diff --git a/scripts/check_circ_type.py b/scripts/check_circ_type.py
deleted file mode 100644
index 9a32014..0000000
--- a/scripts/check_circ_type.py
+++ /dev/null
@@ -1,69 +0,0 @@
-import sys
-import re
-
-igtf = sys.argv[1]
-circf = sys.argv[2]
-
-tid2exons = []
-tids = []
-
-with open(igtf) as gf:
-	pre_tid = ''
-	i = -1
-	for l in gf:
-		ll = l.strip().split()
-		if l[0] == '#' or ll[2] != 'exon':
-			continue
-		ch = ll[0]
-		st = ll[3]
-		end = ll[4]
-		tid = ll[13][1:-2]
-		#print ch,st,end,tid
-
-		if tid != pre_tid:
-			i += 1
-			tid2exons.append([])
-			tid2exons[i].append((ch, st, end))
-			tids.append(tid)
-		else:
-			tid2exons[i].append((ch, st, end))
-
-		pre_tid = tid
-
-print >>sys.stderr, 'Finished loading GTF, loaded {} transcripts. {}'.format(len(tid2exons), len(tids))
-
-with open(circf) as cf:
-	for l in cf:
-		ll = l.strip().split()
-		ch = ll[0]
-		st = '{}'.format(int(ll[1]) + 1)
-		end = ll[2]
-		tid = ll[6].split('.')[0]
-		
-		ind = -1
-		for i in range(len(tid2exons)):
-			if tids[i] == tid:
-				ind = i
-
-		if ind < 0:
-			print >>sys.stderr, 'tid {} not found!'.format(tid)
-
-		st_found = False
-		en_found = False
-		for e in tid2exons[ind]:
-			(ech, est, een) = e
-			if ech == ch and est == st:
-				st_found = True
-			if ech == ch and een == end:
-				en_found = True
-
-		if st_found and en_found:
-			typ = "BothIn"
-		elif st_found or en_found:
-			typ = "OneEnd"
-		else:
-			typ = "None"
-		
-		print '{}\t{}\t{}\t{}'.format(ch, st, end, typ)
-
-
diff --git a/scripts/convert_ciri.py b/scripts/circ_simulation_eval/convert_ciri.py
similarity index 100%
rename from scripts/convert_ciri.py
rename to scripts/circ_simulation_eval/convert_ciri.py
diff --git a/scripts/find_TP.py b/scripts/circ_simulation_eval/find_TP.py
similarity index 100%
rename from scripts/find_TP.py
rename to scripts/circ_simulation_eval/find_TP.py
diff --git a/scripts/missed_circ_classify.py b/scripts/circ_simulation_eval/missed_circ_classify.py
similarity index 100%
rename from scripts/missed_circ_classify.py
rename to scripts/circ_simulation_eval/missed_circ_classify.py
diff --git a/scripts/parse_simul_log.py b/scripts/circ_simulation_eval/parse_simul_log.py
similarity index 100%
rename from scripts/parse_simul_log.py
rename to scripts/circ_simulation_eval/parse_simul_log.py
diff --git a/scripts/read_dist.py b/scripts/circ_simulation_eval/read_dist.py
similarity index 100%
rename from scripts/read_dist.py
rename to scripts/circ_simulation_eval/read_dist.py
diff --git a/scripts/simulator_log_parser.py b/scripts/circ_simulation_eval/simulator_log_parser.py
similarity index 100%
rename from scripts/simulator_log_parser.py
rename to scripts/circ_simulation_eval/simulator_log_parser.py
diff --git a/scripts/compare_circExplorer.py b/scripts/compare_circExplorer.py
deleted file mode 100644
index 32335ef..0000000
--- a/scripts/compare_circExplorer.py
+++ /dev/null
@@ -1,60 +0,0 @@
-import sys
-
-my_report = sys.argv[1]
-ce_report = sys.argv[2]
-out_name = sys.argv[3]
-
-my_calls = {}
-ce_calls = {}
-
-def load_my_file(my_report):
-	with open(my_report) as mf:
