left_id+1][3])    #  large lod
+			
+			if (l2-s2) != 0:
+				lod2_L_pos = round(((lod2-s2)*(l1-s1)/(l2-s2))+s1,4)
+			else:
+				lod2_L_pos = round(((lod2-s2)*(l1-s1)/(0.00001))+s1,4)
+			
+			lod2_L_m = z_dict[left_id][1]
+			if lod2_L_pos < 0:
+			    lod2_L_pos = z_dict[1][2]
+			    lod2_L_m = z_dict[2][1]
+			if ((lod2_L_pos >= s1) and (lod2_L_pos <= l1)):
+			    pass
+			else:
+			    lod2_L_pos = z_dict[1][2]
+			    lod2_L_m = z_dict[1][1]      
+		    else:
+			lod2_L_pos = z_dict[1][2]
+			lod2_L_m = z_dict[1][1]
+		    ans.append(lod2_L_m)
+		    ans.append(lod2_L_pos)
+		    
+		    
+		    # lod2_R calculation
+		    #print "==== lod2_R"
+		    add = 1
+		    right_id = peak_id+1
+		    if right_id <= max(z_dict.keys()):
+			while (z_dict[peak_id+add][3] > lod2) and (right_id < max(z_dict.keys())):
+			    add += 1
+			    right_id = peak_id+add
+			
+			s1 = float(z_dict[right_id-1][2])  # small position
+			s2 = float(z_dict[right_id-1][3])  # small lod
+			l1 = float(z_dict[right_id][2])    # large position
+			l2 = float(z_dict[right_id][3])    #  large lod
+			
+			if (l2-s2) != 0:
+				lod2_R_pos = round(((lod2-s2)*(l1-s1)/(l2-s2))+s1,4)
+			else:
+				lod2_R_pos = round(((lod2-s2)*(l1-s1)/(0.00001))+s1,4)
+			lod2_R_m = z_dict[right_id-1][1]
+
+			if lod2_R_pos > float(z_dict[max(z_dict.keys())][2]):
+			    lod2_R_pos = z_dict[max(z_dict.keys())][2]
+			    lod2_R_m = z_dict[max(z_dict.keys())][1]
+			if ((lod2_R_pos >= s1) and (lod2_R_pos <= l1)):
+			    pass
+			else:
+			    lod2_R_pos = z_dict[max(z_dict.keys())][2]
+			    lod2_R_m = z_dict[max(z_dict.keys())][1]
+		    else:
+			lod2_R_pos = z_dict[max(z_dict.keys())][2]
+			lod2_R_m = z_dict[max(z_dict.keys())][1]
+		    ans.append(lod2_R_m)
+		    ans.append(lod2_R_pos)
+		    
+		    eQTL_dict[i].append(ans)
+		    
+		head = ["LOD1_L_m","LOD1_L_pos","LOD1_R_m","LOD1_R_pos","LOD2_L_m","LOD2_L_pos","LOD2_R_m","LOD2_R_pos"]
+		
+		i = -1
+		eqtfile = open(tempdir+"/QTLs_total_parsed.txt","r")
+		for line in eqtfile:
+		    i += 1
+		    if i == 0:
+			outfile.write(line.strip()+"\t"+"\t".join(head)+"\n")
+		    else: 
+			outfile.write(line.strip()+"\t"+"\t".join(str(x) for x in eQTL_dict[i][5])+"\n")
+		    
+		eqtfile.close()
+		outfile.close()
+		
+		#####################
+		# merge_QTLs.py
+		#####################
+		
+		infile = open(tempdir+"/QTLs_total_parsed_LOD.txt","r")
+		outfile = open(tempdir+"/QTLs_total_parsed_LOD_merged.txt","w")
+		
+		test = ""
+		for line in infile:
+		    l = line.strip().split("\t")
+		    if l[0] == "trait_name":
+			keep = l
+		    else:
+			test = l
+			if keep[0] != test[0]: # if trait names are not the same ---> write keep
+				if keep[0] != "trait_name": # no not include header, only when integrate
+					outfile.write("\t".join(keep)+"\n")
+				keep = test
+			else:
+			    if keep[3] != test[3]: # if chrs are not the same --> write keep 
+				outfile.write("\t".join(keep)+"\n")
+				keep = test
+			    else:
+				if not (((float(keep[11])<0) and (float(test[11])<0)) or ((float(keep[11])>0) and (float(test[11])>0))):  # if additive signs are not the same --> write keep 
+				    outfile.write("\t".join(keep)+"\n")
+				    keep = test
+				else:
+				    #print str((abs(float(test[5])*100-float(keep[5])*100)))
+				    if not (abs(float(test[5])*100-float(keep[5])*100)<float(minimum_cM_between_QTL)): #if minimum cM between QTLs > 20 --> write keep
+					outfile.write("\t".join(keep)+"\n")
+					keep = test
+				    else:
+					if (float(keep[7])<float(test[7])): #if LOD(keep) > LOD(test) --> new keep
+					    keep = test
+		
+		if l[0] != "trait_name":
+			outfile.write("\t".join(keep)+"\n")
+					
+		infile.close()
+		outfile.close()
+				
+						
+		os.system("mv %s/QTLs_total_parsed_LOD_merged.txt %s" %(tempdir,options.output1))
+	
+if __name__=="__main__": 
+    __main__()
+
+
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/qtlmap_15/qtlmap7_15nodes.xml	Fri Mar 18 05:51:39 2016 -0400
@@ -0,0 +1,40 @@
+<tool id="qtlmap7_15nodes" name="Run QTL Cartographer" version="7.0.0">
+	<description> and parse the results</description>
+	<command interpreter="python">
+            qtlmap7_15nodes.py --input1 $input1 --input2 $input2 --input3 $input3 --output1 $output1
+        </command>
+        <inputs>
+            <param label="Phenotype-genotype (.inp) file" name="input1" type="data" format="txt" help="A .inp file with all genotype and phenotype information"></param>
+	    <param label="QTL Cartographer map file" name="input2" type="data" format="txt" help="A .inp file with all genotype and phenotype information"></param>
+	    <param label="Parameters file" name="input3" type="data" format="txt" help="Parameters file with the values of all the parameters for QTL mapping"></param>
+        </inputs>
+	<outputs>
+                <data format="tabular" name="output1" />
+	</outputs>
+	<requirements>
+	</requirements>
+	<tests>
+          <test>
+          </test>
+	</tests>
+	<help>
+		
+**What it does**
+
+Runs QTL Cartographer for QTL/eQTL mapping. Parse the results.  
+
+**Example output file**
+
+eQTL results file, each row correspond to an eQTL (21 columns; only a part of the file is shown)::
+
+ trait_name	trait_number	eQTL_number	chr	peak_marker	peak_position	peak_LR	peak_LOD	R2	TR2	S	additive 	dominance	LOD1_L_m	LOD1_L_pos	LOD1_R_m	LOD1_R_pos	LOD2_L_m	LOD2_L_pos	LOD2_R_m	LOD2_R_pos
+ geneA		4		2		3	15		79.31		14.576	3.162992	0.1093	0.1915	5.2649	-0.0602		0		12		0.6318		15		0.8678		11		0.5984		15		0.8941
+ geneB		5		1		6	7		54.41		12.0029	2.6046293	0.0833	0.1621	5.0323	0.0516		0		6		0.4803		7		0.6296		5		0.4237		7		0.6509
+ geneC		6		1		1	12		81.5		13.2053	2.8655501	0.082	0.2517	154.622	-0.0513		0		11		0.7835		12		0.815		10		0.6549		12		0.815
+ geneC		6		2		5	6		33.92		12.4418	2.6998706	0.0881	0.2653	161.127	0.0546		0		4		0.2652		6		0.4058		2		0.1031		7		0.4629
+ geneF		11		1		9	4		11.74		14.4418	3.1338706	0.0937	0.252	72.2489	-0.0562		0		1		0.0014		4		0.1995		1		0.0001		4		0.2035
+ geneH		12		2		1	9		43.66		16.9545	3.6791265	0.092	0.3558	0.1466	0.0544		0		8		0.4159		9		0.5408		5		0.3295		9		0.5987
+ geneJ		13		1		7	11		66.41		15.6251	3.3906467	0.0965	0.2625	8.2335	-0.0558		0		9		0.5515		11		0.7408		9		0.5464		12		0.7631
+
+        </help>
+</tool>
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/qtlmap_15/readme.txt	Fri Mar 18 05:51:39 2016 -0400
@@ -0,0 +1,23 @@
+======================================================================
+qtlmap_15
+======================================================================
+### This is the second tool in the eQTL mapper pipeline: 
+split_15, qtlmap_15, save_z_15, integrate_15
+
+Link to the workflow (for import): http://chewbacca.bi.up.ac.za:8080/u/nanette/w/15-parallel
+
+QTL Cartographer is employed for eQTL mapping. The results are parsed. 
+
+This tool must be executed 15 times in parallel; every time with a different .inp input file (every time the .map and parameters.txt input files are used). Each execution will produce one .txt output file.  
+
+---------------
+Installation
+---------------
+
+The eQTL mapper pipeline is available for: 
+* command line usage
+* integration into Galaxy servers
+
+
+Requirements:  	Python 2.7
+		QTL Cartographer 1.17
\ No newline at end of file
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Binary file qtlmap_15/test-data/input/._qtlcart8.inp has changed
Binary file qtlmap_15/test-data/input/._qtlcart9.inp has changed
Binary file qtlmap_15/test-data/input/._qtlcart_original.map.txt has changed
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/qtlmap_15/test-data/input/parameters.txt	Fri Mar 18 05:51:39 2016 -0400
@@ -0,0 +1,6 @@
+SRmodel	2
+Zmodel	6
+threshold	11.5
+walking_speed	2.0
+window_size	10.0
+minimum_cM_between_QTL	20.0
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/qtlmap_15/test-data/input/qtlcart1.inp	Fri Mar 18 05:51:39 2016 -0400
@@ -0,0 +1,692 @@
+#bycross
+-SampleSize 100
+-Cross Ri1
+-traits 4
+-otraits 0
+-missingtrait  .
