Mercurial > repos > iuc > cwpair2

changeset 6:c4b926c9831c draft default tip

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cwpair2 commit ca66053a0d915edba3d7f1d4ce014718e7f4f0f2
author iuc
date Thu, 02 May 2019 08:30:22 -0400
parents 71188f3f4b76
children
files cwpair2.py cwpair2.xml cwpair2_macros.xml cwpair2_util.py test-data/closest_d_output2.tabular test-data/closest_mp_output1.gff test-data/closest_mp_output2.gff test-data/closest_o_output2.tabular test-data/cwpair2_input1.gff test-data/largest_d_output2.tabular test-data/largest_mp_output1.gff test-data/largest_mp_output2.gff test-data/largest_o_output2.tabular test-data/mode_d_output2.tabular test-data/mode_mp_output1.gff test-data/mode_mp_output2.gff test-data/mode_o_output2.tabular test-data/statistics1.tabular test-data/statistics2.tabular
diffstat 19 files changed, 2218 insertions(+), 1396 deletions(-) [+]
line wrap: on
line diff
--- a/cwpair2.py	Mon Nov 06 23:19:50 2017 -0500
+++ b/cwpair2.py	Thu May 02 08:30:22 2019 -0400
@@ -62,7 +62,7 @@
         by_file[path].append(stats)
     # Write tabular statistics file.
     keys = ['fname', 'final_mode', 'preview_mode', 'perc95', 'paired', 'orphans']
-    statistics_out = csv.writer(open(args.statistics_output, 'wt'), delimiter='\t')
+    statistics_out = csv.writer(open(args.statistics_output, 'wt'), delimiter='\t', lineterminator="\n")
     statistics_out.writerow(keys)
     for file_path, statistics in by_file.items():
         for stats in statistics:
--- a/cwpair2.xml	Mon Nov 06 23:19:50 2017 -0500
+++ b/cwpair2.xml	Thu May 02 08:30:22 2019 -0400
@@ -1,5 +1,5 @@
 <?xml version="1.0"?>
-<tool id="cwpair2" name="CWPair2" version="@WRAPPER_VERSION@.0">
+<tool id="cwpair2" name="CWPair2" version="1.1.1">
     <description>find matched pairs and unmatched orphans</description>
     <macros>
         <import>cwpair2_macros.xml</import>
@@ -83,9 +83,9 @@
             <param name="output_files" value="matched_pair" />
             <output name="statistics_output" file="statistics1.tabular" ftype="tabular" />
             <output_collection name="MP" type="list">
-                <element name="data_MP_closest_f0u25d100_on_data_1.gff" file="closest_mp_output1.gff" ftype="gff" compare="contains"/>
-                <element name="data_MP_largest_f0u25d100_on_data_1.gff" file="largest_mp_output1.gff" ftype="gff" compare="contains"/>
-                <element name="data_MP_mode_f0u25d100_on_data_1.gff" file="mode_mp_output1.gff" ftype="gff" compare="contains"/>
+                <element name="data_MP_closest_f0u25d100_on_data_1.gff" file="closest_mp_output1.gff" ftype="gff" />
+                <element name="data_MP_largest_f0u25d100_on_data_1.gff" file="largest_mp_output1.gff" ftype="gff" />
+                <element name="data_MP_mode_f0u25d100_on_data_1.gff" file="mode_mp_output1.gff" ftype="gff" />
             </output_collection>
         </test>
         <test>
@@ -106,19 +106,19 @@
                 <element name="histogram_P_mode_f0u50d100_on_data_1.pdf" file="magic.pdf" ftype="pdf" compare="contains" />
             </output_collection>
             <output_collection name="D" type="list">
-                <element name="data_D_closest_f0u50d100_on_data_1.tabular" file="closest_d_output2.tabular" ftype="tabular" compare="contains"/>
-                <element name="data_D_largest_f0u50d100_on_data_1.tabular" file="largest_d_output2.tabular" ftype="tabular" compare="contains"/>
-                <element name="data_D_mode_f0u50d100_on_data_1.tabular" file="mode_d_output2.tabular" ftype="tabular" compare="contains"/>
+                <element name="data_D_closest_f0u50d100_on_data_1.tabular" file="closest_d_output2.tabular" ftype="tabular" />
+                <element name="data_D_largest_f0u50d100_on_data_1.tabular" file="largest_d_output2.tabular" ftype="tabular" />
+                <element name="data_D_mode_f0u50d100_on_data_1.tabular" file="mode_d_output2.tabular" ftype="tabular" />
             </output_collection>
             <output_collection name="O" type="list">
-                <element name="data_O_closest_f0u50d100_on_data_1.tabular" file="closest_o_output2.tabular" ftype="tabular" compare="contains"/>
-                <element name="data_O_largest_f0u50d100_on_data_1.tabular" file="largest_o_output2.tabular" ftype="tabular" compare="contains"/>
-                <element name="data_O_mode_f0u50d100_on_data_1.tabular" file="mode_o_output2.tabular" ftype="tabular" compare="contains"/>
+                <element name="data_O_closest_f0u50d100_on_data_1.tabular" file="closest_o_output2.tabular" ftype="tabular" />
+                <element name="data_O_largest_f0u50d100_on_data_1.tabular" file="largest_o_output2.tabular" ftype="tabular" />
+                <element name="data_O_mode_f0u50d100_on_data_1.tabular" file="mode_o_output2.tabular" ftype="tabular" />
             </output_collection>
             <output_collection name="MP" type="list">
-                <element name="data_MP_closest_f0u50d100_on_data_1.gff" file="closest_mp_output2.gff" ftype="gff" compare="contains"/>
-                <element name="data_MP_largest_f0u50d100_on_data_1.gff" file="largest_mp_output2.gff" ftype="gff" compare="contains"/>
-                <element name="data_MP_mode_f0u50d100_on_data_1.gff" file="mode_mp_output2.gff" ftype="gff" compare="contains"/>
+                <element name="data_MP_closest_f0u50d100_on_data_1.gff" file="closest_mp_output2.gff" ftype="gff" />
+                <element name="data_MP_largest_f0u50d100_on_data_1.gff" file="largest_mp_output2.gff" ftype="gff" />
+                <element name="data_MP_mode_f0u50d100_on_data_1.gff" file="mode_mp_output2.gff" ftype="gff" />
             </output_collection>
         </test>
     </tests>
--- a/cwpair2_macros.xml	Mon Nov 06 23:19:50 2017 -0500
+++ b/cwpair2_macros.xml	Thu May 02 08:30:22 2019 -0400
@@ -1,9 +1,8 @@
 <?xml version='1.0' encoding='UTF-8'?>
 <macros>
-    <token name="@WRAPPER_VERSION@">1.1</token>
     <xml name="requirements">
         <requirements>
-            <requirement type="package" version="1.5.3">matplotlib</requirement>
+            <requirement type="package" version="3.0.3">matplotlib</requirement>
         </requirements>
     </xml>
     <xml name="citations">
@@ -14,7 +13,7 @@
                 title = {None},
                 year = {None},
                 eprint = {None},
-                url = {http://www.huck.psu.edu/content/research/independent-centers-excellence/center-for-eukaryotic-gene-regulation}
+                url = {http://www.cegr.psu.edu/}
             }</citation>
         </citations>
     </xml>
--- a/cwpair2_util.py	Mon Nov 06 23:19:50 2017 -0500
+++ b/cwpair2_util.py	Thu May 02 08:30:22 2019 -0400
@@ -15,7 +15,7 @@
 # Data output formats
 GFF_EXT = 'gff'
 TABULAR_EXT = 'tabular'
-# Statistics historgrams output directory.
+# Statistics histograms output directory.
 HISTOGRAM = 'H'
 # Statistics outputs
 FINAL_PLOTS = 'F'
@@ -46,7 +46,7 @@
 
     def get_bin(self, x):
         """
-        Returns the bin in which a data point falls
+        Returns the centre of the bin in which a data point falls
         """
         return self.start + (x - self.start) // self.binsize * self.binsize + self.binsize / 2.0
 
@@ -64,7 +64,12 @@
         return x, y
 
     def mode(self):
-        return max(self.dist.items(), key=lambda data: data[1])[0]
+        # There could be more than one mode for a frequency distribution,
+        # return the median of the modes to be consistent
+        max_frequency = max(self.dist.values())
+        modes = sorted(_[0] for _ in self.dist.items() if _[1] == max_frequency)
+        median_index = len(modes) // 2
+        return modes[median_index]
 
     def size(self):
         return sum(self.dist.values())
@@ -76,7 +81,7 @@
 
 
 def distance(peak1, peak2):
-    return (peak2[1] + peak2[2]) / 2 - (peak1[1] + peak1[2]) / 2
+    return (peak2[1] + peak2[2]) / 2.0 - (peak1[1] + peak1[2]) / 2.0
 
 
 def gff_row(cname, start, end, score, source, type='.', strand='.', phase='.', attrs={}):
@@ -92,9 +97,11 @@
 def parse_chromosomes(reader):
     # This version of cwpair2 accepts only gff format as input.
     chromosomes = {}
-    next(reader)
     for line in reader:
-        cname, junk, junk, start, end, value, strand, junk, junk = line
+        line = line.rstrip("\r\n")
+        if not line or line.startswith('#'):
+            continue
+        cname, _, _, start, end, value, strand, _, _ = line.split("\t")
         start = int(start)
         end = int(end)
         value = float(value)
@@ -118,7 +125,7 @@
     return values[int(len(values) * 0.95)]
 
 
-def filter(chromosomes, threshold=0.05):
+def peak_filter(chromosomes, threshold):
     """
     Filters the peaks to those above a threshold. Threshold < 1.0 is interpreted
     as a proportion of the maximum, >=1.0 as an absolute value.
@@ -139,7 +146,7 @@
 
 def all_pair_distribution(chromosomes, up_distance, down_distance, binsize):
     dist = FrequencyDistribution(-up_distance, down_distance, binsize=binsize)
-    for cname, data in chromosomes.items():
+    for data in chromosomes.values():
         watson, crick = split_strands(data)
         crick.sort(key=lambda data: float(data[1]))
         keys = make_keys(crick)
@@ -256,7 +263,6 @@
     output_orphans = output_files in ["all", "matched_pair_orphan", "matched_pair_orphan_detail"]
     # Keep track of statistics for the output file
     statistics = {}
-    input = csv.reader(open(dataset_path, 'rt'), delimiter='\t')
     fpath, fname = os.path.split(dataset_path)
     statistics['fname'] = '%s: data %s' % (method, str(galaxy_hid))
     statistics['dir'] = fpath
@@ -276,12 +282,13 @@
     def td_writer(output_type, extension, fname):
         # Returns a tab-delimited writer for a specified output.
         output_file_path = make_path(output_type, extension, fname)
-        return csv.writer(open(output_file_path, 'wt'), delimiter='\t')
+        return csv.writer(open(output_file_path, 'wt'), delimiter='\t', lineterminator="\n")
 
-    try:
-        chromosomes = parse_chromosomes(input)
-    except Exception:
-        stop_err('Unable to parse file "%s".\n%s' % (dataset_path, traceback.format_exc()))
+    with open(dataset_path, 'rt') as input:
+        try:
+            chromosomes = parse_chromosomes(input)
+        except Exception:
+            stop_err('Unable to parse file "%s".\n%s' % (dataset_path, traceback.format_exc()))
     if output_details:
         # Details
         detailed_output = td_writer('data_%s' % DETAILS, TABULAR_EXT, fname)
@@ -303,8 +310,8 @@
         statistics['graph_path'] = make_histogram_path(STATS_GRAPH, fname)
     statistics['perc95'] = perc95(chromosomes)
     if threshold > 0:
-        # Apply filter
-        filter(chromosomes, threshold)
+        # Apply peak_filter
+        peak_filter(chromosomes, threshold)
     if method == 'mode':
         freq = all_pair_distribution(chromosomes, up_distance, down_distance, binsize)
         mode = freq.mode()
--- a/test-data/closest_d_output2.tabular	Mon Nov 06 23:19:50 2017 -0500
+++ b/test-data/closest_d_output2.tabular	Thu May 02 08:30:22 2019 -0400
@@ -1,66 +1,67 @@
-chrom	start	end	value	strand	chrom	start	end	value	strand	midpoint	c-w reads sum	c-w distance (bp)
-chr1	87147	87167	3492.0	+	chr1	87158	87178	2039.0	-	87162	5531.0	11
-chr1	87	107	3211.0	+	chr1	139	159	993.0	-	123	4204.0	52
-chr1	48	68	2842.0	+	chr1	50	70	39.0	-	59	2881.0	2
-chr1	255	275	2810.0	+	chr1	261	281	1278.0	-	268	4088.0	6
-chr1	117	137	2163.0	+	chr1	176	196	14.0	-	156	2177.0	59
-chr1	86954	86974	1948.0	+	chr1	86991	87011	65.0	-	86982	2013.0	37
-chr1	169107	169127	1811.0	+	chr1	169064	169084	76.0	-	169095	1887.0	-43
-chr1	87171	87191	1436.0	+	chr1	87198	87218	2207.0	-	87194	3643.0	27
-chr1	201	221	1411.0	+	chr1	215	235	2611.0	-	218	4022.0	14
-chr1	229741	229761	1380.0	+	chr1	229757	229777	3151.0	-	229759	4531.0	16
-chr1	185076	185096	1309.0	+	chr1	185122	185142	62.0	-	185109	1371.0	46
-chr1	39081	39101	1268.0	+	chr1	39052	39072	82.0	-	39076	1350.0	-29
-chr1	92411	92431	1252.0	+	chr1	92411	92431	136.0	-	92421	1388.0	0
-chr1	203872	203892	1234.0	+	chr1	203835	203855	242.0	-	203863	1476.0	-37
-chr1	70776	70796	1148.0	+	chr1	70788	70808	998.0	-	70792	2146.0	12
-chr1	231	251	1146.0	+	chr1	279	299	1328.0	-	265	2474.0	48
-chr1	87098	87118	1125.0	+	chr1	87101	87121	1134.0	-	87109	2259.0	3
-chr1	6163	6183	1049.0	+	chr1	6254	6274	1076.0	-	6218	2125.0	91
-chr1	25246	25266	995.0	+	chr1	25345	25365	188.0	-	25305	1183.0	99
-chr1	101411	101431	973.0	+	chr1	101367	101387	1388.0	-	101399	2361.0	-44
-chr1	139213	139233	965.0	+	chr1	139228	139248	214.0	-	139230	1179.0	15
-chr1	87019	87039	769.0	+	chr1	87049	87069	422.0	-	87044	1191.0	30
-chr1	124318	124338	749.0	+	chr1	124275	124295	12.0	-	124306	761.0	-43
-chr1	348	368	699.0	+	chr1	373	393	200.0	-	370	899.0	25
-chr1	92543	92563	699.0	+	chr1	92571	92591	90.0	-	92567	789.0	28
-chr1	138868	138888	698.0	+	chr1	138864	138884	13.0	-	138876	711.0	-4
-chr1	307	327	685.0	+	chr1	323	343	486.0	-	325	1171.0	16
-chr1	6413	6433	682.0	+	chr1	6476	6496	567.0	-	6454	1249.0	63
-chr1	72781	72801	657.0	+	chr1	72810	72830	212.0	-	72805	869.0	29
-chr1	22571	22591	609.0	+	chr1	22569	22589	254.0	-	22580	863.0	-2
-chr1	65152	65172	575.0	+	chr1	65148	65168	43.0	-	65160	618.0	-4
-chr1	106034	106054	558.0	+	chr1	106041	106061	14.0	-	106047	572.0	7
-chr1	155028	155048	522.0	+	chr1	155111	155131	1051.0	-	155079	1573.0	83
-chr1	32449	32469	476.0	+	chr1	32497	32517	2.0	-	32483	478.0	48
-chr1	6706	6726	431.0	+	chr1	6702	6722	2.0	-	6714	433.0	-4
-chr1	113782	113802	420.0	+	chr1	113762	113782	296.0	-	113782	716.0	-20
-chr1	228633	228653	371.0	+	chr1	228691	228711	255.0	-	228672	626.0	58
-chr1	438	458	334.0	+	chr1	446	466	170.0	-	452	504.0	8
-chr1	72671	72691	304.0	+	chr1	72771	72791	406.0	-	72731	710.0	100
-chr1	170119	170139	284.0	+	chr1	170129	170149	373.0	-	170134	657.0	10
-chr1	92631	92651	260.0	+	chr1	92639	92659	2137.0	-	92645	2397.0	8
-chr1	136366	136386	248.0	+	chr1	136352	136372	117.0	-	136369	365.0	-14
-chr1	108624	108644	206.0	+	chr1	108579	108599	367.0	-	108611	573.0	-45
-chr1	45678	45698	198.0	+	chr1	45643	45663	295.0	-	45670	493.0	-35
-chr1	368	388	192.0	+	chr1	388	408	167.0	-	388	359.0	20
-chr1	682	702	168.0	+	chr1	634	654	151.0	-	668	319.0	-48