-		for l in mf:
-			ll = l.strip().split()
-			chrom = ll[0]
-			spos = int(ll[1]) - 1
-			epos = int(ll[2])
-			support = int(ll[3])
-
-			my_calls[(chrom, spos, epos)] = support
-
-def load_ce_file(ce_report):
-	with open(ce_report) as ce:
-		for l in ce:
-			ll = l.strip().split()
-			chrom = ll[0]
-			spos = int(ll[1])
-			epos = int(ll[2])
-			lll = ll[3].split('/')
-			support = int(lll[1])
-			#support = int(ll[3])
-
-			ce_calls[(chrom, spos, epos)] = support
-
-# c1 - c2
-def compare(c1, c2, outf):
-	for k in c1.keys():
-		if k not in c2.keys():
-			(c, s, e) = k
-			print >>outf, '{}\t{}\t{}\t{}'.format(c, s, e, c1[k])
-
-def union(c1, c2, outf):
-	for k in c1.keys():
-		if k in c2.keys():
-			(c, s, e) = k
-			print >>outf, '{}\t{}\t{}\t{}\t{}'.format(c, s, e, c1[k], c2[k])
-
-load_my_file(my_report)
-load_ce_file(ce_report)
-
-us_adv = open('{}.us.adv'.format(out_name), 'w')
-compare(my_calls, ce_calls, us_adv)
-us_adv.close()
-
-ce_adv = open('{}.ce.adv'.format(out_name), 'w')
-compare(ce_calls, my_calls, ce_adv)
-ce_adv.close()
-
-both = open('{}.both'.format(out_name), 'w')
-union(my_calls, ce_calls, both)
-both.close()
diff --git a/scripts/compare_multiple_tools/Makefile b/scripts/compare_multiple_tools/Makefile
new file mode 100644
index 0000000..1f9d9e3
--- /dev/null
+++ b/scripts/compare_multiple_tools/Makefile
@@ -0,0 +1,25 @@
+all: OPTIMIZE_FLAGS build
+build: cleanexe mydiff 
+clean: cleanobj
+
+CXX         ?= g++
+
+INCS        := 
+CXXFLAGS    := -Wall $(INCS) -std=c++11
+LDFLAGS     := 
+
+MYOBJ        = diff.o 
+
+
+mydiff: $(MYOBJ)
+	$(CXX) -w $(MYOBJ) -o $@ ${LDFLAGS} ${LIBS}
+
+cleanobj:
+	@rm -f $(MYOBJ)
+
+cleanexe:
+	@rm -f mydiff
+
+OPTIMIZE_FLAGS:
+	$(eval CXXFLAGS = $(CXXFLAGS) -O3)
+
diff --git a/scripts/compare_multiple_tools/diff.cpp b/scripts/compare_multiple_tools/diff.cpp
new file mode 100644
index 0000000..59973fd
--- /dev/null
+++ b/scripts/compare_multiple_tools/diff.cpp
@@ -0,0 +1,162 @@
+#include <map>
+#include <iostream>
+#include <fstream>
+#include <vector>
+#include <algorithm>
+#include <sstream> 
+
+using namespace std;
+
+void separate_by_comma(string s, vector <string>& v) {
+	v.clear();
+	if (s.length() == 0)
+		return;
+
+	std::stringstream ss(s);
+	
+	while (ss.good()) {
+		string substr;
+		getline(ss, substr, ',');
+		v.push_back(substr);
+	}
+}
+
+// b: before
+// a: after
+void get_difference(string b, string a) {
+	vector <string> vb;
+	vector <string> va;
+
+	separate_by_comma(b, vb);
+	separate_by_comma(a, va);
+
+	sort(vb.begin(), vb.end());
+	sort(va.begin(), va.end());
+
+	vector <string> b_a(vb.size());
+	vector <string> a_b(va.size());
+
+	auto it_b_a = std::set_difference(vb.begin(), vb.end(), va.begin(), va.end(), b_a.begin());
+	auto it_a_b = std::set_difference(va.begin(), va.end(), vb.begin(), vb.end(), a_b.begin());
+
+	b_a.resize(it_b_a - b_a.begin());
+	a_b.resize(it_a_b - a_b.begin());
+
+	cout << "\t";
+	if (b_a.begin() == b_a.end())
+		cout << "-";
+	for (auto it = b_a.begin(); it != b_a.end(); ++it)
+		cout << *it << ",";
+
+	cout << "\t";
+	if (a_b.begin() == a_b.end())
+		cout << "-";
