diff --git a/script/trackrun.py b/script/trackrun.py
index 1cf6bf7..e6e79aa 100644
--- a/script/trackrun.py
+++ b/script/trackrun.py
@@ -38,7 +38,7 @@ def __init__(self):
 The command contains:
 pre: prepare the run folder by separating the tracks from the same locus
 clusterj:run the trackcluster in junction mode to get the isoforms and the counting
-cluster:run the trackcluster eon/intron intersection to get the isoforms and the counting
+cluster:run the trackcluster exon/intron intersection to get the isoforms and the counting
 desc: compare the novel isoforms with the existing annotations to give an description for the min edit distance between a novel isoform with its nearest reference annotation
 test: run test for installation 
 ------
@@ -63,7 +63,7 @@ def __init__(self):
 
     def map(self):
         parser = argparse.ArgumentParser(
-            description="minimap2 mapping/samtools process wrapper, will generate prefix_s.bam"
+            description="minimap2 mapping/samtools process wrapper, will generate prefix_s.bam\n"
                         "trackrun.py -t 32 -g gemone.fa -f sample.fastq"
         )
         parser.add_argument("-d", "--folder", default=os.getcwd(),
diff --git a/trackcluster/batch.py b/trackcluster/batch.py
index 8f9174d..088a607 100644
--- a/trackcluster/batch.py
+++ b/trackcluster/batch.py
@@ -21,7 +21,6 @@
 
 # bar for run
 
-
 #random.seed(1234)
 
 
diff --git a/trackcluster/cluster.py b/trackcluster/cluster.py
index 0b124a3..fd1b7a5 100644
--- a/trackcluster/cluster.py
+++ b/trackcluster/cluster.py
@@ -8,6 +8,8 @@
 make dendrogram for further plotting
 The input is a list of
 """
+import os
+
 # self import
 #from trackcluster.track import bigGenePred
 from trackcluster.utils import del_files
@@ -145,6 +147,8 @@ def cal_distance(bigg_list, intronweight=0.5, by="ratio", tmpdir=None):
     :param by: used to cal the distance between two bigg object, can be "ratio", "ratio_short", "length", "length_short"
     :return: D: distance matrix
     """
+    if tmpdir is None:
+        tmpdir=os.getcwd()
     bigg_list.sort(key=operator.attrgetter("chromStart"))
 
     for i in bigg_list:
diff --git a/trackcluster/tracklist.py b/trackcluster/tracklist.py
index 282a1fb..9e67279 100644
--- a/trackcluster/tracklist.py
+++ b/trackcluster/tracklist.py
@@ -157,6 +157,39 @@ def bigglist_to_bedfile(bigg_list,prefix=None, dir=None):
     return (out_exon, out_intron)
 
 
+def bigglist_to_plotbed(bigglist, out):
+    """
+    generate a bigglist which is ready for plotting from the bigglist
+    example as csv or tsv:
+        "","chrom","start","end","strand","isoform_name","tracknum","type"
+        "1","chrII",14647324,14647857,"-","ZC101.2g.1",1,"exon"
+        "2","chrII",14647919,14648142,"-","ZC101.2g.1",1,"exon"
+        "3","chrII",14648551,14648827,"-","ZC101.2g.1",1,"exon"
+        "4","chrII",14648885,14649435,"-","ZC101.2g.1",1,"exon"
+        "5","chrII",14649494,14649607,"-","ZC101.2g.1",1,"exon"
+        "6","chrII",14649650,14649798,"-","ZC101.2g.1",1,"exon"
+        "7","chrII",14649843,14650013,"-","ZC101.2g.1",1,"exon"
+        "8","chrII",14650060,14650279,"-","ZC101.2g.1",1,"exon"
+        "9","chrII",14650325,14650538,"-","ZC101.2g.1",1,"exon"
+        "10","chrII",14650593,14650898,"-","ZC101.2g.1",1,"exon"
+        "11","chrII",14651002,14651037,"-","ZC101.2g.1",1,"exon"
+        "12","chrII",14647858,14647918,"-","ZC101.2g.1",1,"intron"
+        "13","chrII",14648143,14648550,"-","ZC101.2g.1",1,"intron"
+        "14","chrII",14648828,14648884,"-","ZC101.2g.1",1,"intron"
+        "15","chrII",14649436,14649493,"-","ZC101.2g.1",1,"intron"
+        "16","chrII",14649608,14649649,"-","ZC101.2g.1",1,"intron"
+        "17","chrII",14649799,14649842,"-","ZC101.2g.1",1,"intron"
+        "18","chrII",14650014,14650059,"-","ZC101.2g.1",1,"intron"
+        "19","chrII",14650280,14650324,"-","ZC101.2g.1",1,"intron"
+        "20","chrII",14650539,14650592,"-","ZC101.2g.1",1,"intron"
+        "21","chrII",14650899,14651001,"-","ZC101.2g.1",1,"intron"
+        "22","chrII",14647324,14647857,"-","ZC101.2e.1",2,"exon"
+    :param bigglist:
+    :param out:
+    :return:
+    """
+
+
 def wrapper_bedtools_intersect2(bedfile1,bedfile2,outfile=None):
     """
     Using two bedfile to get the intsersection of pairs