-chr1	59190	59210	168.0	+	chr1	59246	59266	397.0	-	59228	565.0	56
-chr1	134170	134190	151.0	+	chr1	134270	134290	508.0	-	134230	659.0	100
-chr1	55495	55515	125.0	+	chr1	55581	55601	831.0	-	55548	956.0	86
-chr1	512	532	101.0	+	chr1	468	488	468.0	-	500	569.0	-44
-chr1	39197	39217	101.0	+	chr1	39258	39278	261.0	-	39237	362.0	61
-chr1	229721	229741	84.0	+	chr1	229784	229804	615.0	-	229762	699.0	63
-chr1	116660	116680	74.0	+	chr1	116619	116639	699.0	-	116649	773.0	-41
-chr1	19216	19236	42.0	+	chr1	19191	19211	736.0	-	19213	778.0	-25
-chr1	230110	230130	42.0	+	chr1	230120	230140	2.0	-	230125	44.0	10
-chr1	31627	31647	40.0	+	chr1	31693	31713	450.0	-	31670	490.0	66
-chr1	180280	180300	38.0	+	chr1	180362	180382	59.0	-	180331	97.0	82
-chr1	98528	98548	34.0	+	chr1	98555	98575	88.0	-	98551	122.0	27
-chr1	230163	230183	23.0	+	chr1	230173	230193	33.0	-	230178	56.0	10
-chr1	173262	173282	11.0	+	chr1	173270	173290	535.0	-	173276	546.0	8
-chr1	230145	230165	8.0	+	chr1	230150	230170	7.0	-	230157	15.0	5
-chr1	95920	95940	5.0	+	chr1	95971	95991	684.0	-	95955	689.0	51
-chr1	199418	199438	5.0	+	chr1	199388	199408	805.0	-	199413	810.0	-30
-chr1	197489	197509	3.0	+	chr1	197562	197582	2.0	-	197535	5.0	73
-chr1	96908	96928	2.0	+	chr1	96911	96931	10.0	-	96919	12.0	3
+chrom	start	end	value	strand	chrom	start	end	value	strand	midpoint	c-w reads sum	c-w distance (bp)
+chr1	87147	87167	3492.0	+	chr1	87158	87178	2039.0	-	87162	5531.0	11.0
+chr1	87	107	3211.0	+	chr1	139	159	993.0	-	123	4204.0	52.0
+chr1	48	68	2842.0	+	chr1	50	70	39.0	-	59	2881.0	2.0
+chr1	255	275	2810.0	+	chr1	261	281	1278.0	-	268	4088.0	6.0
+chr1	117	137	2163.0	+	chr1	176	196	14.0	-	156	2177.0	59.0
+chr1	86954	86974	1948.0	+	chr1	86991	87011	65.0	-	86982	2013.0	37.0
+chr1	169107	169127	1811.0	+	chr1	169064	169084	76.0	-	169095	1887.0	-43.0
+chr1	87171	87191	1436.0	+	chr1	87198	87218	2207.0	-	87194	3643.0	27.0
+chr1	201	221	1411.0	+	chr1	215	235	2611.0	-	218	4022.0	14.0
+chr1	229741	229761	1380.0	+	chr1	229757	229777	3151.0	-	229759	4531.0	16.0
+chr1	185076	185096	1309.0	+	chr1	185122	185142	62.0	-	185109	1371.0	46.0
+chr1	39081	39101	1268.0	+	chr1	39052	39072	82.0	-	39076	1350.0	-29.0
+chr1	92411	92431	1252.0	+	chr1	92411	92431	136.0	-	92421	1388.0	0.0
+chr1	203872	203892	1234.0	+	chr1	203835	203855	242.0	-	203863	1476.0	-37.0
+chr1	70776	70796	1148.0	+	chr1	70788	70808	998.0	-	70792	2146.0	12.0
+chr1	231	251	1146.0	+	chr1	279	299	1328.0	-	265	2474.0	48.0
+chr1	87098	87118	1125.0	+	chr1	87101	87121	1134.0	-	87109	2259.0	3.0
+chr1	6163	6183	1049.0	+	chr1	6254	6274	1076.0	-	6218	2125.0	91.0
+chr1	25246	25266	995.0	+	chr1	25345	25365	188.0	-	25305	1183.0	99.0
+chr1	101411	101431	973.0	+	chr1	101367	101387	1388.0	-	101399	2361.0	-44.0
+chr1	139213	139233	965.0	+	chr1	139228	139248	214.0	-	139230	1179.0	15.0
+chr1	87019	87039	769.0	+	chr1	87049	87069	422.0	-	87044	1191.0	30.0
+chr1	124318	124338	749.0	+	chr1	124275	124295	12.0	-	124306	761.0	-43.0
+chr1	348	368	699.0	+	chr1	373	393	200.0	-	370	899.0	25.0
+chr1	92543	92563	699.0	+	chr1	92571	92591	90.0	-	92567	789.0	28.0
+chr1	138868	138888	698.0	+	chr1	138864	138884	13.0	-	138876	711.0	-4.0
+chr1	307	327	685.0	+	chr1	323	343	486.0	-	325	1171.0	16.0
+chr1	6413	6433	682.0	+	chr1	6476	6496	567.0	-	6454	1249.0	63.0
+chr1	72781	72801	657.0	+	chr1	72810	72830	212.0	-	72805	869.0	29.0
+chr1	22571	22591	609.0	+	chr1	22569	22589	254.0	-	22580	863.0	-2.0
+chr1	65152	65172	575.0	+	chr1	65148	65168	43.0	-	65160	618.0	-4.0
+chr1	106034	106054	558.0	+	chr1	106041	106061	14.0	-	106047	572.0	7.0
+chr1	155028	155048	522.0	+	chr1	155111	155131	1051.0	-	155079	1573.0	83.0
+chr1	32449	32469	476.0	+	chr1	32497	32517	2.0	-	32483	478.0	48.0
+chr1	6706	6726	431.0	+	chr1	6702	6722	2.0	-	6714	433.0	-4.0
+chr1	113782	113802	420.0	+	chr1	113762	113782	296.0	-	113782	716.0	-20.0
+chr1	228633	228653	371.0	+	chr1	228691	228711	255.0	-	228672	626.0	58.0
+chr1	438	458	334.0	+	chr1	446	466	170.0	-	452	504.0	8.0
+chr1	72671	72691	304.0	+	chr1	72771	72791	406.0	-	72731	710.0	100.0
+chr1	170119	170139	284.0	+	chr1	170129	170149	373.0	-	170134	657.0	10.0
+chr1	92631	92651	260.0	+	chr1	92639	92659	2137.0	-	92645	2397.0	8.0
+chr1	136366	136386	248.0	+	chr1	136352	136372	117.0	-	136369	365.0	-14.0
+chr1	108624	108644	206.0	+	chr1	108579	108599	367.0	-	108611	573.0	-45.0
+chr1	45678	45698	198.0	+	chr1	45643	45663	295.0	-	45670	493.0	-35.0
+chr1	368	388	192.0	+	chr1	388	408	167.0	-	388	359.0	20.0
+chr1	682	702	168.0	+	chr1	634	654	151.0	-	668	319.0	-48.0
+chr1	59190	59210	168.0	+	chr1	59246	59266	397.0	-	59228	565.0	56.0
+chr1	134170	134190	151.0	+	chr1	134270	134290	508.0	-	134230	659.0	100.0
+chr1	55495	55515	125.0	+	chr1	55581	55601	831.0	-	55548	956.0	86.0
+chr1	512	532	101.0	+	chr1	468	488	468.0	-	500	569.0	-44.0
+chr1	39197	39217	101.0	+	chr1	39258	39278	261.0	-	39237	362.0	61.0
+chr1	229721	229741	84.0	+	chr1	229784	229804	615.0	-	229762	699.0	63.0
+chr1	116660	116680	74.0	+	chr1	116619	116639	699.0	-	116649	773.0	-41.0
+chr1	19216	19236	42.0	+	chr1	19191	19211	736.0	-	19213	778.0	-25.0
+chr1	230110	230130	42.0	+	chr1	230120	230140	2.0	-	230125	44.0	10.0
+chr1	31627	31647	40.0	+	chr1	31693	31713	450.0	-	31670	490.0	66.0
+chr1	180280	180300	38.0	+	chr1	180362	180382	59.0	-	180331	97.0	82.0
+chr1	98528	98548	34.0	+	chr1	98555	98575	88.0	-	98551	122.0	27.0
+chr1	230163	230183	23.0	+	chr1	230173	230193	33.0	-	230178	56.0	10.0
+chr1	173262	173282	11.0	+	chr1	173270	173290	535.0	-	173276	546.0	8.0
+chr1	230145	230165	8.0	+	chr1	230150	230170	7.0	-	230157	15.0	5.0
+chr1	95920	95940	5.0	+	chr1	95971	95991	684.0	-	95955	689.0	51.0
+chr1	199418	199438	5.0	+	chr1	199388	199408	805.0	-	199413	810.0	-30.0
+chr1	197489	197509	3.0	+	chr1	197562	197582	2.0	-	197535	5.0	73.0
+chr1	96908	96928	2.0	+	chr1	96911	96931	10.0	-	96919	12.0	3.0
+chr1	151369	151389	2.0	+	chr1	151341	151361	593.0	-	151365	595.0	-28.0
--- a/test-data/closest_mp_output1.gff	Mon Nov 06 23:19:50 2017 -0500
+++ b/test-data/closest_mp_output1.gff	Thu May 02 08:30:22 2019 -0400
@@ -1,55 +1,56 @@
-chr1	cwpair	.	87162	87163	5531.0	.	.	cw_distance=11
-chr1	cwpair	.	229759	229760	4531.0	.	.	cw_distance=16
-chr1	cwpair	.	123	124	4204.0	.	.	cw_distance=52
-chr1	cwpair	.	268	269	4088.0	.	.	cw_distance=6
-chr1	cwpair	.	218	219	4022.0	.	.	cw_distance=14
-chr1	cwpair	.	87194	87195	3643.0	.	.	cw_distance=27
-chr1	cwpair	.	59	60	2881.0	.	.	cw_distance=2
-chr1	cwpair	.	265	266	2474.0	.	.	cw_distance=48
-chr1	cwpair	.	92645	92646	2397.0	.	.	cw_distance=8
-chr1	cwpair	.	87109	87110	2259.0	.	.	cw_distance=3
-chr1	cwpair	.	156	157	2177.0	.	.	cw_distance=59
-chr1	cwpair	.	70792	70793	2146.0	.	.	cw_distance=12
-chr1	cwpair	.	6218	6219	2125.0	.	.	cw_distance=91
-chr1	cwpair	.	86982	86983	2013.0	.	.	cw_distance=37
-chr1	cwpair	.	155079	155080	1573.0	.	.	cw_distance=83
-chr1	cwpair	.	92421	92422	1388.0	.	.	cw_distance=0
-chr1	cwpair	.	185109	185110	1371.0	.	.	cw_distance=46
-chr1	cwpair	.	6454	6455	1249.0	.	.	cw_distance=63
-chr1	cwpair	.	87044	87045	1191.0	.	.	cw_distance=30
-chr1	cwpair	.	25305	25306	1183.0	.	.	cw_distance=99
-chr1	cwpair	.	139230	139231	1179.0	.	.	cw_distance=15
-chr1	cwpair	.	325	326	1171.0	.	.	cw_distance=16
-chr1	cwpair	.	55548	55549	956.0	.	.	cw_distance=86
-chr1	cwpair	.	370	371	899.0	.	.	cw_distance=25
-chr1	cwpair	.	72805	72806	869.0	.	.	cw_distance=29
-chr1	cwpair	.	22580	22581	863.0	.	.	cw_distance=-2
-chr1	cwpair	.	92567	92568	789.0	.	.	cw_distance=28
-chr1	cwpair	.	19213	19214	778.0	.	.	cw_distance=-25
-chr1	cwpair	.	113782	113783	716.0	.	.	cw_distance=-20
-chr1	cwpair	.	138876	138877	711.0	.	.	cw_distance=-4
-chr1	cwpair	.	72731	72732	710.0	.	.	cw_distance=100
-chr1	cwpair	.	229762	229763	699.0	.	.	cw_distance=63
-chr1	cwpair	.	95955	95956	689.0	.	.	cw_distance=51
-chr1	cwpair	.	134230	134231	659.0	.	.	cw_distance=100
-chr1	cwpair	.	170134	170135	657.0	.	.	cw_distance=10
-chr1	cwpair	.	228672	228673	626.0	.	.	cw_distance=58
-chr1	cwpair	.	65160	65161	618.0	.	.	cw_distance=-4
-chr1	cwpair	.	106047	106048	572.0	.	.	cw_distance=7
-chr1	cwpair	.	477	478	566.0	.	.	cw_distance=1
-chr1	cwpair	.	59228	59229	565.0	.	.	cw_distance=56
-chr1	cwpair	.	173276	173277	546.0	.	.	cw_distance=8
-chr1	cwpair	.	452	453	504.0	.	.	cw_distance=8
-chr1	cwpair	.	31670	31671	490.0	.	.	cw_distance=66
-chr1	cwpair	.	32483	32484	478.0	.	.	cw_distance=48
-chr1	cwpair	.	6714	6715	433.0	.	.	cw_distance=-4
-chr1	cwpair	.	136369	136370	365.0	.	.	cw_distance=-14
-chr1	cwpair	.	39237	39238	362.0	.	.	cw_distance=61
-chr1	cwpair	.	388	389	359.0	.	.	cw_distance=20
-chr1	cwpair	.	627	628	247.0	.	.	cw_distance=33
-chr1	cwpair	.	98551	98552	122.0	.	.	cw_distance=27
-chr1	cwpair	.	180331	180332	97.0	.	.	cw_distance=82
-chr1	cwpair	.	230178	230179	56.0	.	.	cw_distance=10
-chr1	cwpair	.	230125	230126	44.0	.	.	cw_distance=10
-chr1	cwpair	.	230157	230158	15.0	.	.	cw_distance=5
-chr1	cwpair	.	96919	96920	12.0	.	.	cw_distance=3
+chr1	cwpair	.	87162	87163	5531.0	.	.	cw_distance=11.0
+chr1	cwpair	.	229759	229760	4531.0	.	.	cw_distance=16.0
+chr1	cwpair	.	123	124	4204.0	.	.	cw_distance=52.0
+chr1	cwpair	.	268	269	4088.0	.	.	cw_distance=6.0
+chr1	cwpair	.	218	219	4022.0	.	.	cw_distance=14.0
+chr1	cwpair	.	87194	87195	3643.0	.	.	cw_distance=27.0
+chr1	cwpair	.	59	60	2881.0	.	.	cw_distance=2.0
+chr1	cwpair	.	265	266	2474.0	.	.	cw_distance=48.0
+chr1	cwpair	.	92645	92646	2397.0	.	.	cw_distance=8.0
+chr1	cwpair	.	87109	87110	2259.0	.	.	cw_distance=3.0
+chr1	cwpair	.	156	157	2177.0	.	.	cw_distance=59.0
+chr1	cwpair	.	70792	70793	2146.0	.	.	cw_distance=12.0
+chr1	cwpair	.	6218	6219	2125.0	.	.	cw_distance=91.0
+chr1	cwpair	.	86982	86983	2013.0	.	.	cw_distance=37.0
+chr1	cwpair	.	155079	155080	1573.0	.	.	cw_distance=83.0
+chr1	cwpair	.	92421	92422	1388.0	.	.	cw_distance=0.0
+chr1	cwpair	.	185109	185110	1371.0	.	.	cw_distance=46.0
+chr1	cwpair	.	6454	6455	1249.0	.	.	cw_distance=63.0
+chr1	cwpair	.	87044	87045	1191.0	.	.	cw_distance=30.0
+chr1	cwpair	.	25305	25306	1183.0	.	.	cw_distance=99.0
+chr1	cwpair	.	139230	139231	1179.0	.	.	cw_distance=15.0
+chr1	cwpair	.	325	326	1171.0	.	.	cw_distance=16.0
+chr1	cwpair	.	55548	55549	956.0	.	.	cw_distance=86.0
+chr1	cwpair	.	370	371	899.0	.	.	cw_distance=25.0
+chr1	cwpair	.	72805	72806	869.0	.	.	cw_distance=29.0
+chr1	cwpair	.	22580	22581	863.0	.	.	cw_distance=-2.0
+chr1	cwpair	.	92567	92568	789.0	.	.	cw_distance=28.0
+chr1	cwpair	.	19213	19214	778.0	.	.	cw_distance=-25.0
+chr1	cwpair	.	113782	113783	716.0	.	.	cw_distance=-20.0
+chr1	cwpair	.	138876	138877	711.0	.	.	cw_distance=-4.0
+chr1	cwpair	.	72731	72732	710.0	.	.	cw_distance=100.0
+chr1	cwpair	.	229762	229763	699.0	.	.	cw_distance=63.0
+chr1	cwpair	.	95955	95956	689.0	.	.	cw_distance=51.0
+chr1	cwpair	.	134230	134231	659.0	.	.	cw_distance=100.0
+chr1	cwpair	.	170134	170135	657.0	.	.	cw_distance=10.0
+chr1	cwpair	.	228672	228673	626.0	.	.	cw_distance=58.0
+chr1	cwpair	.	65160	65161	618.0	.	.	cw_distance=-4.0
+chr1	cwpair	.	106047	106048	572.0	.	.	cw_distance=7.0
+chr1	cwpair	.	477	478	566.0	.	.	cw_distance=1.0
+chr1	cwpair	.	59228	59229	565.0	.	.	cw_distance=56.0
+chr1	cwpair	.	173276	173277	546.0	.	.	cw_distance=8.0
+chr1	cwpair	.	452	453	504.0	.	.	cw_distance=8.0
+chr1	cwpair	.	31670	31671	490.0	.	.	cw_distance=66.0
+chr1	cwpair	.	32483	32484	478.0	.	.	cw_distance=48.0
+chr1	cwpair	.	6714	6715	433.0	.	.	cw_distance=-4.0
+chr1	cwpair	.	136369	136370	365.0	.	.	cw_distance=-14.0
+chr1	cwpair	.	39237	39238	362.0	.	.	cw_distance=61.0
+chr1	cwpair	.	388	389	359.0	.	.	cw_distance=20.0
+chr1	cwpair	.	627	628	247.0	.	.	cw_distance=33.0
+chr1	cwpair	.	98551	98552	122.0	.	.	cw_distance=27.0
+chr1	cwpair	.	180331	180332	97.0	.	.	cw_distance=82.0
+chr1	cwpair	.	230178	230179	56.0	.	.	cw_distance=10.0
+chr1	cwpair	.	230125	230126	44.0	.	.	cw_distance=10.0
+chr1	cwpair	.	230157	230158	15.0	.	.	cw_distance=5.0
+chr1	cwpair	.	96919	96920	12.0	.	.	cw_distance=3.0
+chr1	cwpair	.	197535	197536	5.0	.	.	cw_distance=73.0
--- a/test-data/closest_mp_output2.gff	Mon Nov 06 23:19:50 2017 -0500
+++ b/test-data/closest_mp_output2.gff	Thu May 02 08:30:22 2019 -0400
@@ -1,65 +1,66 @@
-chr1	cwpair	.	87162	87163	5531.0	.	.	cw_distance=11
-chr1	cwpair	.	229759	229760	4531.0	.	.	cw_distance=16
-chr1	cwpair	.	123	124	4204.0	.	.	cw_distance=52
-chr1	cwpair	.	268	269	4088.0	.	.	cw_distance=6
-chr1	cwpair	.	218	219	4022.0	.	.	cw_distance=14
-chr1	cwpair	.	87194	87195	3643.0	.	.	cw_distance=27
-chr1	cwpair	.	59	60	2881.0	.	.	cw_distance=2
-chr1	cwpair	.	265	266	2474.0	.	.	cw_distance=48
-chr1	cwpair	.	92645	92646	2397.0	.	.	cw_distance=8
-chr1	cwpair	.	101399	101400	2361.0	.	.	cw_distance=-44
-chr1	cwpair	.	87109	87110	2259.0	.	.	cw_distance=3
-chr1	cwpair	.	156	157	2177.0	.	.	cw_distance=59
-chr1	cwpair	.	70792	70793	2146.0	.	.	cw_distance=12
-chr1	cwpair	.	6218	6219	2125.0	.	.	cw_distance=91
-chr1	cwpair	.	86982	86983	2013.0	.	.	cw_distance=37
-chr1	cwpair	.	169095	169096	1887.0	.	.	cw_distance=-43
-chr1	cwpair	.	155079	155080	1573.0	.	.	cw_distance=83
-chr1	cwpair	.	203863	203864	1476.0	.	.	cw_distance=-37
-chr1	cwpair	.	92421	92422	1388.0	.	.	cw_distance=0
-chr1	cwpair	.	185109	185110	1371.0	.	.	cw_distance=46
-chr1	cwpair	.	39076	39077	1350.0	.	.	cw_distance=-29
-chr1	cwpair	.	6454	6455	1249.0	.	.	cw_distance=63
-chr1	cwpair	.	87044	87045	1191.0	.	.	cw_distance=30
-chr1	cwpair	.	25305	25306	1183.0	.	.	cw_distance=99
-chr1	cwpair	.	139230	139231	1179.0	.	.	cw_distance=15
-chr1	cwpair	.	325	326	1171.0	.	.	cw_distance=16
-chr1	cwpair	.	55548	55549	956.0	.	.	cw_distance=86
-chr1	cwpair	.	370	371	899.0	.	.	cw_distance=25
-chr1	cwpair	.	72805	72806	869.0	.	.	cw_distance=29
-chr1	cwpair	.	22580	22581	863.0	.	.	cw_distance=-2
-chr1	cwpair	.	199413	199414	810.0	.	.	cw_distance=-30
-chr1	cwpair	.	92567	92568	789.0	.	.	cw_distance=28
-chr1	cwpair	.	19213	19214	778.0	.	.	cw_distance=-25
-chr1	cwpair	.	116649	116650	773.0	.	.	cw_distance=-41
-chr1	cwpair	.	124306	124307	761.0	.	.	cw_distance=-43
-chr1	cwpair	.	113782	113783	716.0	.	.	cw_distance=-20
-chr1	cwpair	.	138876	138877	711.0	.	.	cw_distance=-4
-chr1	cwpair	.	72731	72732	710.0	.	.	cw_distance=100
-chr1	cwpair	.	229762	229763	699.0	.	.	cw_distance=63
-chr1	cwpair	.	95955	95956	689.0	.	.	cw_distance=51
-chr1	cwpair	.	134230	134231	659.0	.	.	cw_distance=100
-chr1	cwpair	.	170134	170135	657.0	.	.	cw_distance=10
-chr1	cwpair	.	228672	228673	626.0	.	.	cw_distance=58