+	for (auto it = a_b.begin(); it != a_b.end(); ++it)
+		cout << *it << ",";
+}
+
+int main(int argc, char** argv) {
+	--argc;
+
+	if (argc < 2)
+		cerr << "Usage: " << argv[0] << " FILE1 FILE2 [FILE3 FILE4]\n";
+
+    ifstream fin1;
+    ifstream fin2;
+    ifstream fin3;
+    ifstream fin4;
+
+    fin1.open(argv[1]);
+    fin2.open(argv[2]);
+    fin3.open(argv[3]);
+	fin4.open(argv[4]);
+
+    string a, b, c, rs;
+    int d;
+    map <string, vector<int> > mymap;
+    map <string, pair<string, string> > rsmap;
+    while (fin1 >> a >> b >> c >> d >> rs) {
+        mymap[a+'-'+b+'-'+c] = {d, 0, 0, 0};
+		rsmap[a+'-'+b+'-'+c] = {rs, ""};
+    }
+
+    while (fin2 >> a >> b >> c >> d >> rs) {
+        if (mymap.find(a+'-'+b+'-'+c) != mymap.end()) {
+            mymap[a+'-'+b+'-'+c][1] = d;
+			rsmap[a+'-'+b+'-'+c].second = rs;
+        }
+        else {
+            mymap[a+'-'+b+'-'+c] = {0, d, 0, 0};
+			rsmap[a+'-'+b+'-'+c] = {"", rs};
+        }
+    }
+
+    while (fin3 >> a >> b >> c >> d) {
+        if (mymap.find(a+'-'+b+'-'+c) != mymap.end()) {
+            mymap[a+'-'+b+'-'+c][2] = d;
+        }
+    }
+
+	int ce2b;
+    while (fin4 >> a >> ce2b >> c >> d) {
+		b = to_string(ce2b+1);
+        if (mymap.find(a+'-'+b+'-'+c) != mymap.end()) {
+            mymap[a+'-'+b+'-'+c][3] = d;
+        }
+    }
+
+    map <string, pair<int, int> >::iterator it;
+    int increased = 0, decreased = 0, not_changed = 0, disapeared = 0, newly_added = 0;
+
+	auto rsit = rsmap.begin();
+    for (auto it = mymap.begin(); it != mymap.end(); ++it) {
+        int bb = it->second[0];
+        int aa = it->second[1];
+
+		int ciri = it->second[2];
+		int ce2 = it->second[3];
+
+        if (bb - aa == 0) {
+            not_changed++;
+            cout << "[NC]\t";
+        }
+        else if (bb < aa) {
+            if (bb == 0) {
+                newly_added++;
+                cout << "[NA]\t";
+            }
+            else {
+                increased++;
+                cout << "[++]\t";
+            }
+        }
+        else {
+            if (aa == 0) {
+                disapeared++;
+                cout << "[DI]\t";
+            }
+            else {
+                decreased++;
+                cout << "[--]\t";
+            }
+        }
+
+        cout << it->first << "\t" << bb << "\t" << aa;
+		if (argc > 2)
+        	cout << "\t" << ciri << "\t" << ce2;
+
+		get_difference(rsit->second.first, rsit->second.second);
+
+		cout << endl;
+
+		++rsit;
+
+    }
+
+	fin1.close();
+	fin2.close();
+	fin3.close();
+	fin4.close();
+
+    return 0;
+}
diff --git a/scripts/compare_sam.py b/scripts/compare_sam.py
deleted file mode 100644
index 1b31365..0000000
--- a/scripts/compare_sam.py
+++ /dev/null
@@ -1,107 +0,0 @@
-import sys
-
-sam_fname = sys.argv[1]
-myout_fname = sys.argv[2]
-
-SAMSIZE = 40000000
-LOCDIFTH = 10
-
-sam_locs = [ 0, 0 ]
-sam_locs[0] = [ ]
-sam_locs[1] = [ ]
-
-exact_locs = [ ]
-scat = [ ]
-
-for i in range(SAMSIZE):
-	sam_locs[0].append([])
-	sam_locs[1].append([])
-	exact_locs.append(-1)
-	scat.append(0)
-
-is_r1 = 0
-read = 0
-
-print "Loading sam file..."