+-case yes
+-TranslationTable
+AA	2	A
+Aa	1	*1
+aa	0	B
+A-	12	*2
+a-	10	*3
+--	-1	-
+-start markers
+phi056                A A B B A B B A A A B A B A A A A A A A A A B A 
+B B A B - B B A B B - - A B A B A - - A B A A A A B A A A - B A B B - 
+A - B B B B A B A B A B - - A B A B A - B A A A A B A A B A B A A B A 
+B A B A A B 
+bnl5.62               A A - B A B B A B A B A B B A A A A A A A A B A 
+B A - B - A A A B A - A A B A B A B A A B A A A - B A A A B B A B B - 
+A A B B B B A B A B A A A - A B A B B A B A A - A B A A B A B B A B A 
+B A B A A B 
+umc1041               A A B B A A B A B B A B B A - A B A A A A B B A 
+A A B B - A A A B A B B B B B A - B A A B A A A - A A B - - B A B B B 
+A A B A B A A B A B A A A B A B A B A A B A - A A B A A B A B A A A A 
+B A B B A B 
+umc157a               A A B A B A B A A B B - B A A A B - B A A A A A 
+A B B B - A A A B A A A B B A A B B B A A - B A A B A B A A B A A B B 
+A A B A B A A B B A A A A B A B B A B A A A A B A A B A B A B B A B A 
+B A B B B B 
+bnlg1178              A A A A B A B A A B B - B B A A B B B A A B A A 
+A B B B B A A A B A A A B B A A B B B A A - B A B - A B - A A - A B - 
+A A B A A A A B A A A A B B A - A A B B A A A B A A B - B - B B A B A 
+B A B B B B 
+bnlg1429              A A A A B A B A A B B B B B A A B - B A A B A A 
+A B B B B A A A B A A A B B A A B A B A A - B A B B A B - - A A B B - 
+B A B A A A A B A A A A A B A - A A B A A A A B A A B A B A A B A B A 
+B A B B B B 
+bnlg1627              A A A A B B A A B B A B B A A A B B B A A B A A 
+A B - B B A A A B A A A B B A A B A B A A - B A B B A B B - - A B B - 
+A A B A A A A B A B A A A B A B A A B A A A A B A A B A A A A B A B A 
+A A B B B B 
+umc11a                A A - A B B B A B B A A B A A B B B B A A A - B 
+A B B B A B A A B B B A B B B A B A B A A B B A B - B B A B A B A B B 
+A A B B A A A B - B A A A B A B B A B A B - A B A A B B A B B - A B A 
+B A B B B B 
+bnlg439               A A A A B B A A B B A A - A A B B B B A A A B B 
+A B A B A A A A B B B A B B B B A A B A A B A B B - - B A B A B A B B 
+A B B A A A A B - B B A B B A - B B B B A A A B A - B A B B B - B - A 
+A A B B B B 
+bnlg2238              A A A - B B A A B B A B A A A B B A A A A A A B 
+A B A B A A A A B B B A A B B A A A - A A B A B B A A B A B A B - B B 
+A B B B A A A B B B B A A B A B B B B A A - A A A A A A A A A A B A A 
+A A - B B B 
+Bnlg1811_U            A A A B B A A B B B B B A A A A B A A A A A A B 
+A B A B B B A A B B A A A B B A B A A A B B B B A A B B A B A B A B B 
+A B B B A A A B B B B A A B A B B B B A A A A B - B A B B B A A B A A 
+A A B B A B 
+bnlg2086              A B A A A A A A B B B B A A B - B A A B A A A B 
+A B A B B B A A B A B A A B B B B A A B B - A B B A B B A B B B A B B 
+B B B B A A A B B B A A A B B B - B B A - A A B B A A B B B A A B A A 
+A A A B A B 
+csu61b                B B - A B A A A B B B B A B A - B B B B - B A B 
+B A A B B A A A B A B A A B B B B A - B A A - B - B B B A B B B A B B 
+A B B A A A A B B B A B A B A B - B B A - - A B A A - B B B A - B - A 
+A A B B A B 
+bnlg1057              B B A A A A B A B B B B A B A - B B A B B B B B 
+A B A B B A A A - A B A A B B B A A - A A A - B A - B B A - B B A B B 
+A B - A A A A - B A A B A B A B A B B A - B A B A A - B B B A - B - A 
+A A B B A B 
+umc1122               A B A A B A B A B B A B B B A A A B A B A B B A 
+B B A B B B A A B A B A A B B B A A B A A A B B A B B A A A B A A B A 
+A B A A A A B A B A B B A B A B A B B A A A B B A B B B B B B B B B B 
+A A B A A B 
+Bnlg615_U             A A B A B B A A B A A B A B A B A B A A A B B B 
+B A A A B A A B B B B A A B B B A A B A A B B B A B B A A - B - A B A 
+A A B A B A B B B A B B A B - B A B B A A A B A A B B B A B B B B B B 
+A A B A A B 
+umc1128               A B B A B B B B B B B A A B A B A B A B A B B A 
+A A B A B A A B B B B A A B B B A A B A A B B B A B A A A - B B A B A 
+A A B A B A B B B A B B A B A A A B B A A A B A A B B B A - B B B B B 
+B B B A A B 
+umc166b               A B B A B B B B B B A A A B A B A B A B A A B A 
+B A B A B A A B B B B A A B - B A B B A A - A B A B B A A A B - A B A 
+A A B A B B B B B B B B A B A A A B B A A A A A A A B B A B B B B B B 
+B B B A B B 
+dupssr12              A B B A B B A A A B B A A B A B A B B B A A B - 
+B B B A B A A B B B - A A A B B A B B A A B A B A B B A A A B B A B A 
+B A B A B B B B B B B B A B A B A B B A A A A A A A B B A A B B A B B 
+A B B A A B 
+phi011                A A B A - B A A A B B B A B B A A A B A A A B A 
+B A B A B B A B A B B A B A A B A A A A A B A B B A B A A B B A A B A 
+B B A B B A B A B B B A A B A B A A B A B A A A B B A B B B B A A A B 
+A B A A B B 
+bnlg1720              A A B - - B A B B B B B A B B A A A B A A A B A 
+B A B B A A B B A B - A B B A A A A B A A B B B A B B A A B B A A B A 
+B B A B B B B A A B B A B A B B A A A B B A B A B B B B A B B B A B B 
+B B B A A B 
+umc106a               A A - A A B A B B - B B A B B A A A B A A A B A 
+B A A B A A B B A A A A B B A A A A B A A B B B A B B A A B B A A B A 
+B A - A B B B - A B B - - B A B A A B B B A A B B B B B A B A B A B B 
+A B A A A B 
+umc147b               B B B A A B A A A B B B A B - A A A B A B A B A 
+B A A - A A B B A A A A A B A A B A B A A - B B A B B A A B B A A B A 
+B - A B B B B A A B B B B B A B A A B B B B A B A B B B A B A B A B B 
+A B A A A B 
+umc1111_P             - B B A B A - B A - B - A B A A A A - A A A - A 
+- - B B A A B B A B A A A B A A B A - A A - B B A - - A A A B A B A B 
+A A A A B B B A A A - A B A A B B B A B A - A B A - A A A A A - A B B 
+B B A A A A 
+bnlg2331              A B B B B A B B A A B B A B A A A A B A A A B A 
+B B B B A A B B A B A A A B A A B A A A A B B B B A A A - A B A B A B 
+A A A A B B B A A A B A B A A B B A A B A A A B A - A A A A A A A A B 
+B B B A A A 
+bnlg2123              A B B A A A A B A B - B A B A B B B B - A A B B 
+B B B A A A B B A B A A B B A - B A B A A A B B B A A B A A B B B B B 
+A A A A B B B A A B B A B A A A B A A B B A A B A A B A B A A B A B B 
+B B B B A A 
+bnl6.32               B B - A A A A A A B - B A B A B B B A - B - B B 
+B - A A A A B - A B A A B B A A B B A B A A B B B B A B A B B B B - B 
+A B A A B B B - B A B A B B A A B A B B B B A B A A - A B A A B A B A 
+A B B B A A 
+phi402893             B B A A A A B B B B A A B A B A A B B B B B B B 
+A A B A A A B A B A B A B B B A B A B A B A A - A B B A - A A B B B B 
+A B B A A A B B B A A B A A B A B B A - B B A - B B B B A B - B B B B 
+B B B A B A 
+bnlg1297              B B A A B A B B B A B A B A B A A B B B B B B A 
+B A B A B A B B B A B - B B B A B A B A B A A - A B B A A B A B B B A 
+A B - A A B B A A B A B B B B A B B B B B B A A B B B B A B B B B B B 
+B B B A B B 
+bnlg2042              B - A B B B A B B B B A B B A - B A B B B A - A 
+B A A A A B A B A A B B A B B B B A B A B A A B B B A B B B - A A B A 
+A B A A A B B A A B A - B B B A A A B B - B A - A A B A A A B B B B B 
+A B B B B A 
+umc44b                A A A A - A A A B B B A A B A B B A B A A B B A 
+A A B A A B A B - A A B A B B A B A A B B A - B B A B B B B A A A B A 
+A B A A A B B A A A A B A B A A B A B A B A A A A B A B B B A A B A B 
+A A B B B A 
+csu40                 A A - A B A A - B A B A A A A A A B B A A A B B 
+A A A - A B A B B A B B A B B A B A A B A B B B B A B A B B B A A A B 
+A B B A A B B B A B A B A B B - B B B A A A A A A B A B B B A B B A B 
+A B B A A B 
+umc135                A A A A A - A B A A B A A A A A A B B A A B B B 
+A A A - A B A B B A B B A B B A A A A B A B B B B A A A B B B B A A B 
+A B B B A B B B A - A B A A B - B B A A B A A A A B A - B - A A A - B 
+A B B A A B 
+csu54a                A A A A A A B B B A A A A A A - A B B A A B B B 
+A A A A A B A B B B - A A B B A - A B B B B A B B B A A B B B B A - B 
+A B B B A B B B A - A A A A B - B B A A B A A A A B B A A A A B B B B 
+B A B A A B 
+umc55a                A A A A A A B B B A A A A A B - A B B A A A B B 