-chr1	cwpair	.	65160	65161	618.0	.	.	cw_distance=-4
-chr1	cwpair	.	151365	151366	595.0	.	.	cw_distance=-28
-chr1	cwpair	.	108611	108612	573.0	.	.	cw_distance=-45
-chr1	cwpair	.	106047	106048	572.0	.	.	cw_distance=7
-chr1	cwpair	.	500	501	569.0	.	.	cw_distance=-44
-chr1	cwpair	.	59228	59229	565.0	.	.	cw_distance=56
-chr1	cwpair	.	173276	173277	546.0	.	.	cw_distance=8
-chr1	cwpair	.	452	453	504.0	.	.	cw_distance=8
-chr1	cwpair	.	45670	45671	493.0	.	.	cw_distance=-35
-chr1	cwpair	.	31670	31671	490.0	.	.	cw_distance=66
-chr1	cwpair	.	32483	32484	478.0	.	.	cw_distance=48
-chr1	cwpair	.	6714	6715	433.0	.	.	cw_distance=-4
-chr1	cwpair	.	136369	136370	365.0	.	.	cw_distance=-14
-chr1	cwpair	.	39237	39238	362.0	.	.	cw_distance=61
-chr1	cwpair	.	388	389	359.0	.	.	cw_distance=20
-chr1	cwpair	.	668	669	319.0	.	.	cw_distance=-48
-chr1	cwpair	.	98551	98552	122.0	.	.	cw_distance=27
-chr1	cwpair	.	180331	180332	97.0	.	.	cw_distance=82
-chr1	cwpair	.	230178	230179	56.0	.	.	cw_distance=10
-chr1	cwpair	.	230125	230126	44.0	.	.	cw_distance=10
-chr1	cwpair	.	230157	230158	15.0	.	.	cw_distance=5
-chr1	cwpair	.	96919	96920	12.0	.	.	cw_distance=3
+chr1	cwpair	.	87162	87163	5531.0	.	.	cw_distance=11.0
+chr1	cwpair	.	229759	229760	4531.0	.	.	cw_distance=16.0
+chr1	cwpair	.	123	124	4204.0	.	.	cw_distance=52.0
+chr1	cwpair	.	268	269	4088.0	.	.	cw_distance=6.0
+chr1	cwpair	.	218	219	4022.0	.	.	cw_distance=14.0
+chr1	cwpair	.	87194	87195	3643.0	.	.	cw_distance=27.0
+chr1	cwpair	.	59	60	2881.0	.	.	cw_distance=2.0
+chr1	cwpair	.	265	266	2474.0	.	.	cw_distance=48.0
+chr1	cwpair	.	92645	92646	2397.0	.	.	cw_distance=8.0
+chr1	cwpair	.	101399	101400	2361.0	.	.	cw_distance=-44.0
+chr1	cwpair	.	87109	87110	2259.0	.	.	cw_distance=3.0
+chr1	cwpair	.	156	157	2177.0	.	.	cw_distance=59.0
+chr1	cwpair	.	70792	70793	2146.0	.	.	cw_distance=12.0
+chr1	cwpair	.	6218	6219	2125.0	.	.	cw_distance=91.0
+chr1	cwpair	.	86982	86983	2013.0	.	.	cw_distance=37.0
+chr1	cwpair	.	169095	169096	1887.0	.	.	cw_distance=-43.0
+chr1	cwpair	.	155079	155080	1573.0	.	.	cw_distance=83.0
+chr1	cwpair	.	203863	203864	1476.0	.	.	cw_distance=-37.0
+chr1	cwpair	.	92421	92422	1388.0	.	.	cw_distance=0.0
+chr1	cwpair	.	185109	185110	1371.0	.	.	cw_distance=46.0
+chr1	cwpair	.	39076	39077	1350.0	.	.	cw_distance=-29.0
+chr1	cwpair	.	6454	6455	1249.0	.	.	cw_distance=63.0
+chr1	cwpair	.	87044	87045	1191.0	.	.	cw_distance=30.0
+chr1	cwpair	.	25305	25306	1183.0	.	.	cw_distance=99.0
+chr1	cwpair	.	139230	139231	1179.0	.	.	cw_distance=15.0
+chr1	cwpair	.	325	326	1171.0	.	.	cw_distance=16.0
+chr1	cwpair	.	55548	55549	956.0	.	.	cw_distance=86.0
+chr1	cwpair	.	370	371	899.0	.	.	cw_distance=25.0
+chr1	cwpair	.	72805	72806	869.0	.	.	cw_distance=29.0
+chr1	cwpair	.	22580	22581	863.0	.	.	cw_distance=-2.0
+chr1	cwpair	.	199413	199414	810.0	.	.	cw_distance=-30.0
+chr1	cwpair	.	92567	92568	789.0	.	.	cw_distance=28.0
+chr1	cwpair	.	19213	19214	778.0	.	.	cw_distance=-25.0
+chr1	cwpair	.	116649	116650	773.0	.	.	cw_distance=-41.0
+chr1	cwpair	.	124306	124307	761.0	.	.	cw_distance=-43.0
+chr1	cwpair	.	113782	113783	716.0	.	.	cw_distance=-20.0
+chr1	cwpair	.	138876	138877	711.0	.	.	cw_distance=-4.0
+chr1	cwpair	.	72731	72732	710.0	.	.	cw_distance=100.0
+chr1	cwpair	.	229762	229763	699.0	.	.	cw_distance=63.0
+chr1	cwpair	.	95955	95956	689.0	.	.	cw_distance=51.0
+chr1	cwpair	.	134230	134231	659.0	.	.	cw_distance=100.0
+chr1	cwpair	.	170134	170135	657.0	.	.	cw_distance=10.0
+chr1	cwpair	.	228672	228673	626.0	.	.	cw_distance=58.0
+chr1	cwpair	.	65160	65161	618.0	.	.	cw_distance=-4.0
+chr1	cwpair	.	151365	151366	595.0	.	.	cw_distance=-28.0
+chr1	cwpair	.	108611	108612	573.0	.	.	cw_distance=-45.0
+chr1	cwpair	.	106047	106048	572.0	.	.	cw_distance=7.0
+chr1	cwpair	.	500	501	569.0	.	.	cw_distance=-44.0
+chr1	cwpair	.	59228	59229	565.0	.	.	cw_distance=56.0
+chr1	cwpair	.	173276	173277	546.0	.	.	cw_distance=8.0
+chr1	cwpair	.	452	453	504.0	.	.	cw_distance=8.0
+chr1	cwpair	.	45670	45671	493.0	.	.	cw_distance=-35.0
+chr1	cwpair	.	31670	31671	490.0	.	.	cw_distance=66.0
+chr1	cwpair	.	32483	32484	478.0	.	.	cw_distance=48.0
+chr1	cwpair	.	6714	6715	433.0	.	.	cw_distance=-4.0
+chr1	cwpair	.	136369	136370	365.0	.	.	cw_distance=-14.0
+chr1	cwpair	.	39237	39238	362.0	.	.	cw_distance=61.0
+chr1	cwpair	.	388	389	359.0	.	.	cw_distance=20.0
+chr1	cwpair	.	668	669	319.0	.	.	cw_distance=-48.0
+chr1	cwpair	.	98551	98552	122.0	.	.	cw_distance=27.0
+chr1	cwpair	.	180331	180332	97.0	.	.	cw_distance=82.0
+chr1	cwpair	.	230178	230179	56.0	.	.	cw_distance=10.0
+chr1	cwpair	.	230125	230126	44.0	.	.	cw_distance=10.0
+chr1	cwpair	.	230157	230158	15.0	.	.	cw_distance=5.0
+chr1	cwpair	.	96919	96920	12.0	.	.	cw_distance=3.0
+chr1	cwpair	.	197535	197536	5.0	.	.	cw_distance=73.0
--- a/test-data/closest_o_output2.tabular	Mon Nov 06 23:19:50 2017 -0500
+++ b/test-data/closest_o_output2.tabular	Thu May 02 08:30:22 2019 -0400
@@ -1,100 +1,368 @@
-chrom	strand	start	end	value
-chr1	+	100364	100384	2695.0
-chr1	+	30	50	2140.0
-chr1	+	5379	5399	1572.0
-chr1	+	52440	52460	1562.0
-chr1	+	73234	73254	1492.0
-chr1	+	31096	31116	1481.0
-chr1	+	145253	145273	1394.0
-chr1	+	10641	10661	1359.0
-chr1	+	200580	200600	1298.0
-chr1	+	64772	64792	1292.0
-chr1	+	86886	86906	1253.0
-chr1	+	103207	103227	1229.0
-chr1	+	43835	43855	1173.0
-chr1	+	29570	29590	1130.0
-chr1	+	83774	83794	1125.0
-chr1	+	165827	165847	1109.0
-chr1	+	92775	92795	1105.0
-chr1	+	4748	4768	1077.0
-chr1	+	126733	126753	952.0
-chr1	+	71041	71061	881.0
-chr1	+	35773	35793	866.0
-chr1	+	53097	53117	835.0
-chr1	+	71556	71576	835.0
-chr1	+	30964	30984	829.0
-chr1	+	31019	31039	810.0
-chr1	+	55349	55369	794.0
-chr1	+	203193	203213	789.0
-chr1	+	39794	39814	780.0
-chr1	+	153928	153948	768.0
-chr1	+	179472	179492	696.0
-chr1	+	178117	178137	686.0
-chr1	+	1298	1318	684.0
-chr1	+	87085	87105	676.0
-chr1	+	192754	192774	668.0
-chr1	+	89611	89631	640.0
-chr1	+	20205	20225	634.0
-chr1	+	118428	118448	633.0
-chr1	+	110736	110756	621.0
-chr1	+	48642	48662	610.0
-chr1	+	159372	159392	605.0
-chr1	+	6453	6473	601.0
-chr1	+	112137	112157	601.0
-chr1	+	142905	142925	599.0
-chr1	+	167443	167463	597.0
-chr1	+	126073	126093	590.0
-chr1	+	6233	6253	589.0
-chr1	+	43657	43677	586.0
-chr1	+	134021	134041	572.0
-chr1	+	29864	29884	570.0
-chr1	+	70953	70973	555.0
-chr1	+	87002	87022	550.0
-chr1	+	129555	129575	536.0
-chr1	+	119754	119774	515.0
-chr1	+	43523	43543	505.0
-chr1	+	97898	97918	501.0
-chr1	+	40830	40850	491.0
-chr1	+	153095	153115	490.0
-chr1	+	7303	7323	484.0
-chr1	+	115866	115886	480.0
-chr1	+	129680	129700	464.0
-chr1	+	187155	187175	455.0
-chr1	+	192271	192291	453.0
-chr1	+	160	180	451.0
-chr1	+	150449	150469	436.0
-chr1	+	9367	9387	425.0
-chr1	+	93793	93813	415.0
-chr1	+	87572	87592	407.0
-chr1	+	124845	124865	383.0
-chr1	+	4053	4073	381.0
-chr1	+	136072	136092	380.0
-chr1	+	39942	39962	375.0
-chr1	+	61977	61997	368.0
-chr1	+	2976	2996	356.0
-chr1	+	27978	27998	354.0
-chr1	+	195756	195776	348.0
-chr1	+	172223	172243	338.0
-chr1	+	143657	143677	328.0
-chr1	+	45409	45429	307.0
-chr1	+	45248	45268	305.0
-chr1	+	68564	68584	303.0
-chr1	+	119953	119973	295.0
-chr1	+	48319	48339	290.0
-chr1	+	48772	48792	284.0
-chr1	+	126369	126389	284.0
-chr1	+	116432	116452	267.0
-chr1	+	199649	199669	264.0
-chr1	+	204126	204146	261.0
-chr1	+	130514	130534	243.0
-chr1	+	55692	55712	228.0
-chr1	+	117198	117218	228.0
-chr1	+	42843	42863	218.0
-chr1	+	59583	59603	204.0
-chr1	+	124669	124689	203.0
-chr1	+	2613	2633	202.0
-chr1	+	40264	40284	199.0
-chr1	+	21406	21426	177.0
-chr1	+	20391	20411	173.0
-chr1	+	20626	20646	171.0
-chr1	+	198594	198614	170.0
+chrom	strand	start	end	value
+chr1	+	100364	100384	2695.0
+chr1	+	30	50	2140.0
+chr1	+	5379	5399	1572.0
+chr1	+	52440	52460	1562.0
+chr1	+	73234	73254	1492.0
+chr1	+	31096	31116	1481.0
+chr1	+	145253	145273	1394.0
+chr1	+	10641	10661	1359.0
+chr1	+	200580	200600	1298.0
+chr1	+	64772	64792	1292.0
+chr1	+	86886	86906	1253.0
+chr1	+	103207	103227	1229.0
+chr1	+	43835	43855	1173.0
+chr1	+	29570	29590	1130.0
+chr1	+	83774	83794	1125.0
+chr1	+	165827	165847	1109.0
+chr1	+	92775	92795	1105.0
+chr1	+	4748	4768	1077.0
+chr1	+	126733	126753	952.0
+chr1	+	71041	71061	881.0
+chr1	+	35773	35793	866.0
+chr1	+	53097	53117	835.0
+chr1	+	71556	71576	835.0
+chr1	+	30964	30984	829.0
+chr1	+	31019	31039	810.0
+chr1	+	55349	55369	794.0
+chr1	+	203193	203213	789.0
+chr1	+	39794	39814	780.0
+chr1	+	153928	153948	768.0
+chr1	+	179472	179492	696.0
+chr1	+	178117	178137	686.0
+chr1	+	1298	1318	684.0
+chr1	+	87085	87105	676.0
+chr1	+	192754	192774	668.0
+chr1	+	89611	89631	640.0
+chr1	+	20205	20225	634.0
+chr1	+	118428	118448	633.0
+chr1	+	110736	110756	621.0
+chr1	+	48642	48662	610.0
+chr1	+	159372	159392	605.0
+chr1	+	6453	6473	601.0
+chr1	+	112137	112157	601.0
+chr1	+	142905	142925	599.0
+chr1	+	167443	167463	597.0
+chr1	+	126073	126093	590.0
+chr1	+	6233	6253	589.0
+chr1	+	43657	43677	586.0
+chr1	+	134021	134041	572.0
+chr1	+	29864	29884	570.0
+chr1	+	70953	70973	555.0
+chr1	+	87002	87022	550.0
+chr1	+	129555	129575	536.0
+chr1	+	119754	119774	515.0
+chr1	+	43523	43543	505.0
+chr1	+	97898	97918	501.0
+chr1	+	40830	40850	491.0
+chr1	+	153095	153115	490.0
+chr1	+	7303	7323	484.0
+chr1	+	115866	115886	480.0
+chr1	+	129680	129700	464.0
+chr1	+	187155	187175	455.0
+chr1	+	192271	192291	453.0
+chr1	+	160	180	451.0
+chr1	+	150449	150469	436.0
+chr1	+	9367	9387	425.0
+chr1	+	93793	93813	415.0
+chr1	+	11	31	414.0
+chr1	+	87572	87592	407.0
+chr1	+	124845	124865	383.0
+chr1	+	4053	4073	381.0
+chr1	+	136072	136092	380.0
+chr1	+	39942	39962	375.0
+chr1	+	61977	61997	368.0
+chr1	+	2976	2996	356.0
+chr1	+	27978	27998	354.0
+chr1	+	195756	195776	348.0
+chr1	+	172223	172243	338.0
+chr1	+	143657	143677	328.0
+chr1	+	45409	45429	307.0
+chr1	+	45248	45268	305.0
+chr1	+	68564	68584	303.0
+chr1	+	119953	119973	295.0
+chr1	+	48319	48339	290.0
+chr1	+	48772	48792	284.0
+chr1	+	126369	126389	284.0
+chr1	+	116432	116452	267.0
+chr1	+	199649	199669	264.0
+chr1	+	204126	204146	261.0
+chr1	+	130514	130534	243.0
+chr1	+	55692	55712	228.0
+chr1	+	117198	117218	228.0
+chr1	+	42843	42863	218.0
+chr1	+	59583	59603	204.0
+chr1	+	124669	124689	203.0
+chr1	+	2613	2633	202.0
+chr1	+	40264	40284	199.0
+chr1	+	21406	21426	177.0
+chr1	+	20391	20411	173.0
+chr1	+	20626	20646	171.0
+chr1	+	198594	198614	170.0
+chr1	+	149343	149363	159.0
+chr1	+	121016	121036	155.0
+chr1	+	180652	180672	154.0
+chr1	+	5794	5814	148.0
+chr1	+	187009	187029	139.0
+chr1	+	119736	119756	135.0
+chr1	+	152678	152698	135.0
+chr1	+	47015	47035	133.0
+chr1	+	156252	156272	133.0
+chr1	+	41008	41028	132.0
+chr1	+	147211	147231	130.0
+chr1	+	112900	112920	125.0
+chr1	+	91379	91399	120.0
+chr1	+	227346	227366	114.0
+chr1	+	77731	77751	113.0
+chr1	+	229862	229882	110.0
+chr1	+	147227	147247	101.0
+chr1	+	44687	44707	100.0
+chr1	+	467	487	98.0
+chr1	+	601	621	96.0
+chr1	+	4445	4465	94.0
+chr1	+	110540	110560	91.0
+chr1	+	169159	169179	91.0
+chr1	+	103108	103128	90.0
+chr1	+	121289	121309	89.0
+chr1	+	134559	134579	87.0
+chr1	+	90412	90432	86.0
+chr1	+	133139	133159	84.0
+chr1	+	90040	90060	82.0
+chr1	+	86865	86885	81.0
+chr1	+	59248	59268	80.0
+chr1	+	42925	42945	77.0
+chr1	+	189494	189514	70.0
+chr1	+	146517	146537	69.0
+chr1	+	32145	32165	66.0
+chr1	+	68018	68038	62.0
+chr1	+	210175	210195	62.0
+chr1	+	48431	48451	57.0
+chr1	+	177627	177647	51.0
+chr1	+	97967	97987	50.0
+chr1	+	191408	191428	50.0
+chr1	+	33829	33849	48.0
+chr1	+	76365	76385	47.0
+chr1	+	105499	105519	46.0
+chr1	+	176858	176878	46.0
+chr1	+	92982	93002	44.0
+chr1	+	142139	142159	43.0
+chr1	+	110130	110150	42.0
+chr1	+	151431	151451	38.0
+chr1	+	219301	219321	37.0
+chr1	+	102337	102357	36.0
+chr1	+	134868	134888	36.0
+chr1	+	204214	204234	36.0
+chr1	+	76501	76521	33.0
+chr1	+	179554	179574	31.0
+chr1	+	113226	113246	28.0
+chr1	+	6255	6275	26.0
+chr1	+	5750	5770	25.0
+chr1	+	105942	105962	25.0
+chr1	+	140857	140877	23.0
+chr1	+	166238	166258	21.0
+chr1	+	111317	111337	17.0
+chr1	+	16501	16521	15.0
+chr1	+	22268	22288	15.0
+chr1	+	147322	147342	15.0
+chr1	+	201841	201861	15.0
+chr1	+	7753	7773	14.0
+chr1	+	12305	12325	13.0
+chr1	+	2293	2313	12.0
+chr1	+	16173	16193	12.0
+chr1	+	142950	142970	12.0
+chr1	+	91215	91235	11.0
+chr1	+	39591	39611	10.0
+chr1	+	43147	43167	9.0
+chr1	+	119155	119175	9.0
+chr1	+	20117	20137	8.0
+chr1	+	110602	110622	8.0
+chr1	+	206684	206704	8.0
+chr1	+	188920	188940	7.0
+chr1	+	81481	81501	5.0
+chr1	+	138051	138071	5.0
+chr1	+	167652	167672	5.0
+chr1	+	228150	228170	5.0
+chr1	+	24765	24785	4.0
+chr1	+	183610	183630	4.0
+chr1	+	125727	125747	3.0
+chr1	+	33426	33446	2.0
+chr1	+	49283	49303	2.0
+chr1	+	89663	89683	2.0
+chr1	+	138030	138050	2.0
+chr1	+	156097	156117	2.0
+chr1	+	158038	158058	2.0
+chr1	+	169338	169358	2.0
+chr1	+	175899	175919	2.0
+chr1	+	199141	199161	2.0
+chr1	-	410	430	8.0
+chr1	-	1457	1477	111.0
+chr1	-	1970	1990	629.0
+chr1	-	3148	3168	1420.0
+chr1	-	4892	4912	272.0
+chr1	-	5546	5566	27.0
+chr1	-	7659	7679	243.0
+chr1	-	8596	8616	114.0
+chr1	-	8904	8924	80.0
+chr1	-	9119	9139	22.0
+chr1	-	10107	10127	1622.0
+chr1	-	12157	12177	40.0
+chr1	-	13415	13435	634.0
+chr1	-	16739	16759	3.0
+chr1	-	19145	19165	618.0
+chr1	-	20550	20570	865.0
+chr1	-	22383	22403	141.0
+chr1	-	23046	23066	213.0
+chr1	-	27517	27537	1459.0
+chr1	-	29325	29345	1074.0
+chr1	-	30046	30066	17.0
+chr1	-	31876	31896	1344.0
+chr1	-	37166	37186	1000.0
+chr1	-	38768	38788	1064.0
+chr1	-	38799	38819	9.0
+chr1	-	39000	39020	3.0
+chr1	-	39293	39313	2.0
+chr1	-	41867	41887	7.0
+chr1	-	45565	45585	246.0
+chr1	-	45579	45599	78.0
+chr1	-	46616	46636	741.0
+chr1	-	49660	49680	6.0
+chr1	-	50091	50111	156.0
+chr1	-	51978	51998	633.0
+chr1	-	52308	52328	549.0
+chr1	-	53045	53065	31.0
+chr1	-	55616	55636	984.0
+chr1	-	56542	56562	606.0
+chr1	-	56664	56684	67.0
+chr1	-	56995	57015	1393.0
+chr1	-	57121	57141	4.0
+chr1	-	57212	57232	667.0
+chr1	-	57543	57563	2.0
+chr1	-	59157	59177	168.0
+chr1	-	61877	61897	607.0
+chr1	-	65687	65707	596.0
+chr1	-	66306	66326	2.0
+chr1	-	68423	68443	139.0
+chr1	-	70336	70356	652.0
+chr1	-	74763	74783	430.0
+chr1	-	75897	75917	10.0
+chr1	-	77515	77535	797.0
+chr1	-	77530	77550	513.0
+chr1	-	78813	78833	113.0
+chr1	-	80958	80978	137.0
+chr1	-	81037	81057	4.0
+chr1	-	81972	81992	49.0
+chr1	-	85759	85779	77.0
+chr1	-	86166	86186	969.0
+chr1	-	86280	86300	14.0
+chr1	-	87234	87254	637.0
+chr1	-	87262	87282	505.0
+chr1	-	87289	87309	1270.0
+chr1	-	87327	87347	729.0