-with open(sam_fname) as sf:
-	for l in sf:
-		ll = l.strip().split()
-		rname = int(ll[0].split('.')[1])
-		chrom = ll[2]
-		if chrom == "*":
-			continue
-		
-		read += 1
-		if (read % 200000) == 0:
-			print "# {} lines".format(read)
-		flag = int(ll[1])
-		spos = int(ll[3])
-		
-		cat = ll[-1]
-		scat[rname] = int(cat[-1])
-
-		is_r1 = (flag & 64) / 64
-		sam_locs[is_r1][rname].append( (chrom, spos) )
-
-#print "R1: ", sam_locs[1]
-#print "R2: ", sam_locs[0]
-
-print "Size: ", len(sam_locs[0]) - sam_locs[0].count([]), len(sam_locs[1]) - sam_locs[1].count([])
-
-def closest_vacinity(chrom, p, l):
-	return min( [ abs (x - p) for (ch, x) in l if ch == chrom ] )
-
-# score of each mate:
-# 4: exact match
-# 1: in vacinity
-# 0: not matched
-def set_score(chrom, p, l):
-	cl = 2 * LOCDIFTH
-	
-	try:
-		cl = closest_vacinity(chrom, p, l)
-	except ValueError:
-		cl = LOCDIFTH + 1
-
-	if cl == 0:		#Exact match
-		return 4
-	elif cl <= LOCDIFTH:
-		return 1
-	else:
-		return 0
-
-def check_loc(rname, chrom, p1, p2):
-	s1 = 0
-	s2 = 0
-	
-	s1 += set_score(chrom, p1, sam_locs[1][rname])
-	s1 += set_score(chrom, p2, sam_locs[0][rname])
-
-	s2 += set_score(chrom, p2, sam_locs[1][rname])
-	s2 += set_score(chrom, p1, sam_locs[0][rname])
-
-	return max(s1, s2)
-
-read = 0
-print "Loading my output file..."
-with open(myout_fname) as mf:
-	for l in mf:
-		read += 1
-		if (read % 200000) == 0:
-			print "# {} reads".format(read)
-
-		ll = l.strip().split()
-		rname = int(ll[0].split('.')[1])
-		chrom = ll[1]
-		pos1 = int(ll[2])
-		pos2 = int(ll[10])
-		mtype = int(ll[-1])
-		
-		exact_locs[rname] = max(exact_locs[rname], check_loc(rname, chrom, pos1, pos2))
-
-print "Printing results..."
-for rname in range(len(exact_locs)):
-	if rname % 100000 == 0:
-		print "# {} reads".format(rname)
-	if exact_locs[rname] != -1:
-		print>> sys.stderr, rname, exact_locs[rname], "XC:i:{}".format(scat[rname])
diff --git a/scripts/count_exon.py b/scripts/count_exon.py
deleted file mode 100644
index 18cf495..0000000
--- a/scripts/count_exon.py
+++ /dev/null
@@ -1,27 +0,0 @@
-import sys
-
-gtf_fname = sys.argv[1]
-
-genes = {}
-enums = []
-
-max_enum = 0
-
-with open(gtf_fname) as gf:
-	for l in gf:
-		if l[0] == '#':
-			continue
-		ll = l.strip().split()
-		if ll[2] == "gene":
-			enums.append(max_enum)
-			max_enum = 0
-		if ll[2] != "exon":
-			continue
-		exon_num = int(ll[13][1:-2])
-		max_enum = max(max_enum, exon_num)
-
-enums.append(max_enum)
-
-print enums
-print len(enums)
-print sum(enums)
diff --git a/scripts/count_n.py b/scripts/count_n.py
deleted file mode 100644
index 36b3300..0000000
--- a/scripts/count_n.py
+++ /dev/null
@@ -1,25 +0,0 @@
-import sys
-
-seq_fname = sys.argv[1]
-
-high_th = 50
-
-with open(seq_fname) as sf:
-	rname = '?'