+A A A A - B A A B B B - A - B A B A B B B B A B A B A A B B A B A - A 
+A B B B A B A B A A A A A A B B A B A A B A A A B B B A A A B B B B A 
+B A B A A B 
+umc14b                A B A A A A B B B A A B A B B - A B B A A A B B 
+A A A A - B A A B B B A A B B A A A B B B - A B A B A A B A B B A A B 
+A A B B A B A B A A A A A A B B A B A A A A A A B B B A A A B B B B A 
+B A B A A B 
+csu154a               A A A A B B B B B A A B A B B A A B B A - B B B 
+A A A A A B A A B B B A A B B A B B A B A - A A A A A A A A B B A - A 
+A B B B A B A B A A A A A A - B A A A A A A A A B A A A A A A A B A A 
+B B B A A B 
+umc150b               A A A A B B B B B A A - A B B A A B - A A B B B 
+B B A A A A A A B B B A B B B A B A B B A A B A A B A A A A B B B A A 
+A B B A A B A B A A A A A A - B A A A A A A A B B A B - A A A B B B A 
+B B - A A B 
+umc1551               A A A A B B - B A A A A A B B A A B A B A B A B 
+B A A A A A B - B B B A A B B B B B B B A A B A A B A A A - B - B A A 
+A B B B A B - B A A A A A A - - A A A A B A A B B A B - A A A B - B A 
+A B - A A B 
+umc36a                A A A B - B A B B A - B A B B A B B A A A B A B 
+B A A B A A B - B A B B A A B B A B B B B - B A A B A B B B B B B A A 
+B B B A A B - B A B B A A A - B B A A A B A A B B A B - B A A B B B - 
+A B - B A B 
+csu109a               - A A B B B A B B A - B A B B A A B A A A B A B 
+B B A B A A B - B A B B A A B B A B B B B - B A A B - A B B B B B A A 
+B B B A - B - B A B B A A - B B B A A A B - A B B A B - B A - B B B - 
+A B B A A B 
+umc32a                B A - A B B B A A B A A B A A B A B B A B A B A 
+B B A A A A A - A A B B B B A A A A B A A B B - B - A A - - A A B B B 
+A A A A B B B A B A B B B B B A B A B B A B A A A - B A A A A - B B B 
+B A A A A A 
+phi104127             A A B A B B - A B B A A B - A B A B B A A A B A 
+B A B A A A B A A A B B B B B A A A B A A B B B B B A - B A A A B B B 
+B A A B B B A A B A B B B B B A A A B B A A A B A - - A A A A B B B A 
+B B B A B A 
+bnlg1325              A A B A B - B A B B A B B A A B A B - A A B B A 
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--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
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--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
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--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
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--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
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+-stop traits
+-quit
+-end
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/qtlmap_15/test-data/input/qtlcart15.inp	Fri Mar 18 05:51:39 2016 -0400
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--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
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--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
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--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
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--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
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--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
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+umc157a               A A B A B A B A A B B - B A A A B - B A A A A A 
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--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
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--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
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+umc1393               A A B B B B A A B B B B B A A A A B B A A B A A 
+B B B A A A A B A A B - B B B B B B B B A B B A A B B A B B B B B B B 
+B B A A B A B A B A A B B A B A B B A B A A B A A A B B A B A B B B B 
+- B B A B B 
+bnlg1808              A B B B B B A B B B B B - A - A B B B B A B A A 
+A B B A B A B B B A A A B B B B B B B B A B B A A B B B B B B B B B B 
+A B B A B A B B A A A B B A B A B B A B A A B A B A B B A B A B B B B 
+A B B B B B 
+bnl15.21              A B B B B B A B B A A B A B A B B B B B A B A A 
+A B B - A A B B B B B A B B B B A B A B A B B A A A B B A A B A B B B 
+A B B A B - B B A A A B B A B A B B A B A A B A - A A B A B B A B A B 
+A B B B B B 
+bnlg339               A B B B B B A B B A A B A A B B B B B B A - A A 
+A B A - A - B B B B B A A B B B A B A B B B - A A A B B A A B A B A B 
+A B B A B B B B A A A B B A B A B B A B A A - A A - A B A B B A B A B 
+A B - B - B 
+bnlg155               A B B B B B A A B A B - A - B B B A B B A B A A 
+A B A A A B - B B B A A A B B - A B A B B A B A B A A B A A B A A - B 
+A B B A B B - B A A A B B B B A B B B B A A B A B - A A B A B A B A B 
+A B A B A B 
+bnlg1805              A A B B B B B B B A B B A A B B B A B B A B A A 
+A B A A A A B B B B A A A B A B A B B B B A B A B B A B A A B A A A B 
+A B B A B B B B A A A B A B B B B B A A A A B B B A B A B A B B B B B 
+B B A B A B 
+bnl14.07              A A B B A B B B A A B - B B B B B A A B A B A A 
+B A A B A B A B B A A A B B A B A B B B B A B A - B A B A A B B A A - 
+A B B A B B B B A A A B A B B - A B B A A A B A B A B A B A B - B B B 
+B B A B B B 
+umc1125               A A B B A B B A A A A A A B B B B B A B A B A A 
+B A A B A B A A B A A A B B B B B B B B B A B A B - A B A B B B A B A 
+A B B - B B A B B A A B B B B A A B B B A A A A B A B A B A B A - - A 
+B A B B B B 
+phi082                A A B B A B B B B A A A B B B A B B A B A A A - 
+B A A B B A B A B A A A B B B B B B B A B B B A B B B B A B B B A B A 
+A B B A B A A B A B A A A B A B A B B A - A A A B A B B B B A B A B A 
+B - B B A B 
+umc1799               A A B B A B B B B A A A B B B A B B A B A A B - 
+B B A B B A B A B A A A B B B A A B B A B B B A B B B B A B B B A B A 
+A B B A B B A B A B A A A A A B A B A A - A A A B A B B B B A B A B A 
+B A B B A A 
+npi114a               A B - B B A - B A B B A B A B A A A A B A B B B 
+A B B A - B B A B A A - A A B B A B A A A A B - A A B A B B B B A A B 
+A B B A - B A B B B B A A B A A A A B A A A B B B A A B A B A A A A A 
+A B B A B B 
+umc1327               A A A B - A B B B B B A B B B A A - A B A B A B 
+A B B B A B A A A A B A A A - B B B A A B A A - B A B A B B B B B A B 
+A B A - - B A A B B A A A B A A A A B A A A - B B A A B A B - A A A A 
+B B B A B B 
+npi110a               A A - B B A B B A B B A B A A A A - A B A B A B 
+A B A B A B B A A B B A B A A B B B A A B - A - B A B A A B A A - A B 
+B B A - A B A A B B A A A B A A A B B A A A B B A - A B - B B A B A A 
+B A A A B A 
+umc103a               A A - B B A B - A B B A B A A A A - A A A B B A 
+A B A B A B B A A A B A B A - B B B A A B A A A B A B A A B B B - A B 
+A B A A A B A A B A A A A B A B A A B - A A B - A A A B A B B A B A A 
+B B B A B B 
+bnlg669               A A A B B A B B B B B B B B A A A - A A A A B - 
+A B B B A B B A A A B - B A A B B B A B - A A A B A A A A B B B - A B 
+A B A A A B A A A A B A - B A B A A B A A A B A A A A A A A A A B A A 
+B B B A A A 
+umc1858               A A A A B A B A A B B B - A A A A B A A A B B B 
+B A A B A B A B A A B A B A B B B - A B B B A B B A A A A B B B A B B 
+B - A A A A B A A A B B A B B B B A B A B A B A A A A A A A A A A A B 
+B A B A A A 
+umc1562_P             - A A A B - B A - B B B A B B A A B A A - B - A 
+B A - B A B A B A B B B B - B A B A - B B - A B - - - A B B B B A A A 
+B A A B A - B A B - - B A B B B B B B A A - - - B - A - A - A - - - B 
+B - B A A A 
+umc48a                A B - A B B B A A B B B A B B A A B A A A B A A 
+B A B B A A - B A B B - A B B A B B A B A - A B B A A A - B A B A B - 
+B - A B A A B A A A A A A B A A A B B A A A B A B B A A A A B A A A B 
+B A B A B A 
+asg52a                A B A A B B B A A B B A A A B A A B A A A B A A 
+B A - B A A A - A B B - A B B A B B A B A A A B B A A A B B A B A B - 