+chr1	-	87468	87488	304.0
+chr1	-	88213	88233	301.0
+chr1	-	88376	88396	56.0
+chr1	-	89175	89195	23.0
+chr1	-	91926	91946	10.0
+chr1	-	92541	92561	602.0
+chr1	-	92664	92684	187.0
+chr1	-	94913	94933	1437.0
+chr1	-	96278	96298	166.0
+chr1	-	96315	96335	2.0
+chr1	-	96566	96586	6.0
+chr1	-	101301	101321	48.0
+chr1	-	102072	102092	14.0
+chr1	-	102903	102923	846.0
+chr1	-	104110	104130	117.0
+chr1	-	105663	105683	417.0
+chr1	-	105814	105834	529.0
+chr1	-	105846	105866	177.0
+chr1	-	105889	105909	84.0
+chr1	-	106340	106360	421.0
+chr1	-	108072	108092	72.0
+chr1	-	108263	108283	145.0
+chr1	-	111947	111967	585.0
+chr1	-	114306	114326	2.0
+chr1	-	116148	116168	248.0
+chr1	-	117522	117542	1573.0
+chr1	-	117845	117865	16.0
+chr1	-	118841	118861	7.0
+chr1	-	119430	119450	1093.0
+chr1	-	119596	119616	842.0
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+chr1	-	119669	119689	665.0
+chr1	-	119866	119886	846.0
+chr1	-	119880	119900	1136.0
+chr1	-	120788	120808	105.0
+chr1	-	122624	122644	201.0
+chr1	-	122777	122797	20.0
+chr1	-	123718	123738	751.0
+chr1	-	125840	125860	273.0
+chr1	-	127027	127047	590.0
+chr1	-	130869	130889	718.0
+chr1	-	133644	133664	122.0
+chr1	-	135051	135071	63.0
+chr1	-	137428	137448	1200.0
+chr1	-	137816	137836	695.0
+chr1	-	139627	139647	531.0
+chr1	-	140133	140153	441.0
+chr1	-	140770	140790	556.0
+chr1	-	141182	141202	14.0
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+chr1	-	144669	144689	1192.0
+chr1	-	145383	145403	326.0
+chr1	-	147573	147593	255.0
+chr1	-	148690	148710	2.0
+chr1	-	149704	149724	74.0
+chr1	-	150358	150378	153.0
+chr1	-	152984	153004	106.0
+chr1	-	153812	153832	168.0
+chr1	-	154862	154882	14.0
+chr1	-	155456	155476	23.0
+chr1	-	155897	155917	10.0
+chr1	-	157559	157579	337.0
+chr1	-	166467	166487	582.0
+chr1	-	166631	166651	173.0
+chr1	-	169500	169520	814.0
+chr1	-	170282	170302	63.0
+chr1	-	171063	171083	212.0
+chr1	-	175188	175208	117.0
+chr1	-	175474	175494	1119.0
+chr1	-	176004	176024	1473.0
+chr1	-	177140	177160	93.0
+chr1	-	177386	177406	289.0
+chr1	-	178846	178866	601.0
+chr1	-	178971	178991	723.0
+chr1	-	179116	179136	71.0
+chr1	-	180272	180292	25.0
+chr1	-	180995	181015	299.0
+chr1	-	182588	182608	465.0
+chr1	-	182790	182810	355.0
+chr1	-	185673	185693	190.0
+chr1	-	187422	187442	20.0
+chr1	-	187976	187996	728.0
+chr1	-	196499	196519	224.0
+chr1	-	197060	197080	224.0
+chr1	-	197151	197171	1464.0
+chr1	-	197342	197362	204.0
+chr1	-	198423	198443	598.0
+chr1	-	198953	198973	3.0
+chr1	-	199935	199955	31.0
+chr1	-	201308	201328	1287.0
+chr1	-	201651	201671	892.0
+chr1	-	202977	202997	163.0
+chr1	-	203452	203472	76.0
+chr1	-	206245	206265	22.0
+chr1	-	207675	207695	313.0
+chr1	-	208559	208579	121.0
+chr1	-	209205	209225	176.0
+chr1	-	220863	220883	2.0
+chr1	-	223035	223055	62.0
+chr1	-	225156	225176	2.0
+chr1	-	226777	226797	444.0
+chr1	-	227608	227628	1311.0
+chr1	-	228405	228425	1447.0
+chr1	-	229031	229051	6.0
+chr1	-	229583	229603	62.0
+chr1	-	229665	229685	131.0
+chr1	-	229965	229985	13.0
+chr1	-	230132	230152	2.0
--- a/test-data/cwpair2_input1.gff	Mon Nov 06 23:19:50 2017 -0500
+++ b/test-data/cwpair2_input1.gff	Thu May 02 08:30:22 2019 -0400
@@ -1,499 +1,500 @@
-chr1	genetrack	.	11	31	414	+	.	stddev=2.26073020752
-chr1	genetrack	.	30	50	2140	+	.	stddev=4.43077587195
-chr1	genetrack	.	48	68	2842	+	.	stddev=4.88263527016
-chr1	genetrack	.	87	107	3211	+	.	stddev=5.51553909779
-chr1	genetrack	.	117	137	2163	+	.	stddev=4.21572697137
-chr1	genetrack	.	160	180	451	+	.	stddev=0.724882503432
-chr1	genetrack	.	201	221	1411	+	.	stddev=5.79752503059
-chr1	genetrack	.	231	251	1146	+	.	stddev=1.48216146131
-chr1	genetrack	.	255	275	2810	+	.	stddev=1.35163759113
-chr1	genetrack	.	307	327	685	+	.	stddev=0.0
-chr1	genetrack	.	348	368	699	+	.	stddev=2.60206286017
-chr1	genetrack	.	368	388	192	+	.	stddev=0.0
-chr1	genetrack	.	438	458	334	+	.	stddev=0.109271183179
-chr1	genetrack	.	467	487	98	+	.	stddev=0.0
-chr1	genetrack	.	512	532	101	+	.	stddev=0.792079207921
-chr1	genetrack	.	601	621	96	+	.	stddev=0.0
-chr1	genetrack	.	682	702	168	+	.	stddev=0.0
-chr1	genetrack	.	1298	1318	684	+	.	stddev=0.0
-chr1	genetrack	.	2293	2313	12	+	.	stddev=0.0
-chr1	genetrack	.	2613	2633	202	+	.	stddev=0.0
-chr1	genetrack	.	2976	2996	356	+	.	stddev=0.0
-chr1	genetrack	.	4053	4073	381	+	.	stddev=0.0
-chr1	genetrack	.	4445	4465	94	+	.	stddev=0.0
-chr1	genetrack	.	4748	4768	1077	+	.	stddev=0.0
-chr1	genetrack	.	5379	5399	1572	+	.	stddev=0.0
-chr1	genetrack	.	5750	5770	25	+	.	stddev=0.0
-chr1	genetrack	.	5794	5814	148	+	.	stddev=0.0
-chr1	genetrack	.	6163	6183	1049	+	.	stddev=0.645595472695
-chr1	genetrack	.	6233	6253	589	+	.	stddev=2.54134583729
-chr1	genetrack	.	6255	6275	26	+	.	stddev=0.0
-chr1	genetrack	.	6413	6433	682	+	.	stddev=0.0
-chr1	genetrack	.	6453	6473	601	+	.	stddev=0.0
-chr1	genetrack	.	6706	6726	431	+	.	stddev=0.0
-chr1	genetrack	.	7303	7323	484	+	.	stddev=0.0
-chr1	genetrack	.	7753	7773	14	+	.	stddev=0.0
-chr1	genetrack	.	9367	9387	425	+	.	stddev=0.0
-chr1	genetrack	.	10641	10661	1359	+	.	stddev=0.0
-chr1	genetrack	.	12305	12325	13	+	.	stddev=0.0
-chr1	genetrack	.	16173	16193	12	+	.	stddev=0.0
-chr1	genetrack	.	16501	16521	15	+	.	stddev=0.0
-chr1	genetrack	.	19216	19236	42	+	.	stddev=0.0
-chr1	genetrack	.	20117	20137	8	+	.	stddev=0.0
-chr1	genetrack	.	20205	20225	634	+	.	stddev=0.0
-chr1	genetrack	.	20391	20411	173	+	.	stddev=0.0
-chr1	genetrack	.	20626	20646	171	+	.	stddev=0.0
-chr1	genetrack	.	21406	21426	177	+	.	stddev=0.0
-chr1	genetrack	.	22268	22288	15	+	.	stddev=0.0
-chr1	genetrack	.	22571	22591	609	+	.	stddev=0.0
-chr1	genetrack	.	24765	24785	4	+	.	stddev=0.0
-chr1	genetrack	.	25246	25266	995	+	.	stddev=0.0
-chr1	genetrack	.	27978	27998	354	+	.	stddev=0.0
-chr1	genetrack	.	29570	29590	1130	+	.	stddev=0.0
-chr1	genetrack	.	29864	29884	570	+	.	stddev=0.0
-chr1	genetrack	.	30964	30984	829	+	.	stddev=0.0
-chr1	genetrack	.	31019	31039	810	+	.	stddev=0.0
-chr1	genetrack	.	31096	31116	1481	+	.	stddev=0.0
-chr1	genetrack	.	31627	31647	40	+	.	stddev=0.0
-chr1	genetrack	.	32145	32165	66	+	.	stddev=0.0
-chr1	genetrack	.	32449	32469	476	+	.	stddev=0.0
-chr1	genetrack	.	33426	33446	2	+	.	stddev=0.0
-chr1	genetrack	.	33829	33849	48	+	.	stddev=0.0
-chr1	genetrack	.	35773	35793	866	+	.	stddev=0.0
-chr1	genetrack	.	39081	39101	1268	+	.	stddev=0.0
-chr1	genetrack	.	39197	39217	101	+	.	stddev=0.0
-chr1	genetrack	.	39591	39611	10	+	.	stddev=0.0
-chr1	genetrack	.	39794	39814	780	+	.	stddev=0.0
-chr1	genetrack	.	39942	39962	375	+	.	stddev=0.0
-chr1	genetrack	.	40264	40284	199	+	.	stddev=0.0
-chr1	genetrack	.	40830	40850	491	+	.	stddev=0.0
-chr1	genetrack	.	41008	41028	132	+	.	stddev=0.0
-chr1	genetrack	.	42843	42863	218	+	.	stddev=0.0
-chr1	genetrack	.	42925	42945	77	+	.	stddev=0.0
-chr1	genetrack	.	43147	43167	9	+	.	stddev=0.0
-chr1	genetrack	.	43523	43543	505	+	.	stddev=0.0
-chr1	genetrack	.	43657	43677	586	+	.	stddev=0.0
-chr1	genetrack	.	43835	43855	1173	+	.	stddev=0.0
-chr1	genetrack	.	44687	44707	100	+	.	stddev=0.0
-chr1	genetrack	.	45248	45268	305	+	.	stddev=0.139642881568
-chr1	genetrack	.	45409	45429	307	+	.	stddev=0.0
-chr1	genetrack	.	45678	45698	198	+	.	stddev=0.0
-chr1	genetrack	.	47015	47035	133	+	.	stddev=0.0
-chr1	genetrack	.	48319	48339	290	+	.	stddev=0.0
-chr1	genetrack	.	48431	48451	57	+	.	stddev=0.0
-chr1	genetrack	.	48642	48662	610	+	.	stddev=0.0
-chr1	genetrack	.	48772	48792	284	+	.	stddev=0.0
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-chr1	genetrack	.	59190	59210	168	+	.	stddev=0.0
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-chr1	genetrack	.	61977	61997	368	+	.	stddev=0.0
-chr1	genetrack	.	64772	64792	1292	+	.	stddev=0.0
-chr1	genetrack	.	65152	65172	575	+	.	stddev=0.0
-chr1	genetrack	.	68018	68038	62	+	.	stddev=0.0
-chr1	genetrack	.	68564	68584	303	+	.	stddev=0.0
-chr1	genetrack	.	70776	70796	1148	+	.	stddev=0.0
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-chr1	genetrack	.	91379	91399	120	+	.	stddev=0.0
-chr1	genetrack	.	92411	92431	1252	+	.	stddev=0.169502292497
-chr1	genetrack	.	92543	92563	699	+	.	stddev=0.0
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-chr1	genetrack	.	92775	92795	1105	+	.	stddev=0.923076923077
-chr1	genetrack	.	92982	93002	44	+	.	stddev=0.0
-chr1	genetrack	.	93793	93813	415	+	.	stddev=0.0
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-chr1	genetrack	.	96908	96928	2	+	.	stddev=0.0
-chr1	genetrack	.	97898	97918	501	+	.	stddev=0.0
-chr1	genetrack	.	97967	97987	50	+	.	stddev=0.0
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-chr1	genetrack	.	100364	100384	2695	+	.	stddev=4.98845945981
-chr1	genetrack	.	101411	101431	973	+	.	stddev=0.0
-chr1	genetrack	.	102337	102357	36	+	.	stddev=0.0
-chr1	genetrack	.	103108	103128	90	+	.	stddev=0.0
-chr1	genetrack	.	103207	103227	1229	+	.	stddev=0.0
-chr1	genetrack	.	105499	105519	46	+	.	stddev=0.145830520272
-chr1	genetrack	.	105942	105962	25	+	.	stddev=0.0
-chr1	genetrack	.	106034	106054	558	+	.	stddev=0.0
-chr1	genetrack	.	108624	108644	206	+	.	stddev=0.0
-chr1	genetrack	.	110130	110150	42	+	.	stddev=0.0
-chr1	genetrack	.	110540	110560	91	+	.	stddev=0.0
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-chr1	genetrack	.	110736	110756	621	+	.	stddev=0.0400962950016
-chr1	genetrack	.	111317	111337	17	+	.	stddev=0.0
-chr1	genetrack	.	112137	112157	601	+	.	stddev=0.0
-chr1	genetrack	.	112900	112920	125	+	.	stddev=0.0
-chr1	genetrack	.	113226	113246	28	+	.	stddev=0.0
-chr1	genetrack	.	113782	113802	420	+	.	stddev=0.0
-chr1	genetrack	.	115866	115886	480	+	.	stddev=0.0
-chr1	genetrack	.	116432	116452	267	+	.	stddev=0.0
-chr1	genetrack	.	116660	116680	74	+	.	stddev=0.0
-chr1	genetrack	.	117198	117218	228	+	.	stddev=0.0
-chr1	genetrack	.	118428	118448	633	+	.	stddev=0.039715023981
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-chr1	genetrack	.	119953	119973	295	+	.	stddev=0.0
-chr1	genetrack	.	121016	121036	155	+	.	stddev=0.0
-chr1	genetrack	.	121289	121309	89	+	.	stddev=0.0
-chr1	genetrack	.	124318	124338	749	+	.	stddev=0.0
-chr1	genetrack	.	124669	124689	203	+	.	stddev=0.0
-chr1	genetrack	.	124845	124865	383	+	.	stddev=0.0
-chr1	genetrack	.	125727	125747	3	+	.	stddev=0.0
-chr1	genetrack	.	126073	126093	590	+	.	stddev=0.329075555241
-chr1	genetrack	.	126369	126389	284	+	.	stddev=0.0592345205678
-chr1	genetrack	.	126733	126753	952	+	.	stddev=0.484392920736
-chr1	genetrack	.	129555	129575	536	+	.	stddev=0.0431531100978
-chr1	genetrack	.	129680	129700	464	+	.	stddev=0.0
-chr1	genetrack	.	130514	130534	243	+	.	stddev=0.0
-chr1	genetrack	.	133139	133159	84	+	.	stddev=0.0
-chr1	genetrack	.	134021	134041	572	+	.	stddev=0.0
-chr1	genetrack	.	134170	134190	151	+	.	stddev=0.0
-chr1	genetrack	.	134559	134579	87	+	.	stddev=0.0
-chr1	genetrack	.	134868	134888	36	+	.	stddev=0.0
-chr1	genetrack	.	136072	136092	380	+	.	stddev=0.0
-chr1	genetrack	.	136366	136386	248	+	.	stddev=0.0
-chr1	genetrack	.	138030	138050	2	+	.	stddev=0.0
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-chr1	genetrack	.	175188	175208	117	-	.	stddev=0.0
-chr1	genetrack	.	175474	175494	1119	-	.	stddev=0.0
-chr1	genetrack	.	176004	176024	1473	-	.	stddev=0.0
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+##gff-version 3.2.1
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+chr1	genetrack	.	197342	197362	204	-	.	stddev=0.0
+chr1	genetrack	.	197562	197582	2	-	.	stddev=0.0
+chr1	genetrack	.	198423	198443	598	-	.	stddev=0.0
+chr1	genetrack	.	198953	198973	3	-	.	stddev=0.0
+chr1	genetrack	.	199388	199408	805	-	.	stddev=0.0
+chr1	genetrack	.	199935	199955	31	-	.	stddev=0.0
+chr1	genetrack	.	201308	201328	1287	-	.	stddev=0.0
+chr1	genetrack	.	201651	201671	892	-	.	stddev=0.0
+chr1	genetrack	.	202977	202997	163	-	.	stddev=0.0
+chr1	genetrack	.	203452	203472	76	-	.	stddev=0.0
+chr1	genetrack	.	203835	203855	242	-	.	stddev=0.0
+chr1	genetrack	.	206245	206265	22	-	.	stddev=0.0
+chr1	genetrack	.	207675	207695	313	-	.	stddev=0.0
+chr1	genetrack	.	208559	208579	121	-	.	stddev=0.89393833276
+chr1	genetrack	.	209205	209225	176	-	.	stddev=0.0
+chr1	genetrack	.	220863	220883	2	-	.	stddev=0.0
+chr1	genetrack	.	223035	223055	62	-	.	stddev=0.0
+chr1	genetrack	.	225156	225176	2	-	.	stddev=0.0
+chr1	genetrack	.	226777	226797	444	-	.	stddev=0.0
+chr1	genetrack	.	227608	227628	1311	-	.	stddev=0.0
+chr1	genetrack	.	228405	228425	1447	-	.	stddev=2.78971080368
+chr1	genetrack	.	228691	228711	255	-	.	stddev=0.0
+chr1	genetrack	.	229031	229051	6	-	.	stddev=0.0
+chr1	genetrack	.	229583	229603	62	-	.	stddev=0.0
+chr1	genetrack	.	229665	229685	131	-	.	stddev=0.0
+chr1	genetrack	.	229757	229777	3151	-	.	stddev=2.79078905805
+chr1	genetrack	.	229784	229804	615	-	.	stddev=0.0
+chr1	genetrack	.	229965	229985	13	-	.	stddev=0.0
+chr1	genetrack	.	230120	230140	2	-	.	stddev=0.0
+chr1	genetrack	.	230132	230152	2	-	.	stddev=0.0
+chr1	genetrack	.	230150	230170	7	-	.	stddev=0.699854212224
+chr1	genetrack	.	230173	230193	33	-	.	stddev=0.477212598425
--- a/test-data/largest_d_output2.tabular	Mon Nov 06 23:19:50 2017 -0500
+++ b/test-data/largest_d_output2.tabular	Thu May 02 08:30:22 2019 -0400
@@ -1,64 +1,65 @@
-chrom	start	end	value	strand	chrom	start	end	value	strand	midpoint	c-w reads sum	c-w distance (bp)
-chr1	87147	87167	3492.0	+	chr1	87198	87218	2207.0	-	87182	5699.0	51
-chr1	87	107	3211.0	+	chr1	139	159	993.0	-	123	4204.0	52
-chr1	48	68	2842.0	+	chr1	50	70	39.0	-	59	2881.0	2
-chr1	255	275	2810.0	+	chr1	215	235	2611.0	-	245	5421.0	-40
-chr1	117	137	2163.0	+	chr1	176	196	14.0	-	156	2177.0	59
-chr1	86954	86974	1948.0	+	chr1	87049	87069	422.0	-	87011	2370.0	95
-chr1	169107	169127	1811.0	+	chr1	169064	169084	76.0	-	169095	1887.0	-43
-chr1	87171	87191	1436.0	+	chr1	87158	87178	2039.0	-	87174	3475.0	-13
-chr1	201	221	1411.0	+	chr1	279	299	1328.0	-	250	2739.0	78
-chr1	229741	229761	1380.0	+	chr1	229757	229777	3151.0	-	229759	4531.0	16
-chr1	185076	185096	1309.0	+	chr1	185122	185142	62.0	-	185109	1371.0	46
-chr1	39081	39101	1268.0	+	chr1	39052	39072	82.0	-	39076	1350.0	-29
-chr1	92411	92431	1252.0	+	chr1	92411	92431	136.0	-	92421	1388.0	0
-chr1	203872	203892	1234.0	+	chr1	203835	203855	242.0	-	203863	1476.0	-37
-chr1	70776	70796	1148.0	+	chr1	70788	70808	998.0	-	70792	2146.0	12
-chr1	231	251	1146.0	+	chr1	261	281	1278.0	-	256	2424.0	30
-chr1	87098	87118	1125.0	+	chr1	87101	87121	1134.0	-	87109	2259.0	3
-chr1	6163	6183	1049.0	+	chr1	6254	6274	1076.0	-	6218	2125.0	91