-	seq = ''
-	highn = 0
-	for l in sf:
-		if l[0] == '>':
-			if rname != l[1:]:
-				if rname != '?':
-					print '{}\t{}\t{}\t{}'.format(rname.strip(), len(seq), seq.count('N'), 100.0 * seq.count('N') / len(seq))
-					if 100.0 * seq.count('N') / len(seq) >= high_th:
-						highn += 1
-				rname = l[1:]
-				seq = ''
-			continue
-		seq += l.strip()
-	print '{}\t{}\t{}\t{}'.format(rname.strip(), len(seq), seq.count('N'), 100.0 * seq.count('N') / len(seq))
-	if 100.0 * seq.count('N') / len(seq) >= high_th:
-		highn += 1
-	print '>= {}% N:\t{}'.format(high_th, highn)
diff --git a/scripts/err_sc_dist.py b/scripts/evaluation/err_sc_dist.py
similarity index 100%
rename from scripts/err_sc_dist.py
rename to scripts/evaluation/err_sc_dist.py
diff --git a/scripts/evaluate.py b/scripts/evaluation/evaluate.py
similarity index 100%
rename from scripts/evaluate.py
rename to scripts/evaluation/evaluate.py
diff --git a/scripts/evaluate2.py b/scripts/evaluation/evaluate2.py
similarity index 100%
rename from scripts/evaluate2.py
rename to scripts/evaluation/evaluate2.py
diff --git a/scripts/filter_inversion.py b/scripts/filter_inversion.py
deleted file mode 100644
index b2cc130..0000000
--- a/scripts/filter_inversion.py
+++ /dev/null
@@ -1,75 +0,0 @@
-import sys
-import re
-
-def get_len(cigar):
-	mysum = 0
-	ind = 0
-	lens = re.split("M|D|N|=|X|I|S|H|P", cigar)
-	if lens[-1] == '':
-		del lens[-1]
-
-	#print cigar
-	#print lens
-	for x in lens:
-		ind += len(x)
-		if cigar[ind] in 'MDN=X':
-			mysum += int(x)
-		ind += 1
-	return mysum
-
-chimeric_sam = sys.argv[1]	# sorted
-out_file = sys.argv[2]
-
-inv_rname = open(out_file + '.rname', 'w')
-inv_sam = open(out_file + '.inv.sam', 'w')
-bsj_sam = open(out_file + '.bsj.sam', 'w')
-
-with open(chimeric_sam) as sf:
-	mates = { }
-	for l in sf:
-		if l[0] == '@':
-			continue
-
-		ll = l.strip().split()
-		rname = ll[0]
-		flag = int(ll[1])
-		chrom = ll[2]
-		spos = int(ll[3])
-		cigar = ll[5]
-		seq = ll[9]
-
-		rlen = get_len(cigar)
-		#print rlen
-
-		if rname not in mates.keys():
-			mates[rname] = [ (flag, chrom, seq, l.strip()) ]
-		else:
-			mates[rname].append( (flag, chrom, seq, l.strip()) )
-
-for rname in mates.keys():
-	primaries = []
-	for x in mates[rname]:
-		if x[0] < 256:
-			primaries.append(x)
-
-	inver = True
-	for x in mates[rname]:
-		if x[0] < 256:
-			continue
-
-		for pri in primaries:
-			if x[2] == pri[2]:
-				inver = False
-		
-		if inver:
-			print 'INV', rname
-			print >> inv_rname, rname
-			for y in mates[rname]:
-				print >> inv_sam, y[3]
-
-		else:
-			print 'ORD', rname
-			print >> inv_rname, rname
-			for y in mates[rname]:
-				print >> inv_sam, y[3]
-
diff --git a/scripts/filter_nonexon.py b/scripts/filter_nonexon.py
deleted file mode 100644
index e7a2d62..0000000
--- a/scripts/filter_nonexon.py
+++ /dev/null
@@ -1,111 +0,0 @@
-import sys
-import re
-
-th = 9
-
-def intersect(chrom, beg, end, echrom, ebeg, eend):
-	if chrom != echrom:
-		if beg < ebeg:
-			return 1
-		else:
-			return -1
-	if end < ebeg:
-		return -1
-	if beg > eend:
-		return 1
-	
-	if beg < ebeg:
-		if ebeg - beg < th:
-			return 0
-		else:
-			return -1
-	if end > eend:
-		if end - eend < th:
-			return 0
-		else:
-			return 1
-	return 0
-
-def check_record(chrom, beg, end, last_chrom, last_beg, last_end, gtff):