+B B A B A A A A A A A A A B A A A B B A A A B A B B A A A A B A A A B 
+B A B A B A 
+umc150a               A B A A B B B A A B B A A A B A B - A A A B - A 
+B A - B A B A B A B B - A B B A B B A B A A A B B A A B B B A B A B - 
+B B A A A A B A A A A A A B A A A B B A A A B A B B A A A A A A A A B 
+B A B B B A 
+umc1384               A B A - B A B A A A B A A A B B B - A B A B B A 
+A A B B A B A B A A B A A - B A B A B B A A A B A - B B B B B B B B B 
+B B A B A A B A - A A A A B A A - B B A B A B A B B B B B B A - B B B 
+B A B B B A 
+umc7                  A B A B B A B A A A B A A - A B B - A B A B B A 
+A A - B A B A B A A B A A A B A A A B A A B A B A B B B A B B A B B A 
+B B A B A A B B B A A A A B A A A A B A B A B A A B B B B B A B B B B 
+B - B B A B 
+bnlg1056              A B A B B A B A A A B A A - A B B - A B A B B A 
+A A - B A B A B A A B A A A B A A A B A A B A B A B A B A - B A B B A 
+A B A B A A B B B A A A A B A A - A B A B A B B A B B A B A A B B B B 
+B A A B B B 
+umc39b                A B A B B A B A A A B A A B B B B B B B A B A B 
+A B - B A B A B A B A - A A B A A A B A A B A B A B A B A B B B B A B 
+A B - B A A B B B A A A A B B A B A B A B A B B B B B A - A A B B B B 
+B A A B B B 
+bnlg1272              A A A A A B B A A A A B A B A B A B A A A B B A 
+- B B A A B B A A B B A A A B B B - A - B - B - A A B A - A A A A A A 
+- A A A A B A A A B A B B B - - A A B B A A B A A A A B B B A A B A A 
+B A A A A A 
+umc113a               A A A A A B B B A A A B A B A A A B A B A A B A 
+A B B A A B B A B B B B A A - B B B A B A A A - B A A A B A B A A - A 
+A A B A A A A B - B A B A - - B B B - A B A B A A B A - B - A A B A A 
+B A B A A A 
+umc1170_P             A A A A A B - B A - - A A B A - A B - B A A B A 
+- B B B B A B - B B B - A A A A B B A A A - - A A B A A B A B - A B A 
+A B B A A - B B - B A B B A B A B B A A B A B A A B A A B A - - B A B 
+- A B A A B 
+umc105a               A A A A A B B B A B A B A B B B A B A B A A A B 
+B B B B B A A B B B B B B A A B A B B A B - A A - B B A B A B B A B B 
+B A B A A A B B A B A B B A B A B B A B B A B A B B B B B B A B B B B 
+B A B A A B 
+umc81                 B A - B A B B B A A A A A B B - A B B B B - A A 
+B B A B B B - B B B B B B A B A A B B A B B A B B B A A B A B A B A B 
+B A B B A B - B A B A A B A - B B B A B B B B A B A B A B A A - A B B 
+B A B A B B 
+bnl8.17               B A - B A B A A A B B B B A A B A B A B B - A A 
+A B A B B B - B A - B A A A B A A B A A B B A A A B A A A A A A B A A 
+B B A B A B B A A B A B B A A B B B - B B B B B A A B B B B A B A B B 
+A A A A B B 
+umc1231               B A A B A B A A A B - B B A - B A B A B B B A A 
+- B A B B - - B A B B A A A B A A A B A A - - A A B B A A - A A B A A 
+B B A - A B B A B B A B A A A B B B A A B B B B A B B B B B A B A B B 
+A - A A A B 
+umc1733               A A A A A A B A A B A B B A A A A B A B A A A B 
+A A A A B B A B A B B A A A B B A A A A A A B A A A A A A B B A B B A 
+A A A B A B B A B B A B A A B B A A A A B A B B A B A A B A A A A A B 
+B A A A A B 
+bnlg1588              B A A A A A B A A B A B B A A B A B A B B A A - 
+A A A A A B A B A B B A A A B B B A A A A A A A A A A A A A B A B B A 
+A A A B A B B A B B A B A A B B A A A A B B B B A B A A B A A A A A B 
+B A A A A B 
+bnlg1375              B B A A A B B A A B B B B A A B B - B B B A A A 
+A B A A B B B B A B B A A A B B A - B A A B A A A B B B B B B A A B A 
+A B A B A B B A B B A B A A B A A A A A A B B B A B B A A A A A A A B 
+B A B B A B 
+umc1137               B B A A A A A A A B A B A A A B B A B B A B A A 
+A A A B B B A B A B A A A A B A B B A A A A A A A A B B A B B A A B A 
+A B A A A B B A B B A B A A B B A A A A A B A A A B A B A B A B A A B 
+B A A B A B 
+phi118                B A A A A A B B A A A - A B A A B - B A B A B B 
+A B B B B B B B A A A A A A A B A B B B A A A B - B A B B B A B A B B 
+B - A B A B B A B - B B B A B B A B A B B B A A A - B A B A A B B B B 
+B A A B B A 
+npi285a               - A - B B A B B - - A B - B A A B B B A A A B B 
+A A B - B A B A B A A - A A A A A B B B A - A B A B A B - B A B A B B 
+B A B B A B A B A B B B B B B B A B B B B - A A A B B A B A A B B B A 
+B B B B A A 
+umc1337_P             - A A B B - - A B A A B B A A A A B B A B - A B 
+A A A - B A B A A B A B A A A A A - - B A A B B B B A A A B A B A B B 
+A A A A A - A A A A B B B B A B A B B B A B A A A A - A B A - B - B A 
+A B B A - A 
+umc130                B B - B B B A B B A B A B A A A B B B A B - A B 
+A A A B B A B A A B A B B A - A A B B B A B A B A B A B B - A B A B B 
+A B A A A A A A - B B A B A A B A B A B B B A A A A B A B A B B B B A 
+A B B B A A 
+bnlg1079              B B A B B B A A B A B A A A A A A B B A B A A B 
+A A A B B B B A A B A B B A B A A B B B A B A - A B A A B A B B A B B 
+A B A A A B A A B A B A B - A B A B A B A B A - A A B A B A B B B B - 
+A B B A A A 
+umc1115               A B B B A B A A A B B B A B A A A A B A A A A B 
+B A A A B B B A A B A B - A B A A B - B A B A A A A A A B A A A A A B 
+A B A A B A A A B A B A A A B B A A B A B A A A A A A A B A A A A A A 
+B B B A A A 
+npi232a               A B A B A B B A A B B B A B A A A A A A A A A B 
+B A A A B B B A A B A B B A B B A B A B A A A B A A A A B A A A A A B 
+A B A A A A A A B A B A A A B B A A A A A A A A A A A A A A A A A A A 
+B A B A A A 
+umc44a                A B A B A B B A A B B B B B A A A A A A A A A B 
+B A B A B A B A A - B B A A B A A B A B A A A A - A - A B A B A A - B 
+A B A A A A A B B A A A A A A B A A A A A A A A A A A A A - B A A A A 
+B B B A A A 
+umc182                B B A B A B B A A B B B B B A A B A A B B A A B 
+A A B A B A B A B B B B B A B A A B A B A - A A B A B A B A B A A - B 
+A B B A A B A B B A A A A A A B A B A A A B A A A A A B A B B B A A A 
+B B B A B A 
+bnlg236               B A A B A B A A A B B A B B A A A A A B B A A B 
+A A B A B B B A B B B B B A B A A B A B A A A B B A B A B B B A A A B 
+A B B A A A A B B A A A A A A B A B A A A B A B A - A B A B B A A A A 
+A B B A B A 
+bnl7.49a              B A - B B A A - A A A - A B A A A A A B B A A B 
+A - B A B B - A A B B B - B B A A A A A A - A B B A B A B B B A A - B 
+B A A A A B A A B A B A A A A B A B A A B - A - A B - B - B B - A A A 
+A B B A B A 
+bnlg1450              A A A B A B A A A B - A A B A B A A A B A A A B 
+A B B - A B B A A B B B B B B A A B A A A - A A B A B A B A B A B - B 
+B B A B A B A A - A B A B A B B A B A B B A A B A A A B A B B A B A A 
+A B A A B A 
+umc1038               A A A B B B A B B B B A B A A B A A A B A B A B 
+A B B B A A A A B A B B B - A A - A - B A B B A B B B A B A B A B - B 
+B B B B A B A B A A B A - A B B B B A B A A B B A A A B - B A B B B A 
+A B A A B - 
+-stop markers
+-start traits
+A_92_P029002	429.65	366.25	468.78	436.36	380.34	271.4	283.01	389.6	484.17	359.43	412.19	419.07	425.52	268.52	.	.	344.13	381.45	510	360.08	586.55	575.05	577.04	398.82	.	.	320.58	427.03	.	.	.	.	482.97	490.29	513.3	303.67	498.6	596.61	591.27	509.64	475.68	341.89	392.44	286.5	685.94	1061.29	630.92	653.97	212.69	395.38	488.22	260.61	359.04	336.68	428.48	403.54	325.58	480.31	376.95	466.59	392.79	443.58	302.34	253.51	.	.	.	.	358.38	452.06	375.38	482.5	320.97	293.88	354.85	461.38	556.06	374.57	472.53	457.82	422.02	302.82	396.37	379.9	525.83	579.42	434.5	340.72	525.49	412.65	539.73	399.2	564.56	444.97	435.86	486.86	377.84	312.87	375.87	432.77
+A_92_P028842	203.43	278.08	146.77	241.75	.	.	185.35	240.55	220.33	247.77	219.55	227.77	269.32	179.27	.	.	140.42	279.56	174.34	174.9	248.94	278.4	219.34	336.09	.	.	277	189.29	.	.	.	.	.	.	.	.	243.84	289.59	384.2	158.94	193.3	212.36	276.17	177.59	453.09	545.47	266.23	285.56	.	.	.	.	.	.	.	.	181.09	267.63	166.82	294.71	325.43	145.2	.	.	.	.	.	.	196.2	318.07	261.16	273.23	177.97	197.41	215.7	122.59	419.55	186.13	.	.	228.39	137.62	168.99	131.72	.	.	.	.	270.49	227.11	234.25	178.39	222.41	197.24	274.37	181.97	.	.	.	.