-chr1	25246	25266	995.0	+	chr1	25345	25365	188.0	-	25305	1183.0	99
-chr1	101411	101431	973.0	+	chr1	101367	101387	1388.0	-	101399	2361.0	-44
-chr1	139213	139233	965.0	+	chr1	139228	139248	214.0	-	139230	1179.0	15
-chr1	87019	87039	769.0	+	chr1	86991	87011	65.0	-	87015	834.0	-28
-chr1	124318	124338	749.0	+	chr1	124275	124295	12.0	-	124306	761.0	-43
-chr1	348	368	699.0	+	chr1	323	343	486.0	-	345	1185.0	-25
-chr1	92543	92563	699.0	+	chr1	92639	92659	2137.0	-	92601	2836.0	96
-chr1	138868	138888	698.0	+	chr1	138864	138884	13.0	-	138876	711.0	-4
-chr1	307	327	685.0	+	chr1	373	393	200.0	-	350	885.0	66
-chr1	6413	6433	682.0	+	chr1	6476	6496	567.0	-	6454	1249.0	63
-chr1	72781	72801	657.0	+	chr1	72771	72791	406.0	-	72786	1063.0	-10
-chr1	22571	22591	609.0	+	chr1	22569	22589	254.0	-	22580	863.0	-2
-chr1	65152	65172	575.0	+	chr1	65148	65168	43.0	-	65160	618.0	-4
-chr1	106034	106054	558.0	+	chr1	106041	106061	14.0	-	106047	572.0	7
-chr1	155028	155048	522.0	+	chr1	155111	155131	1051.0	-	155079	1573.0	83
-chr1	32449	32469	476.0	+	chr1	32497	32517	2.0	-	32483	478.0	48
-chr1	6706	6726	431.0	+	chr1	6702	6722	2.0	-	6714	433.0	-4
-chr1	113782	113802	420.0	+	chr1	113762	113782	296.0	-	113782	716.0	-20
-chr1	228633	228653	371.0	+	chr1	228691	228711	255.0	-	228672	626.0	58
-chr1	438	458	334.0	+	chr1	468	488	468.0	-	463	802.0	30
-chr1	170119	170139	284.0	+	chr1	170129	170149	373.0	-	170134	657.0	10
-chr1	92631	92651	260.0	+	chr1	92664	92684	187.0	-	92657	447.0	33
-chr1	136366	136386	248.0	+	chr1	136352	136372	117.0	-	136369	365.0	-14
-chr1	108624	108644	206.0	+	chr1	108579	108599	367.0	-	108611	573.0	-45
-chr1	45678	45698	198.0	+	chr1	45643	45663	295.0	-	45670	493.0	-35
-chr1	368	388	192.0	+	chr1	446	466	170.0	-	417	362.0	78
-chr1	682	702	168.0	+	chr1	634	654	151.0	-	668	319.0	-48
-chr1	59190	59210	168.0	+	chr1	59246	59266	397.0	-	59228	565.0	56
-chr1	134170	134190	151.0	+	chr1	134270	134290	508.0	-	134230	659.0	100
-chr1	55495	55515	125.0	+	chr1	55581	55601	831.0	-	55548	956.0	86
-chr1	39197	39217	101.0	+	chr1	39258	39278	261.0	-	39237	362.0	61
-chr1	229721	229741	84.0	+	chr1	229784	229804	615.0	-	229762	699.0	63
-chr1	116660	116680	74.0	+	chr1	116619	116639	699.0	-	116649	773.0	-41
-chr1	19216	19236	42.0	+	chr1	19191	19211	736.0	-	19213	778.0	-25
-chr1	230110	230130	42.0	+	chr1	230173	230193	33.0	-	230151	75.0	63
-chr1	31627	31647	40.0	+	chr1	31693	31713	450.0	-	31670	490.0	66
-chr1	180280	180300	38.0	+	chr1	180362	180382	59.0	-	180331	97.0	82
-chr1	98528	98548	34.0	+	chr1	98555	98575	88.0	-	98551	122.0	27
-chr1	230163	230183	23.0	+	chr1	230150	230170	7.0	-	230166	30.0	-13
-chr1	173262	173282	11.0	+	chr1	173270	173290	535.0	-	173276	546.0	8
-chr1	230145	230165	8.0	+	chr1	230120	230140	2.0	-	230142	10.0	-25
-chr1	95920	95940	5.0	+	chr1	95971	95991	684.0	-	95955	689.0	51
-chr1	199418	199438	5.0	+	chr1	199388	199408	805.0	-	199413	810.0	-30
-chr1	197489	197509	3.0	+	chr1	197562	197582	2.0	-	197535	5.0	73
-chr1	96908	96928	2.0	+	chr1	96911	96931	10.0	-	96919	12.0	3
+chrom	start	end	value	strand	chrom	start	end	value	strand	midpoint	c-w reads sum	c-w distance (bp)
+chr1	87147	87167	3492.0	+	chr1	87198	87218	2207.0	-	87182	5699.0	51.0
+chr1	87	107	3211.0	+	chr1	139	159	993.0	-	123	4204.0	52.0
+chr1	48	68	2842.0	+	chr1	50	70	39.0	-	59	2881.0	2.0
+chr1	255	275	2810.0	+	chr1	215	235	2611.0	-	245	5421.0	-40.0
+chr1	117	137	2163.0	+	chr1	176	196	14.0	-	156	2177.0	59.0
+chr1	86954	86974	1948.0	+	chr1	87049	87069	422.0	-	87011	2370.0	95.0
+chr1	169107	169127	1811.0	+	chr1	169064	169084	76.0	-	169095	1887.0	-43.0
+chr1	87171	87191	1436.0	+	chr1	87158	87178	2039.0	-	87174	3475.0	-13.0
+chr1	201	221	1411.0	+	chr1	279	299	1328.0	-	250	2739.0	78.0
+chr1	229741	229761	1380.0	+	chr1	229757	229777	3151.0	-	229759	4531.0	16.0
+chr1	185076	185096	1309.0	+	chr1	185122	185142	62.0	-	185109	1371.0	46.0
+chr1	39081	39101	1268.0	+	chr1	39052	39072	82.0	-	39076	1350.0	-29.0
+chr1	92411	92431	1252.0	+	chr1	92411	92431	136.0	-	92421	1388.0	0.0
+chr1	203872	203892	1234.0	+	chr1	203835	203855	242.0	-	203863	1476.0	-37.0
+chr1	70776	70796	1148.0	+	chr1	70788	70808	998.0	-	70792	2146.0	12.0
+chr1	231	251	1146.0	+	chr1	261	281	1278.0	-	256	2424.0	30.0
+chr1	87098	87118	1125.0	+	chr1	87101	87121	1134.0	-	87109	2259.0	3.0
+chr1	6163	6183	1049.0	+	chr1	6254	6274	1076.0	-	6218	2125.0	91.0
+chr1	25246	25266	995.0	+	chr1	25345	25365	188.0	-	25305	1183.0	99.0
+chr1	101411	101431	973.0	+	chr1	101367	101387	1388.0	-	101399	2361.0	-44.0
+chr1	139213	139233	965.0	+	chr1	139228	139248	214.0	-	139230	1179.0	15.0
+chr1	87019	87039	769.0	+	chr1	86991	87011	65.0	-	87015	834.0	-28.0
+chr1	124318	124338	749.0	+	chr1	124275	124295	12.0	-	124306	761.0	-43.0
+chr1	348	368	699.0	+	chr1	323	343	486.0	-	345	1185.0	-25.0
+chr1	92543	92563	699.0	+	chr1	92639	92659	2137.0	-	92601	2836.0	96.0
+chr1	138868	138888	698.0	+	chr1	138864	138884	13.0	-	138876	711.0	-4.0
+chr1	307	327	685.0	+	chr1	373	393	200.0	-	350	885.0	66.0
+chr1	6413	6433	682.0	+	chr1	6476	6496	567.0	-	6454	1249.0	63.0
+chr1	72781	72801	657.0	+	chr1	72771	72791	406.0	-	72786	1063.0	-10.0
+chr1	22571	22591	609.0	+	chr1	22569	22589	254.0	-	22580	863.0	-2.0
+chr1	65152	65172	575.0	+	chr1	65148	65168	43.0	-	65160	618.0	-4.0
+chr1	106034	106054	558.0	+	chr1	106041	106061	14.0	-	106047	572.0	7.0
+chr1	155028	155048	522.0	+	chr1	155111	155131	1051.0	-	155079	1573.0	83.0
+chr1	32449	32469	476.0	+	chr1	32497	32517	2.0	-	32483	478.0	48.0
+chr1	6706	6726	431.0	+	chr1	6702	6722	2.0	-	6714	433.0	-4.0
+chr1	113782	113802	420.0	+	chr1	113762	113782	296.0	-	113782	716.0	-20.0
+chr1	228633	228653	371.0	+	chr1	228691	228711	255.0	-	228672	626.0	58.0
+chr1	438	458	334.0	+	chr1	468	488	468.0	-	463	802.0	30.0
+chr1	170119	170139	284.0	+	chr1	170129	170149	373.0	-	170134	657.0	10.0
+chr1	92631	92651	260.0	+	chr1	92664	92684	187.0	-	92657	447.0	33.0
+chr1	136366	136386	248.0	+	chr1	136352	136372	117.0	-	136369	365.0	-14.0
+chr1	108624	108644	206.0	+	chr1	108579	108599	367.0	-	108611	573.0	-45.0
+chr1	45678	45698	198.0	+	chr1	45643	45663	295.0	-	45670	493.0	-35.0
+chr1	368	388	192.0	+	chr1	446	466	170.0	-	417	362.0	78.0
+chr1	682	702	168.0	+	chr1	634	654	151.0	-	668	319.0	-48.0
+chr1	59190	59210	168.0	+	chr1	59246	59266	397.0	-	59228	565.0	56.0
+chr1	134170	134190	151.0	+	chr1	134270	134290	508.0	-	134230	659.0	100.0
+chr1	55495	55515	125.0	+	chr1	55581	55601	831.0	-	55548	956.0	86.0
+chr1	39197	39217	101.0	+	chr1	39258	39278	261.0	-	39237	362.0	61.0
+chr1	229721	229741	84.0	+	chr1	229784	229804	615.0	-	229762	699.0	63.0
+chr1	116660	116680	74.0	+	chr1	116619	116639	699.0	-	116649	773.0	-41.0
+chr1	19216	19236	42.0	+	chr1	19191	19211	736.0	-	19213	778.0	-25.0
+chr1	230110	230130	42.0	+	chr1	230173	230193	33.0	-	230151	75.0	63.0
+chr1	31627	31647	40.0	+	chr1	31693	31713	450.0	-	31670	490.0	66.0
+chr1	180280	180300	38.0	+	chr1	180362	180382	59.0	-	180331	97.0	82.0
+chr1	98528	98548	34.0	+	chr1	98555	98575	88.0	-	98551	122.0	27.0
+chr1	230163	230183	23.0	+	chr1	230150	230170	7.0	-	230166	30.0	-13.0
+chr1	173262	173282	11.0	+	chr1	173270	173290	535.0	-	173276	546.0	8.0
+chr1	230145	230165	8.0	+	chr1	230120	230140	2.0	-	230142	10.0	-25.0
+chr1	95920	95940	5.0	+	chr1	95971	95991	684.0	-	95955	689.0	51.0
+chr1	199418	199438	5.0	+	chr1	199388	199408	805.0	-	199413	810.0	-30.0
+chr1	197489	197509	3.0	+	chr1	197562	197582	2.0	-	197535	5.0	73.0
+chr1	96908	96928	2.0	+	chr1	96911	96931	10.0	-	96919	12.0	3.0
+chr1	151369	151389	2.0	+	chr1	151341	151361	593.0	-	151365	595.0	-28.0
--- a/test-data/largest_mp_output1.gff	Mon Nov 06 23:19:50 2017 -0500
+++ b/test-data/largest_mp_output1.gff	Thu May 02 08:30:22 2019 -0400
@@ -1,54 +1,55 @@
-chr1	cwpair	.	87182	87183	5699.0	.	.	cw_distance=51
-chr1	cwpair	.	176	177	4774.0	.	.	cw_distance=98
-chr1	cwpair	.	229759	229760	4531.0	.	.	cw_distance=16
-chr1	cwpair	.	123	124	4204.0	.	.	cw_distance=52
-chr1	cwpair	.	277	278	4138.0	.	.	cw_distance=24
-chr1	cwpair	.	87174	87175	3475.0	.	.	cw_distance=-13
-chr1	cwpair	.	59	60	2881.0	.	.	cw_distance=2
-chr1	cwpair	.	92601	92602	2836.0	.	.	cw_distance=96
-chr1	cwpair	.	241	242	2689.0	.	.	cw_distance=60
-chr1	cwpair	.	87011	87012	2370.0	.	.	cw_distance=95
-chr1	cwpair	.	87109	87110	2259.0	.	.	cw_distance=3
-chr1	cwpair	.	70792	70793	2146.0	.	.	cw_distance=12
-chr1	cwpair	.	6218	6219	2125.0	.	.	cw_distance=91
-chr1	cwpair	.	287	288	1632.0	.	.	cw_distance=92
-chr1	cwpair	.	155079	155080	1573.0	.	.	cw_distance=83
-chr1	cwpair	.	92421	92422	1388.0	.	.	cw_distance=0
-chr1	cwpair	.	185109	185110	1371.0	.	.	cw_distance=46
-chr1	cwpair	.	6454	6455	1249.0	.	.	cw_distance=63
-chr1	cwpair	.	25305	25306	1183.0	.	.	cw_distance=99
-chr1	cwpair	.	139230	139231	1179.0	.	.	cw_distance=15
-chr1	cwpair	.	72786	72787	1063.0	.	.	cw_distance=-10
-chr1	cwpair	.	55548	55549	956.0	.	.	cw_distance=86
-chr1	cwpair	.	370	371	899.0	.	.	cw_distance=25
-chr1	cwpair	.	22580	22581	863.0	.	.	cw_distance=-2
-chr1	cwpair	.	357	358	852.0	.	.	cw_distance=81
-chr1	cwpair	.	463	464	802.0	.	.	cw_distance=30
-chr1	cwpair	.	19213	19214	778.0	.	.	cw_distance=-25
-chr1	cwpair	.	113782	113783	716.0	.	.	cw_distance=-20
-chr1	cwpair	.	138876	138877	711.0	.	.	cw_distance=-4
-chr1	cwpair	.	229762	229763	699.0	.	.	cw_distance=63
-chr1	cwpair	.	95955	95956	689.0	.	.	cw_distance=51
-chr1	cwpair	.	134230	134231	659.0	.	.	cw_distance=100
-chr1	cwpair	.	170134	170135	657.0	.	.	cw_distance=10
-chr1	cwpair	.	228672	228673	626.0	.	.	cw_distance=58
-chr1	cwpair	.	65160	65161	618.0	.	.	cw_distance=-4
-chr1	cwpair	.	87006	87007	615.0	.	.	cw_distance=-11
-chr1	cwpair	.	106047	106048	572.0	.	.	cw_distance=7
-chr1	cwpair	.	59228	59229	565.0	.	.	cw_distance=56
-chr1	cwpair	.	173276	173277	546.0	.	.	cw_distance=8
-chr1	cwpair	.	31670	31671	490.0	.	.	cw_distance=66
-chr1	cwpair	.	32483	32484	478.0	.	.	cw_distance=48
-chr1	cwpair	.	178	179	465.0	.	.	cw_distance=16
-chr1	cwpair	.	92657	92658	447.0	.	.	cw_distance=33
-chr1	cwpair	.	6714	6715	433.0	.	.	cw_distance=-4
-chr1	cwpair	.	136369	136370	365.0	.	.	cw_distance=-14
-chr1	cwpair	.	417	418	362.0	.	.	cw_distance=78
-chr1	cwpair	.	39237	39238	362.0	.	.	cw_distance=61
-chr1	cwpair	.	627	628	247.0	.	.	cw_distance=33
-chr1	cwpair	.	98551	98552	122.0	.	.	cw_distance=27
-chr1	cwpair	.	180331	180332	97.0	.	.	cw_distance=82
-chr1	cwpair	.	230151	230152	75.0	.	.	cw_distance=63
-chr1	cwpair	.	230166	230167	30.0	.	.	cw_distance=-13
-chr1	cwpair	.	96919	96920	12.0	.	.	cw_distance=3
-chr1	cwpair	.	230142	230143	10.0	.	.	cw_distance=-25
+chr1	cwpair	.	87182	87183	5699.0	.	.	cw_distance=51.0
+chr1	cwpair	.	176	177	4774.0	.	.	cw_distance=98.0
+chr1	cwpair	.	229759	229760	4531.0	.	.	cw_distance=16.0
+chr1	cwpair	.	123	124	4204.0	.	.	cw_distance=52.0
+chr1	cwpair	.	277	278	4138.0	.	.	cw_distance=24.0
+chr1	cwpair	.	87174	87175	3475.0	.	.	cw_distance=-13.0
+chr1	cwpair	.	59	60	2881.0	.	.	cw_distance=2.0
+chr1	cwpair	.	92601	92602	2836.0	.	.	cw_distance=96.0
+chr1	cwpair	.	241	242	2689.0	.	.	cw_distance=60.0
+chr1	cwpair	.	87011	87012	2370.0	.	.	cw_distance=95.0
+chr1	cwpair	.	87109	87110	2259.0	.	.	cw_distance=3.0
+chr1	cwpair	.	70792	70793	2146.0	.	.	cw_distance=12.0
+chr1	cwpair	.	6218	6219	2125.0	.	.	cw_distance=91.0
+chr1	cwpair	.	287	288	1632.0	.	.	cw_distance=92.0
+chr1	cwpair	.	155079	155080	1573.0	.	.	cw_distance=83.0
+chr1	cwpair	.	92421	92422	1388.0	.	.	cw_distance=0.0
+chr1	cwpair	.	185109	185110	1371.0	.	.	cw_distance=46.0
+chr1	cwpair	.	6454	6455	1249.0	.	.	cw_distance=63.0
+chr1	cwpair	.	25305	25306	1183.0	.	.	cw_distance=99.0
+chr1	cwpair	.	139230	139231	1179.0	.	.	cw_distance=15.0
+chr1	cwpair	.	72786	72787	1063.0	.	.	cw_distance=-10.0
+chr1	cwpair	.	55548	55549	956.0	.	.	cw_distance=86.0
+chr1	cwpair	.	370	371	899.0	.	.	cw_distance=25.0
+chr1	cwpair	.	22580	22581	863.0	.	.	cw_distance=-2.0
+chr1	cwpair	.	357	358	852.0	.	.	cw_distance=81.0
+chr1	cwpair	.	463	464	802.0	.	.	cw_distance=30.0
+chr1	cwpair	.	19213	19214	778.0	.	.	cw_distance=-25.0
+chr1	cwpair	.	113782	113783	716.0	.	.	cw_distance=-20.0
+chr1	cwpair	.	138876	138877	711.0	.	.	cw_distance=-4.0
+chr1	cwpair	.	229762	229763	699.0	.	.	cw_distance=63.0
+chr1	cwpair	.	95955	95956	689.0	.	.	cw_distance=51.0
+chr1	cwpair	.	134230	134231	659.0	.	.	cw_distance=100.0
+chr1	cwpair	.	170134	170135	657.0	.	.	cw_distance=10.0
+chr1	cwpair	.	228672	228673	626.0	.	.	cw_distance=58.0
+chr1	cwpair	.	65160	65161	618.0	.	.	cw_distance=-4.0
+chr1	cwpair	.	87006	87007	615.0	.	.	cw_distance=-11.0
+chr1	cwpair	.	106047	106048	572.0	.	.	cw_distance=7.0
+chr1	cwpair	.	59228	59229	565.0	.	.	cw_distance=56.0
+chr1	cwpair	.	173276	173277	546.0	.	.	cw_distance=8.0
+chr1	cwpair	.	31670	31671	490.0	.	.	cw_distance=66.0
+chr1	cwpair	.	32483	32484	478.0	.	.	cw_distance=48.0
+chr1	cwpair	.	178	179	465.0	.	.	cw_distance=16.0
+chr1	cwpair	.	92657	92658	447.0	.	.	cw_distance=33.0
+chr1	cwpair	.	6714	6715	433.0	.	.	cw_distance=-4.0
+chr1	cwpair	.	136369	136370	365.0	.	.	cw_distance=-14.0
+chr1	cwpair	.	417	418	362.0	.	.	cw_distance=78.0
+chr1	cwpair	.	39237	39238	362.0	.	.	cw_distance=61.0
+chr1	cwpair	.	627	628	247.0	.	.	cw_distance=33.0
+chr1	cwpair	.	98551	98552	122.0	.	.	cw_distance=27.0
+chr1	cwpair	.	180331	180332	97.0	.	.	cw_distance=82.0
+chr1	cwpair	.	230151	230152	75.0	.	.	cw_distance=63.0
+chr1	cwpair	.	230166	230167	30.0	.	.	cw_distance=-13.0
+chr1	cwpair	.	96919	96920	12.0	.	.	cw_distance=3.0
+chr1	cwpair	.	230142	230143	10.0	.	.	cw_distance=-25.0
+chr1	cwpair	.	197535	197536	5.0	.	.	cw_distance=73.0
--- a/test-data/largest_mp_output2.gff	Mon Nov 06 23:19:50 2017 -0500
+++ b/test-data/largest_mp_output2.gff	Thu May 02 08:30:22 2019 -0400
@@ -1,63 +1,64 @@
-chr1	cwpair	.	87182	87183	5699.0	.	.	cw_distance=51
-chr1	cwpair	.	245	246	5421.0	.	.	cw_distance=-40
-chr1	cwpair	.	229759	229760	4531.0	.	.	cw_distance=16
-chr1	cwpair	.	123	124	4204.0	.	.	cw_distance=52
-chr1	cwpair	.	87174	87175	3475.0	.	.	cw_distance=-13
-chr1	cwpair	.	59	60	2881.0	.	.	cw_distance=2
-chr1	cwpair	.	92601	92602	2836.0	.	.	cw_distance=96
-chr1	cwpair	.	250	251	2739.0	.	.	cw_distance=78
-chr1	cwpair	.	256	257	2424.0	.	.	cw_distance=30
-chr1	cwpair	.	87011	87012	2370.0	.	.	cw_distance=95
-chr1	cwpair	.	101399	101400	2361.0	.	.	cw_distance=-44
-chr1	cwpair	.	87109	87110	2259.0	.	.	cw_distance=3
-chr1	cwpair	.	156	157	2177.0	.	.	cw_distance=59
-chr1	cwpair	.	70792	70793	2146.0	.	.	cw_distance=12
-chr1	cwpair	.	6218	6219	2125.0	.	.	cw_distance=91
-chr1	cwpair	.	169095	169096	1887.0	.	.	cw_distance=-43