-	int_res = intersect(chrom, beg, end, last_chrom, last_beg, last_end)
-	#print 'LAST check:', int_res, chrom, beg, end, last_chrom, last_beg, last_end
-	if int_res == -1:
-		return False, (last_chrom, last_beg, last_end)
-
-	if int_res == 0:
-		return True, (last_chrom, last_beg, last_end)
-
-	for l in gtff:
-		if l[0] == '#':
-			continue
-		ll = l.strip().split()
-		if ll[2] != 'exon':
-			continue
-	
-		echrom = ll[0]
-		ebeg = int(ll[3])
-		eend = int(ll[4])
-	
-		int_res = intersect(chrom, beg, end, echrom, ebeg, eend)
-		#print 'XXXX:', int_res, chrom, beg, end, echrom, ebeg, eend
-
-		if int_res == -1:
-			return False, (echrom, ebeg, eend)
-
-		if int_res == 0:
-			return True, (echrom, ebeg, eend)
-
-	return False, ('-1', -1, -1)
-
-def get_len(cigar):
-	mysum = 0
-	ind = 0
-	lens = re.split("M|D|N|=|X|I|S|H|P", cigar)
-	if lens[-1] == '':
-		del lens[-1]
-
-	#print cigar
-	#print lens
-	for x in lens:
-		ind += len(x)
-		if cigar[ind] in 'MDN=X':
-			mysum += int(x)
-		ind += 1
-	return mysum
-
-chimeric_sam = sys.argv[1]
-gtf_file = sys.argv[2]
-out_file = sys.argv[3]
-
-nonexon_rname = open(out_file + '.rname', 'w')	# sorted
-nonexon_sam = open(out_file + '.sam', 'w')	# sorted
-
-with open (gtf_file) as gtff:
-	with open(chimeric_sam) as sf:
-		last_chrom = '0'
-		last_beg = 1000000000
-		last_end = 1000000001
-		for l in sf:
-			if l[0] == '@':
-				continue
-
-			ll = l.strip().split()
-			rname = ll[0]
-			chrom = ll[2]
-			spos = int(ll[3])
-			cigar = ll[5]
-			rlen = get_len(cigar)
-			#print rlen
-
-			res, (ch, b, e) = check_record(chrom, spos, spos + rlen - 1, last_chrom, last_beg, last_end, gtff)
-			if not res:
-				print >> nonexon_rname, rname
-				print 'NO', rname
-				print >> nonexon_sam, l.strip()
-
-			else:
-				print 'YES', rname
-
-			last_chrom = ch
-			last_beg = b
-			last_end = e
diff --git a/scripts/gene_model.py b/scripts/gene_model.py
deleted file mode 100755
index 79afda1..0000000
--- a/scripts/gene_model.py
+++ /dev/null
@@ -1,124 +0,0 @@
-#!/usr/bin/env python
-#-*- encoding:utf-8 -*-
-#
-
-
-import sys, os, math
-from operator import itemgetter
-
-class Usage(Exception):
-	def __init__(self, msg):
-		self.msg = msg
-
-def usage():
-	print '\nUsage: python ' + sys.argv[0] + ' GTF'
-	sys.exit(-1)
-
-####################
-def overlap_interval( s1, e1, s2, e2):
-	ol = 0
-	if ( s1 <= s2 and e2 <= s2 ):
-		ol = e2 - s2 + 1
-	elif ( s2 <= s1 and e1 <= e2 ):
-		ol = e1 - s1 + 1
-	elif ( s2 <= s1 and s1 <= e2 ):
-		ol = e2 - s1 + 1
-	elif ( s1 <= s2 and s2 <= e1 ):
-		ol = e1 - s2 + 1
-	return ol
-
-########## Load GTF with versioon >=75 ##########
-##### 
-# chr -> list of sorted genes: start, end, list_of_isoforms
-# an isoform is a list of exons
-def load_GTF( gtf_file ):
-	gene_dict = {} # from chromosome to a list of sorted gene record
-	gene_list = [] # sorted exon record for a gene
-
-	# tmp struc for exon for a gene
-	coor_dict = {}
-	coor_list = []
-	iso_list  = [] # for promotor
-	
-	gene_name = ""
-	ref = ""
-	start = 0
-	end = 0
-	
-	sr = open( gtf_file, 'r' )
-	for line in sr:
-		if ("#" == line[0]):	
-			continue
-		z_list = line.split("\t")
-		# ignoring all pacthed records 
-		if (  2 < len(z_list[0])):
-			continue
-
-		if ( ref != z_list[0] ):	# storing the list of all genes into a ref entry
-			if 0 < len(coor_list):
- 				iso_list.append( [s, e, coor_list ])