+A_92_P028354	535.05	519.58	458.78	718.73	718.09	500.31	312.98	339.61	696.67	576.64	370.65	653.07	482.29	324.88	601.25	665.53	331.96	498.21	426.63	550.71	1099.57	439.35	656.13	519.95	335.9	375.57	663.62	442.49	726	734.16	.	.	.	.	837.53	809.1	307.34	687.96	938.48	663.27	327.66	590.51	732.21	447.22	603.42	1008.87	564.99	748.7	315.8	675.04	630.33	320.15	531.09	370.98	372.42	510.47	397.79	632.83	644.62	598.79	707.04	490.57	374.72	372.68	262.01	171.09	.	.	434.44	514.02	726.53	278.31	580.62	353.12	403.96	455.08	1240.46	438.83	324.06	642.02	694.18	267.87	610.75	532.2	1036.44	833.27	488.31	474.61	464.14	455	739.11	413.01	642.53	678.35	428.5	506.48	299.08	217.55	567.55	766.83
+A_92_P028042	672.2	581.52	734	640.4	477.57	392.32	617.9	783.12	529.08	485.62	731.3	441.44	555.09	645.07	.	.	494.39	982.64	576.33	636.07	1152.67	957.18	1008.05	648.11	.	.	381.61	604.75	250.04	493.76	459.6	525.16	.	.	356.2	633.97	768.08	582.57	512.51	564.81	602.64	849.56	457.76	476.35	545.32	678.45	600.97	614.59	325.89	411.03	393.29	297.9	555.89	505.81	313.05	508.52	561.87	325.16	500.37	495.4	525.84	347.54	378.23	538.49	185.14	255.54	.	.	.	.	611.07	706.2	332.03	375.7	423.68	613.88	372.91	437.45	812.08	549.87	464.13	335.66	405.03	518.77	508.12	607.98	457.45	305.68	442.61	600.65	766.36	457.72	678.98	623.95	679.13	740.87	462.58	417.28	695.19	337.66
+-stop traits
+-quit
+-end
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/qtlmap_15/test-data/input/qtlcart_original.map.txt	Fri Mar 18 05:51:39 2016 -0400
@@ -0,0 +1,251 @@
+#      671562676   -filetype Rmap.out 
+#
+#	QTL Cartographer v. 1.17e, 27 August 2003
+#	This output file (\\Trin.bi.up.ac.za\duncan\GLS_project\Pipe_line\MeQTL\NewMcd01.map) was created by RMap...
+#
+#	It is 12:22:33 on Tuesday, 24 July 2012
+#
+#
+#
+#    Here is the Map of Markers...
+-s
+-f   2  Map function [1,8]:  Haldane is 1
+-p    0.0000  Extra parameter for map functions [4-8]
+-u  c    The units of measurement is centiMorgans.
+#
+# Markermap parameters
+#
+-c        10  Number of chromosomes.
+-i       167  Total number of markers.
+-m        16  Mean, and...
+-vm   4.9001  ...standard deviation for Markers/Chromosome.
+-d   11.8571  Mean, and...
+-vd   6.0265  ...standard deviation for the intermarker distance.
+-t   -1.#IND  Mean length of material outside the flanking markers.
+#
+          |   Chromosome---->
+--------------------------------------------------------------------------------------------
+Marker    |       1       2       3       4       5       6       7       8       9      10
+--------------------------------------------------------------------------------------------
+-l      0 |   0.0000  0.0000  0.0000  0.0000  0.0000  0.0000  0.0000  0.0000  0.0000  0.0000
+-l      1 |   7.5300 13.2700 11.7500 19.0000  3.2000  5.6200  9.0300 10.7400 17.9400 15.0200
+-l      2 |  11.2400 26.0000 13.8400 10.5900 22.8200  8.9200 11.5700 14.7000  9.5600 17.5500
+-l      3 |  19.9400 25.6300 16.5400  6.3400  7.5600 14.4900 10.2300 13.2900 18.4400 13.4800
+-l      4 |   5.9100 17.1400  9.1100 17.1500  6.6500  6.8300 10.2300 11.4100 19.1100  6.9400
+-l      5 |   4.1100  8.5600 10.0400  3.0800  9.6900  5.7300  4.1400 17.3300 27.0800 22.1800
+-l      6 |   4.4800 10.4300 10.7400 14.0900 11.8600 19.4000 10.2400 15.8400  5.6800  6.3800
+-l      7 |  16.7600 10.7100  6.1200  4.6300 15.4300  4.2800  7.7500 12.7700 22.7000  9.0700
+-l      8 |  11.9000  5.3500  2.3600 17.3300  9.4900  6.4500 13.1400  3.2300  4.2700  8.0500
+-l      9 |  14.2300 15.5300 22.9100  6.1700  7.7200 17.1500 11.3000  3.5800 15.6000  5.9300
+-l     10 |  16.6000  8.8600 26.3700 12.9000  5.2800 26.9500 18.6800 15.3100 18.4000 13.0300
+-l     11 |  14.1300  8.5600  7.0100  8.9700 11.4100  9.7400  4.8500  9.6600  0.0000 12.9000
+-l     12 |  15.8600 16.2000 18.3000  7.6500 13.8900 13.8200  0.0000  3.1300         16.9500
+-l     13 |   6.2800  2.8700  6.1200  9.7600  8.3200 20.3800         10.3200          0.0000
+-l     14 |  15.3100  0.0000 16.3500  9.6600  7.7900  2.5400          0.0000                
+-l     15 |  14.8400         10.9700  4.2500 23.2000 19.9200                                
+-l     16 |   8.1200         10.6200 17.0500 14.6200 13.6300                                
+-l     17 |   6.1800         14.4500  5.5800 11.9000  0.0000                                
+-l     18 |   8.7100          7.6900  9.1900  6.7100                                        
+-l     19 |  33.9500          0.0000  4.9800  6.2800                                        
+-l     20 |  19.7800                  0.0000  0.0000                                        
+-l     21 |   8.9400                                                                        
+-l     22 |  10.2300                                                                        
+-l     23 |  22.0600                                                                        
+-l     24 |   3.1000                                                                        
+-l     25 |  14.8400                                                                        
+-l     26 |   9.3700                                                                        
+-l     27 |   0.0000                                                                        
+--------------------------------------------------------------------------------------------
+-Number   |      27      14      19      20      20      17      12      14      11      13
+
+
+
+Names and positions of the markers 
+
+ Chrom  Mark  Name 
+-b MarkerNames    
+     1     1 phi056
+     1     2 bnl5.62
+     1     3 umc1041
+     1     4 umc157a
+     1     5 bnlg1178
+     1     6 bnlg1429
+     1     7 bnlg1627
+     1     8 umc11a
+     1     9 bnlg439
+     1    10 bnlg2238
+     1    11 Bnlg1811_U
+     1    12 bnlg2086
+     1    13 csu61b
+     1    14 bnlg1057
+     1    15 umc1122
+     1    16 Bnlg615_U
+     1    17 umc1128
+     1    18 umc166b
+     1    19 dupssr12
+     1    20 phi011
+     1    21 bnlg1720
+     1    22 umc106a
+     1    23 umc147b
+     1    24 umc1111_P
+     1    25 bnlg2331
+     1    26 bnlg2123
+     1    27 bnl6.32
+     2     1 phi402893
+     2     2 bnlg1297
+     2     3 bnlg2042
+     2     4 umc44b
+     2     5 csu40
+     2     6 umc135
+     2     7 csu54a
+     2     8 umc55a
+     2     9 umc14b
+     2    10 csu154a
+     2    11 umc150b
+     2    12 umc1551
+     2    13 umc36a
+     2    14 csu109a
+     3     1 umc32a
+     3     2 phi104127
+     3     3 bnlg1325
+     3     4 bnlg1447
+     3     5 umc92a
+     3     6 bnlg1019a
+     3     7 phi053
+     3     8 bnlg420
+     3     9 umc1307
+     3    10 Phi073_U
+     3    11 Bnlg1449_U
+     3    12 bnl10.24a
+     3    13 unknown1
+     3    14 umc3b
+     3    15 umc16a
+     3    16 bnlg1108_P
+     3    17 umc63a
+     3    18 bnlg1182
+     3    19 bnlg1754
+     4     1 umc1017
+     4     2 umc1294
+     4     3 phi021
+     4     4 umc1550
+     4     5 umc1652
+     4     6 bnlg490
+     4     7 csu100