-chr1	cwpair	.	155079	155080	1573.0	.	.	cw_distance=83
-chr1	cwpair	.	203863	203864	1476.0	.	.	cw_distance=-37
-chr1	cwpair	.	92421	92422	1388.0	.	.	cw_distance=0
-chr1	cwpair	.	185109	185110	1371.0	.	.	cw_distance=46
-chr1	cwpair	.	39076	39077	1350.0	.	.	cw_distance=-29
-chr1	cwpair	.	6454	6455	1249.0	.	.	cw_distance=63
-chr1	cwpair	.	345	346	1185.0	.	.	cw_distance=-25
-chr1	cwpair	.	25305	25306	1183.0	.	.	cw_distance=99
-chr1	cwpair	.	139230	139231	1179.0	.	.	cw_distance=15
-chr1	cwpair	.	72786	72787	1063.0	.	.	cw_distance=-10
-chr1	cwpair	.	55548	55549	956.0	.	.	cw_distance=86
-chr1	cwpair	.	350	351	885.0	.	.	cw_distance=66
-chr1	cwpair	.	22580	22581	863.0	.	.	cw_distance=-2
-chr1	cwpair	.	87015	87016	834.0	.	.	cw_distance=-28
-chr1	cwpair	.	199413	199414	810.0	.	.	cw_distance=-30
-chr1	cwpair	.	463	464	802.0	.	.	cw_distance=30
-chr1	cwpair	.	19213	19214	778.0	.	.	cw_distance=-25
-chr1	cwpair	.	116649	116650	773.0	.	.	cw_distance=-41
-chr1	cwpair	.	124306	124307	761.0	.	.	cw_distance=-43
-chr1	cwpair	.	113782	113783	716.0	.	.	cw_distance=-20
-chr1	cwpair	.	138876	138877	711.0	.	.	cw_distance=-4
-chr1	cwpair	.	229762	229763	699.0	.	.	cw_distance=63
-chr1	cwpair	.	95955	95956	689.0	.	.	cw_distance=51
-chr1	cwpair	.	134230	134231	659.0	.	.	cw_distance=100
-chr1	cwpair	.	170134	170135	657.0	.	.	cw_distance=10
-chr1	cwpair	.	228672	228673	626.0	.	.	cw_distance=58
-chr1	cwpair	.	65160	65161	618.0	.	.	cw_distance=-4
-chr1	cwpair	.	151365	151366	595.0	.	.	cw_distance=-28
-chr1	cwpair	.	108611	108612	573.0	.	.	cw_distance=-45
-chr1	cwpair	.	106047	106048	572.0	.	.	cw_distance=7
-chr1	cwpair	.	59228	59229	565.0	.	.	cw_distance=56
-chr1	cwpair	.	173276	173277	546.0	.	.	cw_distance=8
-chr1	cwpair	.	45670	45671	493.0	.	.	cw_distance=-35
-chr1	cwpair	.	31670	31671	490.0	.	.	cw_distance=66
-chr1	cwpair	.	32483	32484	478.0	.	.	cw_distance=48
-chr1	cwpair	.	92657	92658	447.0	.	.	cw_distance=33
-chr1	cwpair	.	6714	6715	433.0	.	.	cw_distance=-4
-chr1	cwpair	.	136369	136370	365.0	.	.	cw_distance=-14
-chr1	cwpair	.	417	418	362.0	.	.	cw_distance=78
-chr1	cwpair	.	39237	39238	362.0	.	.	cw_distance=61
-chr1	cwpair	.	668	669	319.0	.	.	cw_distance=-48
-chr1	cwpair	.	98551	98552	122.0	.	.	cw_distance=27
-chr1	cwpair	.	180331	180332	97.0	.	.	cw_distance=82
-chr1	cwpair	.	230151	230152	75.0	.	.	cw_distance=63
-chr1	cwpair	.	230166	230167	30.0	.	.	cw_distance=-13
-chr1	cwpair	.	96919	96920	12.0	.	.	cw_distance=3
-chr1	cwpair	.	230142	230143	10.0	.	.	cw_distance=-25
+chr1	cwpair	.	87182	87183	5699.0	.	.	cw_distance=51.0
+chr1	cwpair	.	245	246	5421.0	.	.	cw_distance=-40.0
+chr1	cwpair	.	229759	229760	4531.0	.	.	cw_distance=16.0
+chr1	cwpair	.	123	124	4204.0	.	.	cw_distance=52.0
+chr1	cwpair	.	87174	87175	3475.0	.	.	cw_distance=-13.0
+chr1	cwpair	.	59	60	2881.0	.	.	cw_distance=2.0
+chr1	cwpair	.	92601	92602	2836.0	.	.	cw_distance=96.0
+chr1	cwpair	.	250	251	2739.0	.	.	cw_distance=78.0
+chr1	cwpair	.	256	257	2424.0	.	.	cw_distance=30.0
+chr1	cwpair	.	87011	87012	2370.0	.	.	cw_distance=95.0
+chr1	cwpair	.	101399	101400	2361.0	.	.	cw_distance=-44.0
+chr1	cwpair	.	87109	87110	2259.0	.	.	cw_distance=3.0
+chr1	cwpair	.	156	157	2177.0	.	.	cw_distance=59.0
+chr1	cwpair	.	70792	70793	2146.0	.	.	cw_distance=12.0
+chr1	cwpair	.	6218	6219	2125.0	.	.	cw_distance=91.0
+chr1	cwpair	.	169095	169096	1887.0	.	.	cw_distance=-43.0
+chr1	cwpair	.	155079	155080	1573.0	.	.	cw_distance=83.0
+chr1	cwpair	.	203863	203864	1476.0	.	.	cw_distance=-37.0
+chr1	cwpair	.	92421	92422	1388.0	.	.	cw_distance=0.0
+chr1	cwpair	.	185109	185110	1371.0	.	.	cw_distance=46.0
+chr1	cwpair	.	39076	39077	1350.0	.	.	cw_distance=-29.0
+chr1	cwpair	.	6454	6455	1249.0	.	.	cw_distance=63.0
+chr1	cwpair	.	345	346	1185.0	.	.	cw_distance=-25.0
+chr1	cwpair	.	25305	25306	1183.0	.	.	cw_distance=99.0
+chr1	cwpair	.	139230	139231	1179.0	.	.	cw_distance=15.0
+chr1	cwpair	.	72786	72787	1063.0	.	.	cw_distance=-10.0
+chr1	cwpair	.	55548	55549	956.0	.	.	cw_distance=86.0
+chr1	cwpair	.	350	351	885.0	.	.	cw_distance=66.0
+chr1	cwpair	.	22580	22581	863.0	.	.	cw_distance=-2.0
+chr1	cwpair	.	87015	87016	834.0	.	.	cw_distance=-28.0
+chr1	cwpair	.	199413	199414	810.0	.	.	cw_distance=-30.0
+chr1	cwpair	.	463	464	802.0	.	.	cw_distance=30.0
+chr1	cwpair	.	19213	19214	778.0	.	.	cw_distance=-25.0
+chr1	cwpair	.	116649	116650	773.0	.	.	cw_distance=-41.0
+chr1	cwpair	.	124306	124307	761.0	.	.	cw_distance=-43.0
+chr1	cwpair	.	113782	113783	716.0	.	.	cw_distance=-20.0
+chr1	cwpair	.	138876	138877	711.0	.	.	cw_distance=-4.0
+chr1	cwpair	.	229762	229763	699.0	.	.	cw_distance=63.0
+chr1	cwpair	.	95955	95956	689.0	.	.	cw_distance=51.0
+chr1	cwpair	.	134230	134231	659.0	.	.	cw_distance=100.0
+chr1	cwpair	.	170134	170135	657.0	.	.	cw_distance=10.0
+chr1	cwpair	.	228672	228673	626.0	.	.	cw_distance=58.0
+chr1	cwpair	.	65160	65161	618.0	.	.	cw_distance=-4.0
+chr1	cwpair	.	151365	151366	595.0	.	.	cw_distance=-28.0
+chr1	cwpair	.	108611	108612	573.0	.	.	cw_distance=-45.0
+chr1	cwpair	.	106047	106048	572.0	.	.	cw_distance=7.0
+chr1	cwpair	.	59228	59229	565.0	.	.	cw_distance=56.0
+chr1	cwpair	.	173276	173277	546.0	.	.	cw_distance=8.0
+chr1	cwpair	.	45670	45671	493.0	.	.	cw_distance=-35.0
+chr1	cwpair	.	31670	31671	490.0	.	.	cw_distance=66.0
+chr1	cwpair	.	32483	32484	478.0	.	.	cw_distance=48.0
+chr1	cwpair	.	92657	92658	447.0	.	.	cw_distance=33.0
+chr1	cwpair	.	6714	6715	433.0	.	.	cw_distance=-4.0
+chr1	cwpair	.	136369	136370	365.0	.	.	cw_distance=-14.0
+chr1	cwpair	.	417	418	362.0	.	.	cw_distance=78.0
+chr1	cwpair	.	39237	39238	362.0	.	.	cw_distance=61.0
+chr1	cwpair	.	668	669	319.0	.	.	cw_distance=-48.0
+chr1	cwpair	.	98551	98552	122.0	.	.	cw_distance=27.0
+chr1	cwpair	.	180331	180332	97.0	.	.	cw_distance=82.0
+chr1	cwpair	.	230151	230152	75.0	.	.	cw_distance=63.0
+chr1	cwpair	.	230166	230167	30.0	.	.	cw_distance=-13.0
+chr1	cwpair	.	96919	96920	12.0	.	.	cw_distance=3.0
+chr1	cwpair	.	230142	230143	10.0	.	.	cw_distance=-25.0
+chr1	cwpair	.	197535	197536	5.0	.	.	cw_distance=73.0
--- a/test-data/largest_o_output2.tabular	Mon Nov 06 23:19:50 2017 -0500
+++ b/test-data/largest_o_output2.tabular	Thu May 02 08:30:22 2019 -0400
@@ -1,100 +1,372 @@
-chrom	strand	start	end	value
-chr1	+	100364	100384	2695.0
-chr1	+	30	50	2140.0
-chr1	+	5379	5399	1572.0
-chr1	+	52440	52460	1562.0
-chr1	+	73234	73254	1492.0
-chr1	+	31096	31116	1481.0
-chr1	+	145253	145273	1394.0
-chr1	+	10641	10661	1359.0
-chr1	+	200580	200600	1298.0
-chr1	+	64772	64792	1292.0
-chr1	+	86886	86906	1253.0
-chr1	+	103207	103227	1229.0
-chr1	+	43835	43855	1173.0
-chr1	+	29570	29590	1130.0
-chr1	+	83774	83794	1125.0
-chr1	+	165827	165847	1109.0
-chr1	+	92775	92795	1105.0
-chr1	+	4748	4768	1077.0
-chr1	+	126733	126753	952.0
-chr1	+	71041	71061	881.0
-chr1	+	35773	35793	866.0
-chr1	+	53097	53117	835.0
-chr1	+	71556	71576	835.0
-chr1	+	30964	30984	829.0
-chr1	+	31019	31039	810.0
-chr1	+	55349	55369	794.0
-chr1	+	203193	203213	789.0
-chr1	+	39794	39814	780.0
-chr1	+	153928	153948	768.0
-chr1	+	179472	179492	696.0
-chr1	+	178117	178137	686.0
-chr1	+	1298	1318	684.0
-chr1	+	87085	87105	676.0
-chr1	+	192754	192774	668.0
-chr1	+	89611	89631	640.0
-chr1	+	20205	20225	634.0
-chr1	+	118428	118448	633.0
-chr1	+	110736	110756	621.0
-chr1	+	48642	48662	610.0
-chr1	+	159372	159392	605.0
-chr1	+	6453	6473	601.0
-chr1	+	112137	112157	601.0
-chr1	+	142905	142925	599.0
-chr1	+	167443	167463	597.0
-chr1	+	126073	126093	590.0
-chr1	+	6233	6253	589.0
-chr1	+	43657	43677	586.0
-chr1	+	134021	134041	572.0
-chr1	+	29864	29884	570.0
-chr1	+	70953	70973	555.0
-chr1	+	87002	87022	550.0
-chr1	+	129555	129575	536.0
-chr1	+	119754	119774	515.0
-chr1	+	43523	43543	505.0
-chr1	+	97898	97918	501.0
-chr1	+	40830	40850	491.0
-chr1	+	153095	153115	490.0
-chr1	+	7303	7323	484.0
-chr1	+	115866	115886	480.0
-chr1	+	129680	129700	464.0
-chr1	+	187155	187175	455.0
-chr1	+	192271	192291	453.0
-chr1	+	160	180	451.0
-chr1	+	150449	150469	436.0
-chr1	+	9367	9387	425.0
-chr1	+	93793	93813	415.0
-chr1	+	87572	87592	407.0
-chr1	+	124845	124865	383.0
-chr1	+	4053	4073	381.0
-chr1	+	136072	136092	380.0
-chr1	+	39942	39962	375.0
-chr1	+	61977	61997	368.0
-chr1	+	2976	2996	356.0
-chr1	+	27978	27998	354.0
-chr1	+	195756	195776	348.0
-chr1	+	172223	172243	338.0
-chr1	+	143657	143677	328.0
-chr1	+	45409	45429	307.0
-chr1	+	45248	45268	305.0
-chr1	+	72671	72691	304.0
-chr1	+	68564	68584	303.0
-chr1	+	119953	119973	295.0
-chr1	+	48319	48339	290.0
-chr1	+	48772	48792	284.0
-chr1	+	126369	126389	284.0
-chr1	+	116432	116452	267.0
-chr1	+	199649	199669	264.0
-chr1	+	204126	204146	261.0
-chr1	+	130514	130534	243.0
-chr1	+	55692	55712	228.0
-chr1	+	117198	117218	228.0
-chr1	+	42843	42863	218.0
-chr1	+	59583	59603	204.0
-chr1	+	124669	124689	203.0
-chr1	+	2613	2633	202.0
-chr1	+	40264	40284	199.0
-chr1	+	21406	21426	177.0
-chr1	+	20391	20411	173.0
-chr1	+	20626	20646	171.0
+chrom	strand	start	end	value
+chr1	+	100364	100384	2695.0
+chr1	+	30	50	2140.0
+chr1	+	5379	5399	1572.0
+chr1	+	52440	52460	1562.0
+chr1	+	73234	73254	1492.0
+chr1	+	31096	31116	1481.0
+chr1	+	145253	145273	1394.0
+chr1	+	10641	10661	1359.0
+chr1	+	200580	200600	1298.0
+chr1	+	64772	64792	1292.0
+chr1	+	86886	86906	1253.0
+chr1	+	103207	103227	1229.0
+chr1	+	43835	43855	1173.0
+chr1	+	29570	29590	1130.0
+chr1	+	83774	83794	1125.0
+chr1	+	165827	165847	1109.0
+chr1	+	92775	92795	1105.0
+chr1	+	4748	4768	1077.0
+chr1	+	126733	126753	952.0
+chr1	+	71041	71061	881.0
+chr1	+	35773	35793	866.0
+chr1	+	53097	53117	835.0
+chr1	+	71556	71576	835.0
+chr1	+	30964	30984	829.0
+chr1	+	31019	31039	810.0
+chr1	+	55349	55369	794.0
+chr1	+	203193	203213	789.0
+chr1	+	39794	39814	780.0
+chr1	+	153928	153948	768.0
+chr1	+	179472	179492	696.0
+chr1	+	178117	178137	686.0
+chr1	+	1298	1318	684.0
+chr1	+	87085	87105	676.0
+chr1	+	192754	192774	668.0
+chr1	+	89611	89631	640.0
+chr1	+	20205	20225	634.0
+chr1	+	118428	118448	633.0
+chr1	+	110736	110756	621.0
+chr1	+	48642	48662	610.0
+chr1	+	159372	159392	605.0
+chr1	+	6453	6473	601.0
+chr1	+	112137	112157	601.0
+chr1	+	142905	142925	599.0
+chr1	+	167443	167463	597.0
+chr1	+	126073	126093	590.0
+chr1	+	6233	6253	589.0
+chr1	+	43657	43677	586.0
+chr1	+	134021	134041	572.0
+chr1	+	29864	29884	570.0
+chr1	+	70953	70973	555.0
+chr1	+	87002	87022	550.0
+chr1	+	129555	129575	536.0
+chr1	+	119754	119774	515.0
+chr1	+	43523	43543	505.0
+chr1	+	97898	97918	501.0
+chr1	+	40830	40850	491.0
+chr1	+	153095	153115	490.0
+chr1	+	7303	7323	484.0
+chr1	+	115866	115886	480.0
+chr1	+	129680	129700	464.0
+chr1	+	187155	187175	455.0
+chr1	+	192271	192291	453.0
+chr1	+	160	180	451.0
+chr1	+	150449	150469	436.0
+chr1	+	9367	9387	425.0
+chr1	+	93793	93813	415.0
+chr1	+	11	31	414.0
+chr1	+	87572	87592	407.0
+chr1	+	124845	124865	383.0
+chr1	+	4053	4073	381.0
+chr1	+	136072	136092	380.0
+chr1	+	39942	39962	375.0
+chr1	+	61977	61997	368.0
+chr1	+	2976	2996	356.0
+chr1	+	27978	27998	354.0
+chr1	+	195756	195776	348.0
+chr1	+	172223	172243	338.0
+chr1	+	143657	143677	328.0
+chr1	+	45409	45429	307.0
+chr1	+	45248	45268	305.0
+chr1	+	72671	72691	304.0
+chr1	+	68564	68584	303.0
+chr1	+	119953	119973	295.0
+chr1	+	48319	48339	290.0
+chr1	+	48772	48792	284.0
+chr1	+	126369	126389	284.0
+chr1	+	116432	116452	267.0
+chr1	+	199649	199669	264.0
+chr1	+	204126	204146	261.0
+chr1	+	130514	130534	243.0
+chr1	+	55692	55712	228.0
+chr1	+	117198	117218	228.0
+chr1	+	42843	42863	218.0
+chr1	+	59583	59603	204.0
+chr1	+	124669	124689	203.0
+chr1	+	2613	2633	202.0
+chr1	+	40264	40284	199.0
+chr1	+	21406	21426	177.0
+chr1	+	20391	20411	173.0
+chr1	+	20626	20646	171.0
+chr1	+	198594	198614	170.0
+chr1	+	149343	149363	159.0
+chr1	+	121016	121036	155.0
+chr1	+	180652	180672	154.0
+chr1	+	5794	5814	148.0
+chr1	+	187009	187029	139.0
+chr1	+	119736	119756	135.0
+chr1	+	152678	152698	135.0
+chr1	+	47015	47035	133.0
+chr1	+	156252	156272	133.0
+chr1	+	41008	41028	132.0
+chr1	+	147211	147231	130.0
+chr1	+	112900	112920	125.0
+chr1	+	91379	91399	120.0
+chr1	+	227346	227366	114.0
+chr1	+	77731	77751	113.0
+chr1	+	229862	229882	110.0
+chr1	+	512	532	101.0
+chr1	+	147227	147247	101.0
+chr1	+	44687	44707	100.0
+chr1	+	467	487	98.0
+chr1	+	601	621	96.0
+chr1	+	4445	4465	94.0
+chr1	+	110540	110560	91.0
+chr1	+	169159	169179	91.0
+chr1	+	103108	103128	90.0
+chr1	+	121289	121309	89.0
+chr1	+	134559	134579	87.0
+chr1	+	90412	90432	86.0
+chr1	+	133139	133159	84.0
+chr1	+	90040	90060	82.0
+chr1	+	86865	86885	81.0
+chr1	+	59248	59268	80.0
+chr1	+	42925	42945	77.0
+chr1	+	189494	189514	70.0
+chr1	+	146517	146537	69.0
+chr1	+	32145	32165	66.0
+chr1	+	68018	68038	62.0
+chr1	+	210175	210195	62.0
+chr1	+	48431	48451	57.0
+chr1	+	177627	177647	51.0
+chr1	+	97967	97987	50.0
+chr1	+	191408	191428	50.0
+chr1	+	33829	33849	48.0
+chr1	+	76365	76385	47.0
+chr1	+	105499	105519	46.0
+chr1	+	176858	176878	46.0
+chr1	+	92982	93002	44.0
+chr1	+	142139	142159	43.0
+chr1	+	110130	110150	42.0
+chr1	+	151431	151451	38.0
+chr1	+	219301	219321	37.0
+chr1	+	102337	102357	36.0
+chr1	+	134868	134888	36.0
+chr1	+	204214	204234	36.0
+chr1	+	76501	76521	33.0
+chr1	+	179554	179574	31.0
+chr1	+	113226	113246	28.0
+chr1	+	6255	6275	26.0
+chr1	+	5750	5770	25.0
+chr1	+	105942	105962	25.0
+chr1	+	140857	140877	23.0
+chr1	+	166238	166258	21.0
+chr1	+	111317	111337	17.0
+chr1	+	16501	16521	15.0
+chr1	+	22268	22288	15.0
+chr1	+	147322	147342	15.0
+chr1	+	201841	201861	15.0
+chr1	+	7753	7773	14.0
+chr1	+	12305	12325	13.0
+chr1	+	2293	2313	12.0
+chr1	+	16173	16193	12.0
+chr1	+	142950	142970	12.0
+chr1	+	91215	91235	11.0
+chr1	+	39591	39611	10.0
+chr1	+	43147	43167	9.0
+chr1	+	119155	119175	9.0
+chr1	+	20117	20137	8.0
+chr1	+	110602	110622	8.0
+chr1	+	206684	206704	8.0
+chr1	+	188920	188940	7.0
+chr1	+	81481	81501	5.0
+chr1	+	138051	138071	5.0
+chr1	+	167652	167672	5.0
+chr1	+	228150	228170	5.0
+chr1	+	24765	24785	4.0
+chr1	+	183610	183630	4.0
+chr1	+	125727	125747	3.0
+chr1	+	33426	33446	2.0
+chr1	+	49283	49303	2.0
+chr1	+	89663	89683	2.0
+chr1	+	138030	138050	2.0
+chr1	+	156097	156117	2.0
+chr1	+	158038	158058	2.0
+chr1	+	169338	169358	2.0
+chr1	+	175899	175919	2.0
+chr1	+	199141	199161	2.0
+chr1	-	388	408	167.0
+chr1	-	410	430	8.0
+chr1	-	1457	1477	111.0
+chr1	-	1970	1990	629.0
+chr1	-	3148	3168	1420.0
+chr1	-	4892	4912	272.0
+chr1	-	5546	5566	27.0
+chr1	-	7659	7679	243.0
+chr1	-	8596	8616	114.0
+chr1	-	8904	8924	80.0
+chr1	-	9119	9139	22.0
+chr1	-	10107	10127	1622.0