-			if 0 < len(iso_list):
-				iso_list.sort( key = itemgetter(0,1) )
-				gene_list.append( [ ref, start, end, gene_name, iso_list ])
-			if ( 0 < len(gene_list) ):
-				gene_list.sort( key=itemgetter(1,2) )
-				gene_dict[ ref ] = gene_list
-				print "Loading Chromosome " + ref + " with " + str(len(gene_list))  + " genes"
-			
-			gene_list = []
-			iso_list  = []
-			coor_list = []
-			start = 0
-			end = 0
-			ref = z_list[0]
-			print "Starting Chromosome " +ref
-
-		if ("gene" == z_list[2]):
-			if 0 < len(coor_list):
-				iso_list.append( [ s, e, coor_list ] )
-			if 0 < len(iso_list):
-				iso_list.sort( key = itemgetter(0,1) )
-				gene_list.append( [ ref, start, end, gene_name, iso_list ])
-			coor_list = []
-			iso_list  = []
-			coor_dict = {}
-
-			gene_name = line.split("\"")[5]
-			start = int(z_list[3])
-			end   = int(z_list[4])
-		
-		if ("transcript" == z_list[2]):
-			if 0 < len(coor_list):
-				iso_list.append( [ s, e, coor_list ] )
-			s = int(z_list[3])
-			e = int(z_list[4])
-			coor_list = []
-		elif ("exon" == z_list[2]):
-			coor_list.append( [ int(z_list[3]), int(z_list[4]) ] )	
-
-	sr.close()
-
-	# Last exon
-	if 0 < len(coor_list):
-		iso_list.append( [ s, e, coor_list ] )
-	if 0 < len(iso_list):
-		iso_list.sort( key = itemgetter(0,1) )
-		#iso_list.sort(key = itemgetter(1,2) )
-		gene_list.append( [ ref, start, end, gene_name, iso_list ])
-	if ( 0 < len(gene_list) ):
-		gene_list.sort( key=itemgetter(1,2) )
-		gene_dict[ ref ] = gene_list
-		print "Loading Chromosome " + ref + " with " + str(len(gene_list))  + " genes"
-
-	return gene_dict
-#########################	
-def main():
-	args = sys.argv[1:]
-	if len(args) != 1:
-		usage()
-
-	gene_model = load_GTF( sys.argv[1] )
-		
-#########################	
-if __name__ == "__main__":
-	sys.exit(main())
diff --git a/scripts/gmc.py b/scripts/gmc.py
deleted file mode 100644
index df31ff1..0000000
--- a/scripts/gmc.py
+++ /dev/null
@@ -1,88 +0,0 @@
-import sys
-
-gtf_fname = sys.argv[1]
-junc_fname = sys.argv[2]
-
-th = 5
-exons = [ ]
-starts = { }
-ends = { }
-
-def valid_start_bsj(exons, chrom, start, end):
-	for exon in exons:
-		if chrom != exon[0]:
-			continue
-		if abs(exon[1] - start) <= th:
-			return True
-	return False
-
-def valid_end_bsj(exons, chrom, start, end):
-	for exon in exons:
-		if chrom != exon[0]:
-			continue
-		if abs(exon[2] - end) <= th:
-			return True
-	return False
-
-def find_target(mlist, beg, end, target):
-	if end - beg <= 0:
-		return False
-	mid = (beg + end) / 2
-	if target > mlist[mid] + th:
-		return find_target(mlist, mid+1, end, target)
-	if target < mlist[mid] - th:
-		return find_target(mlist, beg, mid, target)
-
-	# abs(mlist[mid] - target) < th
-	return True
-
-with open(gtf_fname) as gf:
-	for l in gf:
-		if l[0] == '#':
-			continue
-		
-		l = l.strip().split()
-		type = l[2]
-		if type != 'exon':
-			continue
-
-		chrom = l[0]
-		if chrom not in starts.keys():
-			starts[chrom] = []
-		if chrom not in ends.keys():
-			ends[chrom] = []
-
-		start = int(l[3])
-		end = int(l[4])
-		exons.append((chrom, start, end))
-		starts[chrom].append(start)
-		ends[chrom].append(end)
-
-#print exons
-for ch in starts.keys():
-	starts[ch].sort()
-	ends[ch].sort()
-
-with open(junc_fname) as jf:
-	line = 0
-	for ll in jf:
-		if line % 1000 == 0:
-			print >>sys.stderr, line
-		line += 1