+     4     8 umc156a
+     4     9 bnlg2291
+     4    10 umc19
+     4    11 mmc0341
+     4    12 umc133a
+     4    13 umc15a
+     4    14 csu11b
+     4    15 npi593a
+     4    16 bnlg589
+     4    17 umc1720_P
+     4    18 bnlg1337
+     4    19 phi019
+     4    20 phi006
+     5     1 bnl8.33
+     5     2 npi409
+     5     3 umc147a
+     5     4 umc90
+     5     5 umc107b
+     5     6 Bnlg105_U
+     5     7 bnlg1046
+     5     8 umc166a
+     5     9 bnl6.22
+     5    10 csu36b
+     5    11 DupSSR10_U
+     5    12 bnl5.71a
+     5    13 umc1155_P
+     5    14 npi237
+     5    15 umc54
+     5    16 bnlg1346
+     5    17 bnlg118
+     5    18 umc1225
+     5    19 umc104b
+     5    20 bnlg1885
+     6     1 umc85a
+     6     2 bnlg426
+     6     3 umc36c
+     6     4 umc1572_P
+     6     5 Bnlg2191_U
+     6     6 bnlg2151
+     6     7 umc1887
+     6     8 umc65a
+     6     9 umc1014
+     6    10 bnlg1922
+     6    11 umc1413_P
+     6    12 mmc0241
+     6    13 umc1424_P
+     6    14 umc36
+     6    15 umc39
+     6    16 bnlg1740
+     6    17 umc2059
+     7     1 csu13
+     7     2 bnlg1094
+     7     3 umc1393
+     7     4 bnlg1808
+     7     5 bnl15.21
+     7     6 bnlg339
+     7     7 bnlg155
+     7     8 bnlg1805
+     7     9 bnl14.07
+     7    10 umc1125
+     7    11 phi082
+     7    12 umc1799
+     8     1 npi114a
+     8     2 umc1327
+     8     3 npi110a
+     8     4 umc103a
+     8     5 bnlg669
+     8     6 umc1858
+     8     7 umc1562_P
+     8     8 umc48a
+     8     9 asg52a
+     8    10 umc150a
+     8    11 umc1384
+     8    12 umc7
+     8    13 bnlg1056
+     8    14 umc39b
+     9     1 bnlg1272
+     9     2 umc113a
+     9     3 umc1170_P
+     9     4 umc105a
+     9     5 umc81
+     9     6 bnl8.17
+     9     7 umc1231
+     9     8 umc1733
+     9     9 bnlg1588
+     9    10 bnlg1375
+     9    11 umc1137
+    10     1 phi118
+    10     2 npi285a
+    10     3 umc1337_P
+    10     4 umc130
+    10     5 bnlg1079
+    10     6 umc1115
+    10     7 npi232a
+    10     8 umc44a
+    10     9 umc182
+    10    10 bnlg236
+    10    11 bnl7.49a
+    10    12 bnlg1450
+    10    13 umc1038
+-e MarkerNames
+
+
+
+Names of the Chromosomes
+
+-b  ChromosomeNames    
+     1            Ch1
+     2            Ch2
+     3            Ch3
+     4            Ch4
+     5            Ch5
+     6            Ch6
+     7            Ch7
+     8            Ch8
+     9            Ch9
+    10            Ch10
+-e ChromosomeNames
Binary file qtlmap_15/test-data/output/._qtl_out_1.txt has changed
Binary file qtlmap_15/test-data/output/._qtl_out_10.txt has changed
Binary file qtlmap_15/test-data/output/._qtl_out_11.txt has changed
Binary file qtlmap_15/test-data/output/._qtl_out_12.txt has changed
Binary file qtlmap_15/test-data/output/._qtl_out_13.txt has changed
Binary file qtlmap_15/test-data/output/._qtl_out_14.txt has changed
Binary file qtlmap_15/test-data/output/._qtl_out_15.txt has changed
Binary file qtlmap_15/test-data/output/._qtl_out_2.txt has changed
Binary file qtlmap_15/test-data/output/._qtl_out_3.txt has changed
Binary file qtlmap_15/test-data/output/._qtl_out_4.txt has changed
Binary file qtlmap_15/test-data/output/._qtl_out_5.txt has changed
Binary file qtlmap_15/test-data/output/._qtl_out_6.txt has changed
Binary file qtlmap_15/test-data/output/._qtl_out_7.txt has changed
Binary file qtlmap_15/test-data/output/._qtl_out_8.txt has changed
Binary file qtlmap_15/test-data/output/._qtl_out_9.txt has changed
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/qtlmap_15/test-data/output/qtl_out_1.txt	Fri Mar 18 05:51:39 2016 -0400
@@ -0,0 +1,10 @@
+A_92_P039116	1	1	6	13	1.5339	15.9210885	3.4548762045	0.1919114	0.3879427	77.2994584	-311.3306014	0.0000000	13	1.4516	15	1.7163	13	1.4181	15	1.7956
+A_92_P039116	1	3	9	6	0.9214	15.3291347	3.3264222299	0.1176972	0.3098947	73.0022134	-249.9855214	0.0000000	5	0.8372	6	0.9652	5	0.7772	6	0.9724
+A_92_P039116	1	4	9	8	1.2052	13.9017110	3.016671287	0.1050450	0.3111284	71.1474755	245.1582644	0.0000000	7	1.2011	9	1.3362	7	1.1768	9	1.3935
+A_92_P038628	2	1	9	1	0.1601	24.5310019	5.3232274123	0.1989293	0.5098951	52.0670152	-701.7675097	0.0000000	1	0.0725	2	0.2239	1	0.0379	2	0.2472
+A_92_P038628	2	2	10	1	0.0201	12.8665772	2.7920472524	0.0951165	0.4914030	48.4981968	-480.0477241	0.0000000	1	0.0001	1	0.1196	1	0.0001	1	0.1444
+A_92_P038150	4	1	6	9	0.7773	13.7094809	2.9749573553	0.1131346	0.5435596	1.1541518	394.9822315	0.0000000	8	0.6819	9	0.8709	6	0.6046	9	0.8844
+A_92_P038150	4	2	9	9	1.2479	13.7334120	2.980150404	0.0784721	0.4919043	1.3007608	351.9779719	0.0000000	7	1.1444	9	1.3206	7	1.0201	9	1.3679
+A_92_P038150	4	3	10	2	0.1503	14.0299522	3.0444996274	0.0845627	0.4961190	1.2914158	342.6938285	0.0000000	1	0.0422	2	0.2273	1	0.0001	2	0.2856
+A_92_P038150	4	4	10	3	0.4058	15.3264104	3.3258310568	0.1320742	0.5272216	1.1053058	-483.3117444	0.0000000	3	0.3449	6	0.797	2	0.32	6	0.8084
+A_92_P038150	4	5	10	5	0.6500	39.1826820	8.502641994	0.3966235	0.5336773	19.1694948	-742.6937805	0.0000000	5	0.5749	5	0.7461	5	0.5467	5	0.7508
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/qtlmap_15/test-data/output/qtl_out_10.txt	Fri Mar 18 05:51:39 2016 -0400
@@ -0,0 +1,10 @@
+A_92_P027554	1	1	2	13	1.6825	12.7611437	2.7691681829	0.1018072	0.3903601	4.4296057	167.8795132	0.0000000	12	1.5655	13	1.6825	11	1.4988	13	1.6825
+A_92_P027554	1	2	3	13	1.5510	20.3857124	4.4236995908	0.1619413	0.4031766	2.7686481	-211.1740827	0.0000000	12	1.4823	13	1.5956	12	1.4466	14	1.706
+A_92_P027554	1	4	10	4	0.4606	17.5002478	3.7975537726	0.1313607	0.3906483	3.3345446	-188.6856642	0.0000000	3	0.3584	4	0.5233	2	0.3245	5	0.6256
+A_92_P027390	2	1	6	8	0.6528	18.1173076	3.9314557492	0.2563745	0.6640015	0.4052638	47.1173201	0.0000000	6	0.5578	8	0.693	6	0.5159	8	0.7133
+A_92_P027390	2	2	6	12	1.3157	17.7087013	3.8427881821	0.3257878	0.6980663	0.4043924	-51.5935951	0.0000000	12	1.2576	12	1.3818	11	1.2481	12	1.3906
+A_92_P027072	3	2	7	11	1.1032	44.9795778	9.7605683826	0.2969825	0.5035042	4.6985714	1843.6463564	0.0000000	11	1.0867	11	1.1032	11	1.0772	11	1.1032
+A_92_P027072	3	3	9	8	1.2052	14.5812965	3.1641413405	0.0775113	0.5066064	4.4592073	985.5528170	0.0000000	7	1.1257	8	1.2359	7	1.0763	9	1.3895
+A_92_P026747	4	1	3	1	0.0401	24.1515872	5.2408944224	0.3905649	0.6410914	3.8219363	37.8546571	0.0000000	1	0.0081	1	0.1007	1	0.0001	1	0.1048
+A_92_P026747	4	2	3	9	0.8051	13.3190279	2.8902290543	0.1942427	0.5175014	30.0430325	-26.6445313	0.0000000	7	0.7614	9	0.9686	7	0.7247	9	1.0276
+A_92_P026747	4	3	6	5	0.3587	11.9666148	2.5967554116	0.1700650	0.5144391	28.6662391	25.6423152	0.0000000	3	0.2763	5	0.4027	3	0.1899	6	0.5236
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/qtlmap_15/test-data/output/qtl_out_11.txt	Fri Mar 18 05:51:39 2016 -0400
@@ -0,0 +1,4 @@
+A_92_P025313	1	1	3	13	1.5510	20.6064068	4.4715902756	0.1710257	0.2747041	1109.4668897	-1905.2184858	0.0000000	12	1.5085	13	1.5862	12	1.4679	14	1.7055