+chr1	-	12157	12177	40.0
+chr1	-	13415	13435	634.0
+chr1	-	16739	16759	3.0
+chr1	-	19145	19165	618.0
+chr1	-	20550	20570	865.0
+chr1	-	22383	22403	141.0
+chr1	-	23046	23066	213.0
+chr1	-	27517	27537	1459.0
+chr1	-	29325	29345	1074.0
+chr1	-	30046	30066	17.0
+chr1	-	31876	31896	1344.0
+chr1	-	37166	37186	1000.0
+chr1	-	38768	38788	1064.0
+chr1	-	38799	38819	9.0
+chr1	-	39000	39020	3.0
+chr1	-	39293	39313	2.0
+chr1	-	41867	41887	7.0
+chr1	-	45565	45585	246.0
+chr1	-	45579	45599	78.0
+chr1	-	46616	46636	741.0
+chr1	-	49660	49680	6.0
+chr1	-	50091	50111	156.0
+chr1	-	51978	51998	633.0
+chr1	-	52308	52328	549.0
+chr1	-	53045	53065	31.0
+chr1	-	55616	55636	984.0
+chr1	-	56542	56562	606.0
+chr1	-	56664	56684	67.0
+chr1	-	56995	57015	1393.0
+chr1	-	57121	57141	4.0
+chr1	-	57212	57232	667.0
+chr1	-	57543	57563	2.0
+chr1	-	59157	59177	168.0
+chr1	-	61877	61897	607.0
+chr1	-	65687	65707	596.0
+chr1	-	66306	66326	2.0
+chr1	-	68423	68443	139.0
+chr1	-	70336	70356	652.0
+chr1	-	72810	72830	212.0
+chr1	-	74763	74783	430.0
+chr1	-	75897	75917	10.0
+chr1	-	77515	77535	797.0
+chr1	-	77530	77550	513.0
+chr1	-	78813	78833	113.0
+chr1	-	80958	80978	137.0
+chr1	-	81037	81057	4.0
+chr1	-	81972	81992	49.0
+chr1	-	85759	85779	77.0
+chr1	-	86166	86186	969.0
+chr1	-	86280	86300	14.0
+chr1	-	87234	87254	637.0
+chr1	-	87262	87282	505.0
+chr1	-	87289	87309	1270.0
+chr1	-	87327	87347	729.0
+chr1	-	87468	87488	304.0
+chr1	-	88213	88233	301.0
+chr1	-	88376	88396	56.0
+chr1	-	89175	89195	23.0
+chr1	-	91926	91946	10.0
+chr1	-	92541	92561	602.0
+chr1	-	92571	92591	90.0
+chr1	-	94913	94933	1437.0
+chr1	-	96278	96298	166.0
+chr1	-	96315	96335	2.0
+chr1	-	96566	96586	6.0
+chr1	-	101301	101321	48.0
+chr1	-	102072	102092	14.0
+chr1	-	102903	102923	846.0
+chr1	-	104110	104130	117.0
+chr1	-	105663	105683	417.0
+chr1	-	105814	105834	529.0
+chr1	-	105846	105866	177.0
+chr1	-	105889	105909	84.0
+chr1	-	106340	106360	421.0
+chr1	-	108072	108092	72.0
+chr1	-	108263	108283	145.0
+chr1	-	111947	111967	585.0
+chr1	-	114306	114326	2.0
+chr1	-	116148	116168	248.0
+chr1	-	117522	117542	1573.0
+chr1	-	117845	117865	16.0
+chr1	-	118841	118861	7.0
+chr1	-	119430	119450	1093.0
+chr1	-	119596	119616	842.0
+chr1	-	119657	119677	499.0
+chr1	-	119669	119689	665.0
+chr1	-	119866	119886	846.0
+chr1	-	119880	119900	1136.0
+chr1	-	120788	120808	105.0
+chr1	-	122624	122644	201.0
+chr1	-	122777	122797	20.0
+chr1	-	123718	123738	751.0
+chr1	-	125840	125860	273.0
+chr1	-	127027	127047	590.0
+chr1	-	130869	130889	718.0
+chr1	-	133644	133664	122.0
+chr1	-	135051	135071	63.0
+chr1	-	137428	137448	1200.0
+chr1	-	137816	137836	695.0
+chr1	-	139627	139647	531.0
+chr1	-	140133	140153	441.0
+chr1	-	140770	140790	556.0
+chr1	-	141182	141202	14.0
+chr1	-	143551	143571	3.0
+chr1	-	144669	144689	1192.0
+chr1	-	145383	145403	326.0
+chr1	-	147573	147593	255.0
+chr1	-	148690	148710	2.0
+chr1	-	149704	149724	74.0
+chr1	-	150358	150378	153.0
+chr1	-	152984	153004	106.0
+chr1	-	153812	153832	168.0
+chr1	-	154862	154882	14.0
+chr1	-	155456	155476	23.0
+chr1	-	155897	155917	10.0
+chr1	-	157559	157579	337.0
+chr1	-	166467	166487	582.0
+chr1	-	166631	166651	173.0
+chr1	-	169500	169520	814.0
+chr1	-	170282	170302	63.0
+chr1	-	171063	171083	212.0
+chr1	-	175188	175208	117.0
+chr1	-	175474	175494	1119.0
+chr1	-	176004	176024	1473.0
+chr1	-	177140	177160	93.0
+chr1	-	177386	177406	289.0
+chr1	-	178846	178866	601.0
+chr1	-	178971	178991	723.0
+chr1	-	179116	179136	71.0
+chr1	-	180272	180292	25.0
+chr1	-	180995	181015	299.0
+chr1	-	182588	182608	465.0
+chr1	-	182790	182810	355.0
+chr1	-	185673	185693	190.0
+chr1	-	187422	187442	20.0
+chr1	-	187976	187996	728.0
+chr1	-	196499	196519	224.0
+chr1	-	197060	197080	224.0
+chr1	-	197151	197171	1464.0
+chr1	-	197342	197362	204.0
+chr1	-	198423	198443	598.0
+chr1	-	198953	198973	3.0
+chr1	-	199935	199955	31.0
+chr1	-	201308	201328	1287.0
+chr1	-	201651	201671	892.0
+chr1	-	202977	202997	163.0
+chr1	-	203452	203472	76.0
+chr1	-	206245	206265	22.0
+chr1	-	207675	207695	313.0
+chr1	-	208559	208579	121.0
+chr1	-	209205	209225	176.0
+chr1	-	220863	220883	2.0
+chr1	-	223035	223055	62.0
+chr1	-	225156	225176	2.0
+chr1	-	226777	226797	444.0
+chr1	-	227608	227628	1311.0
+chr1	-	228405	228425	1447.0
+chr1	-	229031	229051	6.0
+chr1	-	229583	229603	62.0
+chr1	-	229665	229685	131.0
+chr1	-	229965	229985	13.0
+chr1	-	230132	230152	2.0
--- a/test-data/mode_d_output2.tabular	Mon Nov 06 23:19:50 2017 -0500
+++ b/test-data/mode_d_output2.tabular	Thu May 02 08:30:22 2019 -0400
@@ -1,67 +1,67 @@
-chrom	start	end	value	strand	chrom	start	end	value	strand	midpoint	c-w reads sum	c-w distance (bp)
-chr1	87147	87167	3492.0	+	chr1	87158	87178	2039.0	-	87162	5531.0	11.0
-chr1	87	107	3211.0	+	chr1	139	159	993.0	-	123	4204.0	52.0
-chr1	48	68	2842.0	+	chr1	50	70	39.0	-	59	2881.0	2.0
-chr1	255	275	2810.0	+	chr1	279	299	1328.0	-	277	4138.0	24.0
-chr1	117	137	2163.0	+	chr1	176	196	14.0	-	156	2177.0	59.0
-chr1	86954	86974	1948.0	+	chr1	86991	87011	65.0	-	86982	2013.0	37.0
-chr1	169107	169127	1811.0	+	chr1	169064	169084	76.0	-	169095	1887.0	-43.0
-chr1	87171	87191	1436.0	+	chr1	87198	87218	2207.0	-	87194	3643.0	27.0
-chr1	201	221	1411.0	+	chr1	215	235	2611.0	-	218	4022.0	14.0
-chr1	229741	229761	1380.0	+	chr1	229757	229777	3151.0	-	229759	4531.0	16.0
-chr1	185076	185096	1309.0	+	chr1	185122	185142	62.0	-	185109	1371.0	46.0
-chr1	39081	39101	1268.0	+	chr1	39052	39072	82.0	-	39076	1350.0	-29.0
-chr1	92411	92431	1252.0	+	chr1	92411	92431	136.0	-	92421	1388.0	0.0
-chr1	203872	203892	1234.0	+	chr1	203835	203855	242.0	-	203863	1476.0	-37.0
-chr1	70776	70796	1148.0	+	chr1	70788	70808	998.0	-	70792	2146.0	12.0
-chr1	231	251	1146.0	+	chr1	261	281	1278.0	-	256	2424.0	30.0
-chr1	87098	87118	1125.0	+	chr1	87101	87121	1134.0	-	87109	2259.0	3.0
-chr1	6163	6183	1049.0	+	chr1	6254	6274	1076.0	-	6218	2125.0	91.0
-chr1	25246	25266	995.0	+	chr1	25345	25365	188.0	-	25305	1183.0	99.0
-chr1	101411	101431	973.0	+	chr1	101367	101387	1388.0	-	101399	2361.0	-44.0
-chr1	139213	139233	965.0	+	chr1	139228	139248	214.0	-	139230	1179.0	15.0
-chr1	87019	87039	769.0	+	chr1	87049	87069	422.0	-	87044	1191.0	30.0
-chr1	124318	124338	749.0	+	chr1	124275	124295	12.0	-	124306	761.0	-43.0
-chr1	348	368	699.0	+	chr1	373	393	200.0	-	370	899.0	25.0
-chr1	92543	92563	699.0	+	chr1	92571	92591	90.0	-	92567	789.0	28.0
-chr1	138868	138888	698.0	+	chr1	138864	138884	13.0	-	138876	711.0	-4.0
-chr1	307	327	685.0	+	chr1	323	343	486.0	-	325	1171.0	16.0
-chr1	6413	6433	682.0	+	chr1	6476	6496	567.0	-	6454	1249.0	63.0
-chr1	72781	72801	657.0	+	chr1	72810	72830	212.0	-	72805	869.0	29.0
-chr1	22571	22591	609.0	+	chr1	22569	22589	254.0	-	22580	863.0	-2.0
-chr1	65152	65172	575.0	+	chr1	65148	65168	43.0	-	65160	618.0	-4.0
-chr1	106034	106054	558.0	+	chr1	106041	106061	14.0	-	106047	572.0	7.0
-chr1	155028	155048	522.0	+	chr1	155111	155131	1051.0	-	155079	1573.0	83.0
-chr1	32449	32469	476.0	+	chr1	32497	32517	2.0	-	32483	478.0	48.0
-chr1	6706	6726	431.0	+	chr1	6702	6722	2.0	-	6714	433.0	-4.0
-chr1	113782	113802	420.0	+	chr1	113762	113782	296.0	-	113782	716.0	-20.0
-chr1	228633	228653	371.0	+	chr1	228691	228711	255.0	-	228672	626.0	58.0
-chr1	438	458	334.0	+	chr1	446	466	170.0	-	452	504.0	8.0
-chr1	72671	72691	304.0	+	chr1	72771	72791	406.0	-	72731	710.0	100.0
-chr1	170119	170139	284.0	+	chr1	170129	170149	373.0	-	170134	657.0	10.0
-chr1	92631	92651	260.0	+	chr1	92639	92659	2137.0	-	92645	2397.0	8.0
-chr1	136366	136386	248.0	+	chr1	136352	136372	117.0	-	136369	365.0	-14.0
-chr1	108624	108644	206.0	+	chr1	108579	108599	367.0	-	108611	573.0	-45.0
-chr1	45678	45698	198.0	+	chr1	45643	45663	295.0	-	45670	493.0	-35.0
-chr1	368	388	192.0	+	chr1	388	408	167.0	-	388	359.0	20.0
-chr1	682	702	168.0	+	chr1	634	654	151.0	-	668	319.0	-48.0
-chr1	59190	59210	168.0	+	chr1	59246	59266	397.0	-	59228	565.0	56.0
-chr1	134170	134190	151.0	+	chr1	134270	134290	508.0	-	134230	659.0	100.0
-chr1	55495	55515	125.0	+	chr1	55581	55601	831.0	-	55548	956.0	86.0
-chr1	512	532	101.0	+	chr1	468	488	468.0	-	500	569.0	-44.0
-chr1	39197	39217	101.0	+	chr1	39258	39278	261.0	-	39237	362.0	61.0
-chr1	229721	229741	84.0	+	chr1	229784	229804	615.0	-	229762	699.0	63.0
-chr1	116660	116680	74.0	+	chr1	116619	116639	699.0	-	116649	773.0	-41.0
-chr1	19216	19236	42.0	+	chr1	19191	19211	736.0	-	19213	778.0	-25.0
-chr1	230110	230130	42.0	+	chr1	230132	230152	2.0	-	230131	44.0	22.0
-chr1	31627	31647	40.0	+	chr1	31693	31713	450.0	-	31670	490.0	66.0
-chr1	180280	180300	38.0	+	chr1	180272	180292	25.0	-	180286	63.0	-8.0
-chr1	98528	98548	34.0	+	chr1	98555	98575	88.0	-	98551	122.0	27.0
-chr1	230163	230183	23.0	+	chr1	230173	230193	33.0	-	230178	56.0	10.0
-chr1	173262	173282	11.0	+	chr1	173270	173290	535.0	-	173276	546.0	8.0
-chr1	230145	230165	8.0	+	chr1	230150	230170	7.0	-	230157	15.0	5.0
-chr1	95920	95940	5.0	+	chr1	95971	95991	684.0	-	95955	689.0	51.0
-chr1	199418	199438	5.0	+	chr1	199388	199408	805.0	-	199413	810.0	-30.0
-chr1	197489	197509	3.0	+	chr1	197562	197582	2.0	-	197535	5.0	73.0
-chr1	96908	96928	2.0	+	chr1	96911	96931	10.0	-	96919	12.0	3.0
-chr1	151369	151389	2.0	+	chr1	151341	151361	593.0	-	151365	595.0	-28.0
+chrom	start	end	value	strand	chrom	start	end	value	strand	midpoint	c-w reads sum	c-w distance (bp)
+chr1	87147	87167	3492.0	+	chr1	87158	87178	2039.0	-	87162	5531.0	11.0
+chr1	87	107	3211.0	+	chr1	139	159	993.0	-	123	4204.0	52.0
+chr1	48	68	2842.0	+	chr1	50	70	39.0	-	59	2881.0	2.0
+chr1	255	275	2810.0	+	chr1	279	299	1328.0	-	277	4138.0	24.0
+chr1	117	137	2163.0	+	chr1	176	196	14.0	-	156	2177.0	59.0
+chr1	86954	86974	1948.0	+	chr1	86991	87011	65.0	-	86982	2013.0	37.0
+chr1	169107	169127	1811.0	+	chr1	169064	169084	76.0	-	169095	1887.0	-43.0
+chr1	87171	87191	1436.0	+	chr1	87198	87218	2207.0	-	87194	3643.0	27.0
+chr1	201	221	1411.0	+	chr1	215	235	2611.0	-	218	4022.0	14.0
+chr1	229741	229761	1380.0	+	chr1	229757	229777	3151.0	-	229759	4531.0	16.0
+chr1	185076	185096	1309.0	+	chr1	185122	185142	62.0	-	185109	1371.0	46.0
+chr1	39081	39101	1268.0	+	chr1	39052	39072	82.0	-	39076	1350.0	-29.0
+chr1	92411	92431	1252.0	+	chr1	92411	92431	136.0	-	92421	1388.0	0.0
+chr1	203872	203892	1234.0	+	chr1	203835	203855	242.0	-	203863	1476.0	-37.0
+chr1	70776	70796	1148.0	+	chr1	70788	70808	998.0	-	70792	2146.0	12.0
+chr1	231	251	1146.0	+	chr1	261	281	1278.0	-	256	2424.0	30.0
+chr1	87098	87118	1125.0	+	chr1	87101	87121	1134.0	-	87109	2259.0	3.0
+chr1	6163	6183	1049.0	+	chr1	6254	6274	1076.0	-	6218	2125.0	91.0
+chr1	25246	25266	995.0	+	chr1	25345	25365	188.0	-	25305	1183.0	99.0
+chr1	101411	101431	973.0	+	chr1	101367	101387	1388.0	-	101399	2361.0	-44.0
+chr1	139213	139233	965.0	+	chr1	139228	139248	214.0	-	139230	1179.0	15.0
+chr1	87019	87039	769.0	+	chr1	87049	87069	422.0	-	87044	1191.0	30.0
+chr1	124318	124338	749.0	+	chr1	124275	124295	12.0	-	124306	761.0	-43.0
+chr1	348	368	699.0	+	chr1	373	393	200.0	-	370	899.0	25.0
+chr1	92543	92563	699.0	+	chr1	92571	92591	90.0	-	92567	789.0	28.0
+chr1	138868	138888	698.0	+	chr1	138864	138884	13.0	-	138876	711.0	-4.0
+chr1	307	327	685.0	+	chr1	323	343	486.0	-	325	1171.0	16.0
+chr1	6413	6433	682.0	+	chr1	6476	6496	567.0	-	6454	1249.0	63.0
+chr1	72781	72801	657.0	+	chr1	72810	72830	212.0	-	72805	869.0	29.0
+chr1	22571	22591	609.0	+	chr1	22569	22589	254.0	-	22580	863.0	-2.0
+chr1	65152	65172	575.0	+	chr1	65148	65168	43.0	-	65160	618.0	-4.0
+chr1	106034	106054	558.0	+	chr1	106041	106061	14.0	-	106047	572.0	7.0
+chr1	155028	155048	522.0	+	chr1	155111	155131	1051.0	-	155079	1573.0	83.0
+chr1	32449	32469	476.0	+	chr1	32497	32517	2.0	-	32483	478.0	48.0
+chr1	6706	6726	431.0	+	chr1	6702	6722	2.0	-	6714	433.0	-4.0
+chr1	113782	113802	420.0	+	chr1	113762	113782	296.0	-	113782	716.0	-20.0
+chr1	228633	228653	371.0	+	chr1	228691	228711	255.0	-	228672	626.0	58.0
+chr1	438	458	334.0	+	chr1	446	466	170.0	-	452	504.0	8.0
+chr1	72671	72691	304.0	+	chr1	72771	72791	406.0	-	72731	710.0	100.0
+chr1	170119	170139	284.0	+	chr1	170129	170149	373.0	-	170134	657.0	10.0
+chr1	92631	92651	260.0	+	chr1	92639	92659	2137.0	-	92645	2397.0	8.0
+chr1	136366	136386	248.0	+	chr1	136352	136372	117.0	-	136369	365.0	-14.0
+chr1	108624	108644	206.0	+	chr1	108579	108599	367.0	-	108611	573.0	-45.0
+chr1	45678	45698	198.0	+	chr1	45643	45663	295.0	-	45670	493.0	-35.0
+chr1	368	388	192.0	+	chr1	388	408	167.0	-	388	359.0	20.0
+chr1	682	702	168.0	+	chr1	634	654	151.0	-	668	319.0	-48.0
+chr1	59190	59210	168.0	+	chr1	59246	59266	397.0	-	59228	565.0	56.0
+chr1	134170	134190	151.0	+	chr1	134270	134290	508.0	-	134230	659.0	100.0
+chr1	55495	55515	125.0	+	chr1	55581	55601	831.0	-	55548	956.0	86.0
+chr1	512	532	101.0	+	chr1	468	488	468.0	-	500	569.0	-44.0
+chr1	39197	39217	101.0	+	chr1	39258	39278	261.0	-	39237	362.0	61.0
+chr1	229721	229741	84.0	+	chr1	229784	229804	615.0	-	229762	699.0	63.0
+chr1	116660	116680	74.0	+	chr1	116619	116639	699.0	-	116649	773.0	-41.0
+chr1	19216	19236	42.0	+	chr1	19191	19211	736.0	-	19213	778.0	-25.0
+chr1	230110	230130	42.0	+	chr1	230132	230152	2.0	-	230131	44.0	22.0
+chr1	31627	31647	40.0	+	chr1	31693	31713	450.0	-	31670	490.0	66.0
+chr1	180280	180300	38.0	+	chr1	180272	180292	25.0	-	180286	63.0	-8.0
+chr1	98528	98548	34.0	+	chr1	98555	98575	88.0	-	98551	122.0	27.0
+chr1	230163	230183	23.0	+	chr1	230173	230193	33.0	-	230178	56.0	10.0
+chr1	173262	173282	11.0	+	chr1	173270	173290	535.0	-	173276	546.0	8.0
+chr1	230145	230165	8.0	+	chr1	230150	230170	7.0	-	230157	15.0	5.0
+chr1	95920	95940	5.0	+	chr1	95971	95991	684.0	-	95955	689.0	51.0
+chr1	199418	199438	5.0	+	chr1	199388	199408	805.0	-	199413	810.0	-30.0
+chr1	197489	197509	3.0	+	chr1	197562	197582	2.0	-	197535	5.0	73.0
+chr1	96908	96928	2.0	+	chr1	96911	96931	10.0	-	96919	12.0	3.0
+chr1	151369	151389	2.0	+	chr1	151341	151361	593.0	-	151365	595.0	-28.0
--- a/test-data/mode_mp_output1.gff	Mon Nov 06 23:19:50 2017 -0500
+++ b/test-data/mode_mp_output1.gff	Thu May 02 08:30:22 2019 -0400
@@ -1,56 +1,57 @@
-chr1	cwpair	.	87162	87163	5531.0	.	.	cw_distance=11.0
-chr1	cwpair	.	229759	229760	4531.0	.	.	cw_distance=16.0
-chr1	cwpair	.	123	124	4204.0	.	.	cw_distance=52.0
-chr1	cwpair	.	277	278	4138.0	.	.	cw_distance=24.0
-chr1	cwpair	.	218	219	4022.0	.	.	cw_distance=14.0
-chr1	cwpair	.	87194	87195	3643.0	.	.	cw_distance=27.0
-chr1	cwpair	.	59	60	2881.0	.	.	cw_distance=2.0
-chr1	cwpair	.	256	257	2424.0	.	.	cw_distance=30.0
-chr1	cwpair	.	92645	92646	2397.0	.	.	cw_distance=8.0
-chr1	cwpair	.	87109	87110	2259.0	.	.	cw_distance=3.0