-		ll = ll.strip()
-		l = ll.split()
-		if len(l) < 9:
-			continue
-		chrom = l[1]
-		start = int(l[2])
-		end = int(l[3])
-		if not find_target(ends[chrom], 0, len(ends[chrom]), end):
-			continue
-
-		chrom = l[5]
-		start = int(l[6])
-		end = int(l[7])
-		#if valid_start_bsj(exons, chrom, start, end):
-		if find_target(starts[chrom], 0, len(starts[chrom]), start):
-			print ll
-
diff --git a/scripts/gtf_mod.py b/scripts/gtf_mod.py
deleted file mode 100644
index 18c38b9..0000000
--- a/scripts/gtf_mod.py
+++ /dev/null
@@ -1,64 +0,0 @@
-import re
-import sys
-
-fname = sys.argv[1]
-lens = [0,
-		0,	#chr 1
-		81195210 + 78077248 + 59128983 + 3,
-		81195210 + 78077248 + 59128983 + 243199373 + 63025520 + 48129895 + 51304566 + 7,
-		81195210 + 78077248 + 59128983 + 243199373 + 63025520 + 48129895 + 51304566 + 198022430 + 8,
-		0,
-		180915260 + 1,
-		180915260 + 171115067 + 2,
-		180915260 + 171115067 + 159138663 + 3,
-		180915260 + 171115067 + 159138663 + 146364022 + 4,
-		249250621 + 1,
-		249250621 + 135534747 + 2,
-		249250621 + 135534747 + 135006516 + 3,
-		249250621 + 135534747 + 135006516 + 133851895 + 4,
-		249250621 + 135534747 + 135006516 + 133851895 + 115169878 + 5,
-		249250621 + 135534747 + 135006516 + 133851895 + 115169878 + 107349540 + 6,
-		249250621 + 135534747 + 135006516 + 133851895 + 115169878 + 107349540 + 102531392 + 7,
-		0,
-		81195210 + 1,
-		81195210 + 78077248 + 2,
-		81195210 + 78077248 + 59128983 + 243199373 + 4,
-		81195210 + 78077248 + 59128983 + 243199373 + 63025520 + 5,
-		81195210 + 78077248 + 59128983 + 243199373 + 63025520 + 48129895 + 6,
-		180915260 + 171115067 + 159138663 + 146364022 + 141213431 + 5,						#MT
-		180915260 + 171115067 + 159138663 + 146364022 + 141213431 + 16569 + 6,				#X
-		180915260 + 171115067 + 159138663 + 146364022 + 141213431 + 16569 + 155270560 + 7	#Y
-		]
-
-ch2int = { str(x): x for x in range(1, 23) }
-ch2int["MT"] = 23
-ch2int["X"] = 24
-ch2int["Y"] = 25
-#print ch2int
-
-with open(fname, "r") as f:
-	for l in f:
-		l = l.strip();
-		if l[0] == "#":
-			print l
-			continue
-
-		ll = re.split("\t", l)
-
-		if ll[0] not in ch2int.keys():
-			print l
-			continue
-		ch = ch2int[ll[0]]
-	
-		st = int(ll[3])
-		end = int(ll[4])
-		new_contig = ""
-		if ch in [1, 10, 11, 12, 13, 14, 15, 16]:
-			new_contig = "1"
-		elif ch in [2, 3, 4, 17, 18, 19, 20, 21, 22]:
-			new_contig = "2"
-		else:
-			new_contig = "3"
-				
-		print "\t".join( [ new_contig, ll[1], ll[2], str(st + lens[ch]), str(end + lens[ch]) ] + ll[5:] )
-
diff --git a/scripts/make_bed.py b/scripts/make_bed.py
deleted file mode 100644
index a9daa2b..0000000
--- a/scripts/make_bed.py
+++ /dev/null
@@ -1,38 +0,0 @@
-import sys
-import re
-
-def get_len(cigar):
-	mysum = 0
-	ind = 0
-	lens = re.split("M|D|N|=|X|I|S|H|P", cigar)
-	if lens[-1] == '':
-		del lens[-1]
-
-	#print cigar
-	#print lens
-	for x in lens:
-		ind += len(x)
-		if cigar[ind] in 'MDN=X':
-			mysum += int(x)
-		ind += 1
-	return mysum
-
-chimeric_sam = sys.argv[1]
-bed_out = sys.argv[2]
-
-bedf = open(bed_out, 'w')
-
-with open(chimeric_sam) as sf:
-	for l in sf:
-		if l[0] == '@':
-			continue
-
-		ll = l.strip().split()
-		rname = ll[0]
-		chrom = ll[2]
-		spos = int(ll[3])
-		cigar = ll[5]
-		rlen = get_len(cigar)
-		#print rlen
-
-		print >>bedf, '{}\t{}\t{}\t{}'.format(chrom, spos-2, spos+rlen, rname)