+A_92_P024994	2	1	5	2	0.2121	17.4534281	3.7873938977	0.2637088	0.6641010	15.0444221	320.9327481	0.0000000	2	0.0364	3	0.2867	1	0.026	3	0.3122
+A_92_P024836	3	1	4	12	1.2626	14.9192368	3.2374743856	0.1173577	0.3739031	13.0708073	-100.1363730	0.0000000	11	1.143	13	1.3648	11	1.1137	14	1.4605
+A_92_P024836	3	2	8	8	0.9609	16.4094504	3.5608507368	0.1247620	0.3640049	12.1550179	111.8531092	0.0000000	7	0.8899	9	0.9997	7	0.8506	10	1.1185
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/qtlmap_15/test-data/output/qtl_out_12.txt	Fri Mar 18 05:51:39 2016 -0400
@@ -0,0 +1,7 @@
+A_92_P024516	1	1	1	19	2.0214	20.5892047	4.4678574199	0.1627540	0.2898391	12.5794392	255.4967487	0.0000000	18	1.9865	19	2.1519	18	1.9586	19	2.2042
+A_92_P024516	1	3	1	23	2.7904	11.7412564	2.5478526388	0.1205252	0.3260419	11.5022960	-218.6650149	0.0000000	21	2.6455	23	2.9188	21	2.6407	23	2.9708
+A_92_P023713	2	1	2	1	0.1001	15.0930867	3.2751998139	0.1490762	0.3233012	1.0763490	252.8027941	0.0000000	1	0.0085	2	0.2729	1	0.0001	2	0.3274
+A_92_P023713	2	3	5	16	1.6832	20.6465042	4.4802914114	0.2378846	0.3902667	0.2904053	323.5459459	0.0000000	15	1.6398	16	1.7329	15	1.6326	16	1.7647
+A_92_P023713	2	5	6	3	0.2255	13.1162156	2.8462187852	0.1138979	0.3974125	3.4227484	-218.8805035	0.0000000	1	0.0163	4	0.3178	1	0.0001	4	0.3477
+A_92_P023551	3	1	1	14	1.6098	12.1963674	2.6466117258	0.1372960	0.3800574	4.6993484	133.4043424	0.0000000	14	1.5338	15	1.6972	13	1.4897	15	1.7507
+A_92_P023551	3	2	10	1	0.0601	19.0928858	4.1431562186	0.2468352	0.4758394	0.5013347	175.2143455	0.0000000	1	0.0045	1	0.1223	1	0.0001	1	0.1422
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/qtlmap_15/test-data/output/qtl_out_13.txt	Fri Mar 18 05:51:39 2016 -0400
@@ -0,0 +1,4 @@
+A_92_P023080	3	1	1	1	0.0601	37.7011957	8.1811594669	0.2848013	0.9322797	1.6358983	104.0142532	0.0000000	1	0.0317	2	0.1189	1	0.0187	2	0.1296
+A_92_P023080	3	3	1	20	2.3609	13.6788863	2.9683183271	0.0553721	0.8882827	3.8493444	-32.3646289	0.0000000	19	2.2733	20	2.4304	19	2.2101	20	2.4852
+A_92_P023080	3	4	7	11	1.1032	31.0287041	6.7332287897	0.1789058	0.8966296	3.4735566	-67.0784555	0.0000000	10	1.0607	11	1.1032	10	1.0104	11	1.1032
+A_92_P023080	3	5	8	5	0.5015	51.6576621	11.2097126757	0.4555327	0.8732000	3.3751192	-96.9461713	0.0000000	4	0.4549	5	0.5372	4	0.4234	5	0.5707
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/qtlmap_15/test-data/output/qtl_out_14.txt	Fri Mar 18 05:51:39 2016 -0400
@@ -0,0 +1,7 @@
+A_92_P022918	1	1	8	1	0.0401	31.7555607	6.8909566719	0.3030513	0.5086103	5.0865774	-681.3026366	0.0000000	1	0.0111	1	0.0817	1	0.0001	1	0.0967
+A_92_P022755	2	1	3	16	1.9454	12.2519892	2.6586816564	0.1092460	0.4087476	8.3542742	-1752.0761466	0.0000000	15	1.8842	17	2.1202	15	1.8784	17	2.1344
+A_92_P022755	2	4	8	4	0.4274	20.6933638	4.4904599446	0.1369886	0.5115352	6.5683702	1984.0754662	0.0000000	3	0.2923	5	0.5831	3	0.264	5	0.6403
+A_92_P022755	2	6	9	7	0.9782	16.3122115	3.5397498955	0.1202802	0.3841991	7.0636630	-1823.7633241	0.0000000	6	0.9287	7	1.0488	5	0.8089	7	1.0942
+A_92_P022755	2	7	10	11	1.1764	13.8857650	3.013211005	0.1003230	0.3792059	7.0186621	-1705.3060098	0.0000000	10	1.1196	11	1.225	10	1.0773	11	1.2614
+A_92_P022592	3	1	1	13	1.4670	14.1819258	3.0774778986	0.1495470	0.3618150	9.7749401	-73.0555529	0.0000000	13	1.4278	14	1.5786	12	1.4169	14	1.6308
+A_92_P022592	3	2	1	18	2.0143	11.8257352	2.5661845384	0.1011971	0.3249504	7.5422339	52.5612035	0.0000000	18	1.9421	19	2.1435	17	1.8757	19	2.2445
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/qtlmap_15/test-data/output/qtl_out_15.txt	Fri Mar 18 05:51:39 2016 -0400
@@ -0,0 +1,7 @@
+A_92_P022110	1	1	1	18	2.0143	12.0455951	2.6138941367	0.0928423	0.3268055	0.5377619	140.2867239	0.0000000	17	1.9036	19	2.1396	16	1.8722	19	2.2243
+A_92_P022110	1	2	10	12	1.4054	13.2804218	2.8818515306	0.1419048	0.3733549	0.3170982	-169.0318841	0.0000000	12	1.3123	12	1.4654	11	1.2993	12	1.4654
+A_92_P021792	2	1	1	14	1.6098	13.7867804	2.9917313468	0.1154861	0.4159935	1.5415854	-187.9840206	0.0000000	14	1.526	15	1.7162	13	1.4892	15	1.7577
+A_92_P021792	2	2	1	19	2.0214	21.2959774	4.6212270958	0.1459124	0.3894262	1.6071086	212.4539382	0.0000000	18	1.973	19	2.1178	18	1.9474	19	2.1703
+A_92_P021792	2	3	7	3	0.2061	14.4512266	3.1359161722	0.0953207	0.3877693	1.6159454	-166.6958319	0.0000000	2	0.1497	3	0.2588	2	0.1091	3	0.2887
+A_92_P021792	2	4	10	10	1.0861	19.1017279	4.1450749543	0.1666632	0.4539051	0.0927683	-215.6184203	0.0000000	9	1.0403	10	1.1595	9	1.0153	10	1.1695
+A_92_P021634	3	1	6	16	1.9423	30.9698873	6.7204655441	0.2910527	0.3081694	2.0286370	795.9301198	0.0000000	16	1.9009	16	1.9423	16	1.8746	16	1.9423
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/qtlmap_15/test-data/output/qtl_out_2.txt	Fri Mar 18 05:51:39 2016 -0400
@@ -0,0 +1,12 @@
+A_92_P037834	1	1	4	5	0.5309	24.0416490	5.217037833	0.1788150	0.4904768	20.2186322	-215.1013986	0.0000000	4	0.483	5	0.5471	4	0.4502	5	0.5558
+A_92_P037834	1	2	5	19	1.9955	12.8100275	2.7797759675	0.1007023	0.5007851	24.0032764	-164.1721772	0.0000000	18	1.9338	19	2.0355	16	1.7878	19	2.0355
+A_92_P037834	1	3	7	3	0.2861	28.3465676	6.1512051692	0.2712756	0.5525036	11.0181706	274.5318342	0.0000000	3	0.2457	4	0.3541	3	0.2299	4	0.382
+A_92_P037509	2	1	2	5	0.8205	20.9015193	4.5356296881	0.1920072	0.8228764	0.6300379	50.7070865	0.0000000	4	0.7702	5	0.8741	4	0.7317	5	0.8958
+A_92_P037509	2	2	3	14	1.7522	14.5634804	3.1602752468	0.1395012	0.8505212	0.6992039	43.6613918	0.0000000	14	1.6705	15	1.84	14	1.6376	15	1.8775
+A_92_P037509	2	3	6	15	1.7431	18.4634837	4.0065759629	0.1907638	0.8576937	0.9327344	52.4041957	0.0000000	15	1.6376	16	1.9224	14	1.6228	16	1.9367
+A_92_P037509	2	5	8	5	0.5015	28.4825171	6.1807062107	0.3078012	0.8259992	0.6597413	-63.9160300	0.0000000	4	0.4414	5	0.5539	4	0.419	5	0.5893
+A_92_P037035	3	1	2	8	1.1375	32.8400994	7.1263015698	0.2303759	0.5341618	178.1779135	-434.9303913	0.0000000	7	1.0942	8	1.1598	7	1.0586	8	1.1634
+A_92_P037035	3	2	2	10	1.3263	16.5244802	3.5858122034	0.0980168	0.5049068	100.6701175	284.2624983	0.0000000	9	1.322	10	1.3666	9	1.3177	10	1.4038
+A_92_P037035	3	3	9	7	0.9782	39.2967801	8.5274012817	0.2607592	0.5063220	118.6289643	-382.9703278	0.0000000	6	0.9547	7	1.0159	6	0.9389	7	1.046
+A_92_P036877	4	1	2	7	1.0104	13.6743073	2.9673246841	0.1091632	0.3352177	193.4943050	151.5554180	0.0000000	6	0.934	7	1.0843	5	0.9044	7	1.113
+A_92_P036877	4	2	4	11	1.1329	15.8680278	3.4433620326	0.1814249	0.3996043	198.2704407	-204.6505552	0.0000000	11	1.1138	11	1.1821	10	1.1081	13	1.3664
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/qtlmap_15/test-data/output/qtl_out_3.txt	Fri Mar 18 05:51:39 2016 -0400
@@ -0,0 +1,10 @@
+A_92_P036723	1	1	3	2	0.1176	25.5451801	5.5433040817	0.3367142	0.7495437	0.1420987	30.1380150	0.0000000	1	0.0634	2	0.1606	1	0.0373	2	0.193
+A_92_P036723	1	2	3	5	0.5925	12.4777349	2.7076684733	0.1140458	0.8663131	0.6745923	19.2755898	0.0000000	5	0.5496	5	0.6126	5	0.5279	5	0.6129
+A_92_P036723	1	4	3	18	2.1961	20.6998468	4.4918667556	0.2566942	0.7530538	0.1563160	27.1528712	0.0000000	18	2.1488	18	2.1961	17	2.0507	18	2.1961
+A_92_P036723	1	5	6	14	1.5977	11.7592146	2.5517495682	0.1189907	0.7522249	0.1368680	-18.8320617	0.0000000	13	1.4591	15	1.6792	12	1.3915	15	1.8129
+A_92_P036564	2	1	1	17	1.9125	14.0649598	3.0520962766	0.1257104	0.3385352	8.3880503	178.1987126	0.0000000	16	1.8419	18	2.0148	16	1.8028	18	2.0189
+A_92_P036564	2	3	4	12	1.2426	11.7618881	2.5523297177	0.1027206	0.3215265	9.5874467	-163.3414051	0.0000000	11	1.1355	13	1.361	10	1.0381	13	1.3718
+A_92_P036402	3	1	3	3	0.3960	11.9578142	2.5948456814	0.1717407	0.6684378	37.0007748	33.8745914	0.0000000	2	0.2539	5	0.5279	2	0.2406	5	0.6001
+A_92_P036402	3	2	10	12	1.4654	13.2511287	2.8754949279	0.1735358	0.6527381	31.4598473	31.5911238	0.0000000	12	1.3866	12	1.4654	12	1.327	12	1.4654
+A_92_P036241	4	1	5	17	1.7894	12.4339606	2.6981694502	0.0944238	0.3150629	15.8341283	-207.6782322	0.0000000	16	1.733	17	1.8612	16	1.6728	17	1.8975
+A_92_P036241	4	2	10	1	0.0401	11.8407342	2.5694393214	0.1081500	0.3340395	19.0765856	221.2449803	0.0000000	1	0.0001	1	0.1413	1	0.0001	1	0.1475
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/qtlmap_15/test-data/output/qtl_out_4.txt	Fri Mar 18 05:51:39 2016 -0400
@@ -0,0 +1,6 @@
+A_92_P036076	1	1	6	1	0.0201	12.0508049	2.6150246633	0.0638608	0.7313758	5.7647286	-148.2950721	0.0000000	1	0.0001	3	0.2309	1	0.0001	3	0.288
+A_92_P036076	1	2	8	4	0.3874	63.8836181	13.8627451277	0.5007644	0.7018512	12.7850245	-411.4754368	0.0000000	3	0.3594	4	0.4126	3	0.3341	4	0.4342
+A_92_P035602	2	1	3	7	0.7403	33.6744317	7.3073516789	0.3067255	0.5170118	11.8654223	-88.4458067	0.0000000	6	0.7166	7	0.7641	6	0.6808	7	0.7728
+A_92_P035118	3	1	2	6	0.9061	11.9240992	2.5875295264	0.1226207	0.4624417	11.3460016	-51.7009439	0.0000000	5	0.854	6	0.9836	3	0.6382	6	1.0072
+A_92_P035118	3	2	2	10	1.4063	20.1741062	4.3777810454	0.2324464	0.5069494	0.0863209	84.9271020	0.0000000	10	1.3551	11	1.4363	10	1.3341	11	1.492
+A_92_P035118	3	4	10	8	0.9063	13.5647584	2.9435525728	0.1296273	0.4429836	11.9072611	58.1585016	0.0000000	7	0.8506	8	0.9832	5	0.7509	9	1.0316
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/qtlmap_15/test-data/output/qtl_out_5.txt	Fri Mar 18 05:51:39 2016 -0400
@@ -0,0 +1,6 @@
+A_92_P034794	1	2	10	2	0.1903	13.7851819	2.9913844723	0.1500800	0.4826392	1.3172075	37.9229818	0.0000000	1	0.0205	2	0.2714	1	0.0001	2	0.3136
+A_92_P034308	2	1	1	10	1.0811	21.5408069	4.6743550973	0.2277382	0.7592832	1.5834036	-33.7902103	0.0000000	10	0.994	11	1.2061	10	0.9663	11	1.2428
+A_92_P034308	2	2	3	18	2.1361	37.6966811	8.1801797987	0.4294746	0.7461673	0.5001206	-46.4689965	0.0000000	17	2.0979	18	2.1767	17	2.0704	18	2.1961
+A_92_P034308	2	4	6	15	1.6231	15.0777058	3.2718621586	0.1278544	0.7208327	0.6238438	-25.3129593	0.0000000	14	1.6037	15	1.7696	12	1.3838	15	1.8092
+A_92_P033825	3	1	5	12	1.2112	26.3566078	5.7193838926	0.2959435	0.6404193	5.3064385	75.0605964	0.0000000	12	1.1492	13	1.2967	12	1.124	13	1.3275
+A_92_P033667	4	1	1	10	1.0011	32.5164489	7.0560694113	0.2841753	0.6066141	14.4318293	-402.5391792	0.0000000	9	0.9597	10	1.0702	9	0.9144	10	1.1011
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/qtlmap_15/test-data/output/qtl_out_6.txt	Fri Mar 18 05:51:39 2016 -0400
@@ -0,0 +1,11 @@
+A_92_P033184	1	1	2	6	0.9061	14.8587743	3.2243540231	0.2333258	0.6091560	22.0542994	-38.6663227	0.0000000	5	0.8719	6	0.9577	5	0.8433	6	0.9883
+A_92_P033019	2	1	4	1	0.0001	18.0264218	3.9117335306	0.2358947	0.7043399	1.1338535	-36.1921190	0.0000000	1	0.0001	1	0.1049	1	0.0001	1	0.1658
+A_92_P033019	2	3	4	14	1.3767	24.4933746	5.3150622882	0.3512706	0.6952266	0.7481420	-44.9542340	0.0000000	13	1.3132	14	1.4571	13	1.291	14	1.4719
+A_92_P033019	2	4	8	9	1.0132	12.4174801	2.6945931817	0.1576451	0.7132070	1.5293308	-31.2505707	0.0000000	8	0.9674	10	1.0946	6	0.8291	10	1.1515
+A_92_P032694	3	1	7	8	0.6320	32.1699934	6.9808885678	0.2420005	0.6003624	24.9291265	344.4116975	0.0000000	7	0.5956	8	0.6784	7	0.5757	8	0.7048
+A_92_P032694	3	2	7	10	0.8764	13.4413200	2.91676644	0.0878881	0.5980498	25.7814583	206.5255165	0.0000000	9	0.7973	10	1.0197	5	0.4516	10	1.0602
+A_92_P032375	4	1	5	16	1.7032	16.9984527	3.6886642359	0.1302289	0.5128756	27.8335593	107.9491425	0.0000000	15	1.5695	16	1.7838	15	1.5206	16	1.7866
+A_92_P032375	4	2	7	7	0.5545	25.7188796	5.5809968732	0.1610310	0.4683558	29.9770539	119.3799447	0.0000000	6	0.5181	7	0.583	6	0.4944	7	0.6026
+A_92_P032375	4	3	8	1	0.1001	19.6244369	4.2585028073	0.1304073	0.4749124	32.9505567	-126.1800898	0.0000000	1	0.0263	2	0.1759	1	0.0001	2	0.2199
+A_92_P032375	4	4	8	5	0.5015	12.1700046	2.6408909982	0.0729679	0.4682935	31.2541491	94.9172785	0.0000000	4	0.4357	5	0.5812	4	0.4057	5	0.6382
+A_92_P032375	4	5	9	8	1.2252	11.9054995	2.5834933915	0.0724122	0.4722985	30.5643015	83.1749874	0.0000000	7	1.1385	9	1.3136	7	1.083	9	1.3852
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/qtlmap_15/test-data/output/qtl_out_7.txt	Fri Mar 18 05:51:39 2016 -0400
@@ -0,0 +1,3 @@
+A_92_P031891	1	1	3	6	0.7129	12.1291440	2.632024248	0.1463481	0.4572059	3.3024336	22.7464054	0.0000000	6	0.6425	7	0.7575	5	0.6128	9	0.8513
+A_92_P031571	2	1	1	9	0.8188	15.5773107	3.3802764219	0.1576819	0.6595742	4.9462336	30.4289126	0.0000000	8	0.7654	9	0.9028	8	0.7266	9	0.9461
+A_92_P030934	4	1	1	12	1.3484	12.7269818	2.7617550506	0.1554477	0.3181084	11.0051898	1307.8971923	0.0000000	11	1.2068	12	1.4126	10	1.1262	12	1.4225
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/qtlmap_15/test-data/output/qtl_out_8.txt	Fri Mar 18 05:51:39 2016 -0400
@@ -0,0 +1,5 @@
+A_92_P030772	1	1	1	12	1.2884	14.6017579	3.1685814643	0.1322083	0.3547828	68.3702870	92.1827784	0.0000000	11	1.1967	12	1.3849	11	1.1334	12	1.4137
+A_92_P030772	1	2	2	8	1.1175	12.2942458	2.6678513386	0.0951207	0.3365067	55.8325996	91.5133766	0.0000000	7	1.0195	8	1.1608	6	1.0079	8	1.1701
+A_92_P029488	3	1	1	23	2.7504	12.7423639	2.7650929663	0.0886911	0.3771941	0.6115715	-170.6386723	0.0000000	22	2.6575	23	2.8791	21	2.6432	23	2.9422
+A_92_P029488	3	2	4	14	1.4567	15.7422210	3.416061957	0.1252436	0.3938654	0.8032518	-197.3601638	0.0000000	14	1.3938	15	1.5144	13	1.342	16	1.6101
+A_92_P029164	4	2	2	12	1.5405	22.4499094	4.8716303398	0.3269444	0.5618480	132.0731880	-1222.1310894	0.0000000	11	1.4693	12	1.6362	11	1.4302	12	1.6609
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/qtlmap_15/test-data/output/qtl_out_9.txt	Fri Mar 18 05:51:39 2016 -0400
@@ -0,0 +1,5 @@
+A_92_P028842	2	1	2	7	1.0904	28.2461323	6.1294107091	0.3118840	0.5439671	5.6068692	-54.5035913	0.0000000	7	1.0324	8	1.1416	7	1.0179	8	1.1585
+A_92_P028842	2	2	3	12	1.3680	18.5426079	4.0237459143	0.1741882	0.5155299	3.8667059	-33.5409799	0.0000000	11	1.3328	12	1.4349	11	1.3142	12	1.4792
+A_92_P028042	4	1	1	11	1.2671	38.7087949	8.3998084933	0.3305027	0.4144519	2.1621607	120.1256345	0.0000000	11	1.2357	11	1.2675	11	1.2082	11	1.2679
+A_92_P028042	4	2	1	14	1.4898	13.3623833	2.8996371761	0.1034618	0.3996348	4.3479198	-71.0505158	0.0000000	13	1.4431	14	1.547	10	1.123	14	1.5891
+A_92_P028042	4	4	9	10	1.4239	17.8301407	3.8691405319	0.1743896	0.4645963	0.1983911	73.9224765	0.0000000	9	1.3211	10	1.4971	9	1.2873	10	1.5309