-chr1	cwpair	.	156	157	2177.0	.	.	cw_distance=59.0
-chr1	cwpair	.	70792	70793	2146.0	.	.	cw_distance=12.0
-chr1	cwpair	.	6218	6219	2125.0	.	.	cw_distance=91.0
-chr1	cwpair	.	86982	86983	2013.0	.	.	cw_distance=37.0
-chr1	cwpair	.	155079	155080	1573.0	.	.	cw_distance=83.0
-chr1	cwpair	.	92421	92422	1388.0	.	.	cw_distance=0.0
-chr1	cwpair	.	185109	185110	1371.0	.	.	cw_distance=46.0
-chr1	cwpair	.	6454	6455	1249.0	.	.	cw_distance=63.0
-chr1	cwpair	.	87044	87045	1191.0	.	.	cw_distance=30.0
-chr1	cwpair	.	25305	25306	1183.0	.	.	cw_distance=99.0
-chr1	cwpair	.	139230	139231	1179.0	.	.	cw_distance=15.0
-chr1	cwpair	.	325	326	1171.0	.	.	cw_distance=16.0
-chr1	cwpair	.	55548	55549	956.0	.	.	cw_distance=86.0
-chr1	cwpair	.	370	371	899.0	.	.	cw_distance=25.0
-chr1	cwpair	.	72805	72806	869.0	.	.	cw_distance=29.0
-chr1	cwpair	.	22580	22581	863.0	.	.	cw_distance=-2.0
-chr1	cwpair	.	92567	92568	789.0	.	.	cw_distance=28.0
-chr1	cwpair	.	19213	19214	778.0	.	.	cw_distance=-25.0
-chr1	cwpair	.	113782	113783	716.0	.	.	cw_distance=-20.0
-chr1	cwpair	.	138876	138877	711.0	.	.	cw_distance=-4.0
-chr1	cwpair	.	72731	72732	710.0	.	.	cw_distance=100.0
-chr1	cwpair	.	229762	229763	699.0	.	.	cw_distance=63.0
-chr1	cwpair	.	95955	95956	689.0	.	.	cw_distance=51.0
-chr1	cwpair	.	134230	134231	659.0	.	.	cw_distance=100.0
-chr1	cwpair	.	170134	170135	657.0	.	.	cw_distance=10.0
-chr1	cwpair	.	228672	228673	626.0	.	.	cw_distance=58.0
-chr1	cwpair	.	65160	65161	618.0	.	.	cw_distance=-4.0
-chr1	cwpair	.	106047	106048	572.0	.	.	cw_distance=7.0
-chr1	cwpair	.	477	478	566.0	.	.	cw_distance=1.0
-chr1	cwpair	.	59228	59229	565.0	.	.	cw_distance=56.0
-chr1	cwpair	.	173276	173277	546.0	.	.	cw_distance=8.0
-chr1	cwpair	.	452	453	504.0	.	.	cw_distance=8.0
-chr1	cwpair	.	31670	31671	490.0	.	.	cw_distance=66.0
-chr1	cwpair	.	32483	32484	478.0	.	.	cw_distance=48.0
-chr1	cwpair	.	6714	6715	433.0	.	.	cw_distance=-4.0
-chr1	cwpair	.	136369	136370	365.0	.	.	cw_distance=-14.0
-chr1	cwpair	.	39237	39238	362.0	.	.	cw_distance=61.0
-chr1	cwpair	.	388	389	359.0	.	.	cw_distance=20.0
-chr1	cwpair	.	627	628	247.0	.	.	cw_distance=33.0
-chr1	cwpair	.	98551	98552	122.0	.	.	cw_distance=27.0
-chr1	cwpair	.	180286	180287	63.0	.	.	cw_distance=-8.0
-chr1	cwpair	.	230178	230179	56.0	.	.	cw_distance=10.0
-chr1	cwpair	.	230131	230132	44.0	.	.	cw_distance=22.0
-chr1	cwpair	.	230157	230158	15.0	.	.	cw_distance=5.0
-chr1	cwpair	.	96919	96920	12.0	.	.	cw_distance=3.0
-chr1	cwpair	.	197535	197536	5.0	.	.	cw_distance=73.0
+chr1	cwpair	.	87182	87183	5699.0	.	.	cw_distance=51.0
+chr1	cwpair	.	123	124	4204.0	.	.	cw_distance=52.0
+chr1	cwpair	.	299	300	3296.0	.	.	cw_distance=68.0
+chr1	cwpair	.	229749	229750	3235.0	.	.	cw_distance=36.0
+chr1	cwpair	.	87138	87139	3164.0	.	.	cw_distance=60.0
+chr1	cwpair	.	197	198	3062.0	.	.	cw_distance=55.0
+chr1	cwpair	.	59	60	2881.0	.	.	cw_distance=2.0
+chr1	cwpair	.	92601	92602	2836.0	.	.	cw_distance=96.0
+chr1	cwpair	.	241	242	2689.0	.	.	cw_distance=60.0
+chr1	cwpair	.	265	266	2474.0	.	.	cw_distance=48.0
+chr1	cwpair	.	156	157	2177.0	.	.	cw_distance=59.0
+chr1	cwpair	.	70792	70793	2146.0	.	.	cw_distance=12.0
+chr1	cwpair	.	6218	6219	2125.0	.	.	cw_distance=91.0
+chr1	cwpair	.	87212	87213	2073.0	.	.	cw_distance=63.0
+chr1	cwpair	.	86982	86983	2013.0	.	.	cw_distance=37.0
+chr1	cwpair	.	229772	229773	1995.0	.	.	cw_distance=43.0
+chr1	cwpair	.	87070	87071	1903.0	.	.	cw_distance=82.0
+chr1	cwpair	.	155079	155080	1573.0	.	.	cw_distance=83.0
+chr1	cwpair	.	92421	92422	1388.0	.	.	cw_distance=0.0
+chr1	cwpair	.	185109	185110	1371.0	.	.	cw_distance=46.0
+chr1	cwpair	.	6454	6455	1249.0	.	.	cw_distance=63.0
+chr1	cwpair	.	25305	25306	1183.0	.	.	cw_distance=99.0
+chr1	cwpair	.	139230	139231	1179.0	.	.	cw_distance=15.0
+chr1	cwpair	.	87035	87036	972.0	.	.	cw_distance=47.0
+chr1	cwpair	.	55548	55549	956.0	.	.	cw_distance=86.0
+chr1	cwpair	.	350	351	885.0	.	.	cw_distance=66.0
+chr1	cwpair	.	72805	72806	869.0	.	.	cw_distance=29.0
+chr1	cwpair	.	22580	22581	863.0	.	.	cw_distance=-2.0
+chr1	cwpair	.	463	464	802.0	.	.	cw_distance=30.0
+chr1	cwpair	.	19213	19214	778.0	.	.	cw_distance=-25.0
+chr1	cwpair	.	113782	113783	716.0	.	.	cw_distance=-20.0
+chr1	cwpair	.	138876	138877	711.0	.	.	cw_distance=-4.0
+chr1	cwpair	.	72731	72732	710.0	.	.	cw_distance=100.0
+chr1	cwpair	.	389	390	707.0	.	.	cw_distance=62.0
+chr1	cwpair	.	95955	95956	689.0	.	.	cw_distance=51.0
+chr1	cwpair	.	134230	134231	659.0	.	.	cw_distance=100.0
+chr1	cwpair	.	170134	170135	657.0	.	.	cw_distance=10.0
+chr1	cwpair	.	228672	228673	626.0	.	.	cw_distance=58.0
+chr1	cwpair	.	65160	65161	618.0	.	.	cw_distance=-4.0
+chr1	cwpair	.	106047	106048	572.0	.	.	cw_distance=7.0
+chr1	cwpair	.	59228	59229	565.0	.	.	cw_distance=56.0
+chr1	cwpair	.	173276	173277	546.0	.	.	cw_distance=8.0
+chr1	cwpair	.	31670	31671	490.0	.	.	cw_distance=66.0
+chr1	cwpair	.	32483	32484	478.0	.	.	cw_distance=48.0
+chr1	cwpair	.	92657	92658	447.0	.	.	cw_distance=33.0
+chr1	cwpair	.	6714	6715	433.0	.	.	cw_distance=-4.0
+chr1	cwpair	.	136369	136370	365.0	.	.	cw_distance=-14.0
+chr1	cwpair	.	417	418	362.0	.	.	cw_distance=78.0
+chr1	cwpair	.	39237	39238	362.0	.	.	cw_distance=61.0
+chr1	cwpair	.	627	628	247.0	.	.	cw_distance=33.0
+chr1	cwpair	.	98551	98552	122.0	.	.	cw_distance=27.0
+chr1	cwpair	.	180331	180332	97.0	.	.	cw_distance=82.0
+chr1	cwpair	.	230151	230152	75.0	.	.	cw_distance=63.0
+chr1	cwpair	.	230166	230167	30.0	.	.	cw_distance=-13.0
+chr1	cwpair	.	96919	96920	12.0	.	.	cw_distance=3.0
+chr1	cwpair	.	230148	230149	10.0	.	.	cw_distance=-13.0
+chr1	cwpair	.	197535	197536	5.0	.	.	cw_distance=73.0
--- a/test-data/mode_mp_output2.gff	Mon Nov 06 23:19:50 2017 -0500
+++ b/test-data/mode_mp_output2.gff	Thu May 02 08:30:22 2019 -0400
@@ -1,66 +1,66 @@
-chr1	cwpair	.	87162	87163	5531.0	.	.	cw_distance=11.0
-chr1	cwpair	.	229759	229760	4531.0	.	.	cw_distance=16.0
-chr1	cwpair	.	123	124	4204.0	.	.	cw_distance=52.0
-chr1	cwpair	.	277	278	4138.0	.	.	cw_distance=24.0
-chr1	cwpair	.	218	219	4022.0	.	.	cw_distance=14.0
-chr1	cwpair	.	87194	87195	3643.0	.	.	cw_distance=27.0
-chr1	cwpair	.	59	60	2881.0	.	.	cw_distance=2.0
-chr1	cwpair	.	256	257	2424.0	.	.	cw_distance=30.0
-chr1	cwpair	.	92645	92646	2397.0	.	.	cw_distance=8.0
-chr1	cwpair	.	101399	101400	2361.0	.	.	cw_distance=-44.0
-chr1	cwpair	.	87109	87110	2259.0	.	.	cw_distance=3.0
-chr1	cwpair	.	156	157	2177.0	.	.	cw_distance=59.0
-chr1	cwpair	.	70792	70793	2146.0	.	.	cw_distance=12.0
-chr1	cwpair	.	6218	6219	2125.0	.	.	cw_distance=91.0
-chr1	cwpair	.	86982	86983	2013.0	.	.	cw_distance=37.0
-chr1	cwpair	.	169095	169096	1887.0	.	.	cw_distance=-43.0
-chr1	cwpair	.	155079	155080	1573.0	.	.	cw_distance=83.0
-chr1	cwpair	.	203863	203864	1476.0	.	.	cw_distance=-37.0
-chr1	cwpair	.	92421	92422	1388.0	.	.	cw_distance=0.0
-chr1	cwpair	.	185109	185110	1371.0	.	.	cw_distance=46.0
-chr1	cwpair	.	39076	39077	1350.0	.	.	cw_distance=-29.0
-chr1	cwpair	.	6454	6455	1249.0	.	.	cw_distance=63.0
-chr1	cwpair	.	87044	87045	1191.0	.	.	cw_distance=30.0
-chr1	cwpair	.	25305	25306	1183.0	.	.	cw_distance=99.0
-chr1	cwpair	.	139230	139231	1179.0	.	.	cw_distance=15.0
-chr1	cwpair	.	325	326	1171.0	.	.	cw_distance=16.0
-chr1	cwpair	.	55548	55549	956.0	.	.	cw_distance=86.0
-chr1	cwpair	.	370	371	899.0	.	.	cw_distance=25.0
-chr1	cwpair	.	72805	72806	869.0	.	.	cw_distance=29.0
-chr1	cwpair	.	22580	22581	863.0	.	.	cw_distance=-2.0
-chr1	cwpair	.	199413	199414	810.0	.	.	cw_distance=-30.0
-chr1	cwpair	.	92567	92568	789.0	.	.	cw_distance=28.0
-chr1	cwpair	.	19213	19214	778.0	.	.	cw_distance=-25.0
-chr1	cwpair	.	116649	116650	773.0	.	.	cw_distance=-41.0
-chr1	cwpair	.	124306	124307	761.0	.	.	cw_distance=-43.0
-chr1	cwpair	.	113782	113783	716.0	.	.	cw_distance=-20.0
-chr1	cwpair	.	138876	138877	711.0	.	.	cw_distance=-4.0
-chr1	cwpair	.	72731	72732	710.0	.	.	cw_distance=100.0
-chr1	cwpair	.	229762	229763	699.0	.	.	cw_distance=63.0
-chr1	cwpair	.	95955	95956	689.0	.	.	cw_distance=51.0
-chr1	cwpair	.	134230	134231	659.0	.	.	cw_distance=100.0
-chr1	cwpair	.	170134	170135	657.0	.	.	cw_distance=10.0
-chr1	cwpair	.	228672	228673	626.0	.	.	cw_distance=58.0
-chr1	cwpair	.	65160	65161	618.0	.	.	cw_distance=-4.0
-chr1	cwpair	.	151365	151366	595.0	.	.	cw_distance=-28.0
-chr1	cwpair	.	108611	108612	573.0	.	.	cw_distance=-45.0
-chr1	cwpair	.	106047	106048	572.0	.	.	cw_distance=7.0
-chr1	cwpair	.	500	501	569.0	.	.	cw_distance=-44.0
-chr1	cwpair	.	59228	59229	565.0	.	.	cw_distance=56.0
-chr1	cwpair	.	173276	173277	546.0	.	.	cw_distance=8.0
-chr1	cwpair	.	452	453	504.0	.	.	cw_distance=8.0
-chr1	cwpair	.	45670	45671	493.0	.	.	cw_distance=-35.0
-chr1	cwpair	.	31670	31671	490.0	.	.	cw_distance=66.0
-chr1	cwpair	.	32483	32484	478.0	.	.	cw_distance=48.0
-chr1	cwpair	.	6714	6715	433.0	.	.	cw_distance=-4.0
-chr1	cwpair	.	136369	136370	365.0	.	.	cw_distance=-14.0
-chr1	cwpair	.	39237	39238	362.0	.	.	cw_distance=61.0
-chr1	cwpair	.	388	389	359.0	.	.	cw_distance=20.0
-chr1	cwpair	.	668	669	319.0	.	.	cw_distance=-48.0
-chr1	cwpair	.	98551	98552	122.0	.	.	cw_distance=27.0
-chr1	cwpair	.	180286	180287	63.0	.	.	cw_distance=-8.0
-chr1	cwpair	.	230178	230179	56.0	.	.	cw_distance=10.0
-chr1	cwpair	.	230131	230132	44.0	.	.	cw_distance=22.0
-chr1	cwpair	.	230157	230158	15.0	.	.	cw_distance=5.0
-chr1	cwpair	.	96919	96920	12.0	.	.	cw_distance=3.0
-chr1	cwpair	.	197535	197536	5.0	.	.	cw_distance=73.0
+chr1	cwpair	.	87162	87163	5531.0	.	.	cw_distance=11.0
+chr1	cwpair	.	229759	229760	4531.0	.	.	cw_distance=16.0
+chr1	cwpair	.	123	124	4204.0	.	.	cw_distance=52.0
+chr1	cwpair	.	277	278	4138.0	.	.	cw_distance=24.0
+chr1	cwpair	.	218	219	4022.0	.	.	cw_distance=14.0
+chr1	cwpair	.	87194	87195	3643.0	.	.	cw_distance=27.0
+chr1	cwpair	.	59	60	2881.0	.	.	cw_distance=2.0
+chr1	cwpair	.	256	257	2424.0	.	.	cw_distance=30.0
+chr1	cwpair	.	92645	92646	2397.0	.	.	cw_distance=8.0
+chr1	cwpair	.	101399	101400	2361.0	.	.	cw_distance=-44.0
+chr1	cwpair	.	87109	87110	2259.0	.	.	cw_distance=3.0
+chr1	cwpair	.	156	157	2177.0	.	.	cw_distance=59.0
+chr1	cwpair	.	70792	70793	2146.0	.	.	cw_distance=12.0
+chr1	cwpair	.	6218	6219	2125.0	.	.	cw_distance=91.0
+chr1	cwpair	.	86982	86983	2013.0	.	.	cw_distance=37.0
+chr1	cwpair	.	169095	169096	1887.0	.	.	cw_distance=-43.0
+chr1	cwpair	.	155079	155080	1573.0	.	.	cw_distance=83.0
+chr1	cwpair	.	203863	203864	1476.0	.	.	cw_distance=-37.0
+chr1	cwpair	.	92421	92422	1388.0	.	.	cw_distance=0.0
+chr1	cwpair	.	185109	185110	1371.0	.	.	cw_distance=46.0
+chr1	cwpair	.	39076	39077	1350.0	.	.	cw_distance=-29.0
+chr1	cwpair	.	6454	6455	1249.0	.	.	cw_distance=63.0
+chr1	cwpair	.	87044	87045	1191.0	.	.	cw_distance=30.0
+chr1	cwpair	.	25305	25306	1183.0	.	.	cw_distance=99.0
+chr1	cwpair	.	139230	139231	1179.0	.	.	cw_distance=15.0
+chr1	cwpair	.	325	326	1171.0	.	.	cw_distance=16.0
+chr1	cwpair	.	55548	55549	956.0	.	.	cw_distance=86.0
+chr1	cwpair	.	370	371	899.0	.	.	cw_distance=25.0
+chr1	cwpair	.	72805	72806	869.0	.	.	cw_distance=29.0
+chr1	cwpair	.	22580	22581	863.0	.	.	cw_distance=-2.0
+chr1	cwpair	.	199413	199414	810.0	.	.	cw_distance=-30.0
+chr1	cwpair	.	92567	92568	789.0	.	.	cw_distance=28.0
+chr1	cwpair	.	19213	19214	778.0	.	.	cw_distance=-25.0
+chr1	cwpair	.	116649	116650	773.0	.	.	cw_distance=-41.0
+chr1	cwpair	.	124306	124307	761.0	.	.	cw_distance=-43.0
+chr1	cwpair	.	113782	113783	716.0	.	.	cw_distance=-20.0
+chr1	cwpair	.	138876	138877	711.0	.	.	cw_distance=-4.0
+chr1	cwpair	.	72731	72732	710.0	.	.	cw_distance=100.0
+chr1	cwpair	.	229762	229763	699.0	.	.	cw_distance=63.0
+chr1	cwpair	.	95955	95956	689.0	.	.	cw_distance=51.0
+chr1	cwpair	.	134230	134231	659.0	.	.	cw_distance=100.0
+chr1	cwpair	.	170134	170135	657.0	.	.	cw_distance=10.0
+chr1	cwpair	.	228672	228673	626.0	.	.	cw_distance=58.0
+chr1	cwpair	.	65160	65161	618.0	.	.	cw_distance=-4.0
+chr1	cwpair	.	151365	151366	595.0	.	.	cw_distance=-28.0
+chr1	cwpair	.	108611	108612	573.0	.	.	cw_distance=-45.0
+chr1	cwpair	.	106047	106048	572.0	.	.	cw_distance=7.0
+chr1	cwpair	.	500	501	569.0	.	.	cw_distance=-44.0
+chr1	cwpair	.	59228	59229	565.0	.	.	cw_distance=56.0
+chr1	cwpair	.	173276	173277	546.0	.	.	cw_distance=8.0
+chr1	cwpair	.	452	453	504.0	.	.	cw_distance=8.0
+chr1	cwpair	.	45670	45671	493.0	.	.	cw_distance=-35.0
+chr1	cwpair	.	31670	31671	490.0	.	.	cw_distance=66.0
+chr1	cwpair	.	32483	32484	478.0	.	.	cw_distance=48.0
+chr1	cwpair	.	6714	6715	433.0	.	.	cw_distance=-4.0
+chr1	cwpair	.	136369	136370	365.0	.	.	cw_distance=-14.0
+chr1	cwpair	.	39237	39238	362.0	.	.	cw_distance=61.0
+chr1	cwpair	.	388	389	359.0	.	.	cw_distance=20.0
+chr1	cwpair	.	668	669	319.0	.	.	cw_distance=-48.0
+chr1	cwpair	.	98551	98552	122.0	.	.	cw_distance=27.0
+chr1	cwpair	.	180286	180287	63.0	.	.	cw_distance=-8.0
+chr1	cwpair	.	230178	230179	56.0	.	.	cw_distance=10.0
+chr1	cwpair	.	230131	230132	44.0	.	.	cw_distance=22.0
+chr1	cwpair	.	230157	230158	15.0	.	.	cw_distance=5.0
+chr1	cwpair	.	96919	96920	12.0	.	.	cw_distance=3.0
+chr1	cwpair	.	197535	197536	5.0	.	.	cw_distance=73.0
--- a/test-data/mode_o_output2.tabular	Mon Nov 06 23:19:50 2017 -0500
+++ b/test-data/mode_o_output2.tabular	Thu May 02 08:30:22 2019 -0400
@@ -1,100 +1,368 @@
-chrom	strand	start	end	value
-chr1	+	100364	100384	2695.0
-chr1	+	30	50	2140.0
-chr1	+	5379	5399	1572.0
-chr1	+	52440	52460	1562.0
-chr1	+	73234	73254	1492.0
-chr1	+	31096	31116	1481.0
-chr1	+	145253	145273	1394.0
-chr1	+	10641	10661	1359.0
-chr1	+	200580	200600	1298.0
-chr1	+	64772	64792	1292.0
-chr1	+	86886	86906	1253.0
-chr1	+	103207	103227	1229.0
-chr1	+	43835	43855	1173.0
-chr1	+	29570	29590	1130.0
-chr1	+	83774	83794	1125.0
-chr1	+	165827	165847	1109.0
-chr1	+	92775	92795	1105.0
-chr1	+	4748	4768	1077.0
-chr1	+	126733	126753	952.0
-chr1	+	71041	71061	881.0
-chr1	+	35773	35793	866.0
-chr1	+	53097	53117	835.0
-chr1	+	71556	71576	835.0
-chr1	+	30964	30984	829.0
-chr1	+	31019	31039	810.0
-chr1	+	55349	55369	794.0
-chr1	+	203193	203213	789.0
-chr1	+	39794	39814	780.0
-chr1	+	153928	153948	768.0
-chr1	+	179472	179492	696.0
-chr1	+	178117	178137	686.0
-chr1	+	1298	1318	684.0
-chr1	+	192754	192774	668.0
-chr1	+	89611	89631	640.0
-chr1	+	20205	20225	634.0
-chr1	+	118428	118448	633.0
-chr1	+	110736	110756	621.0
-chr1	+	48642	48662	610.0
-chr1	+	159372	159392	605.0
-chr1	+	6453	6473	601.0
-chr1	+	112137	112157	601.0
-chr1	+	142905	142925	599.0
-chr1	+	167443	167463	597.0
-chr1	+	126073	126093	590.0
-chr1	+	6233	6253	589.0
-chr1	+	43657	43677	586.0
-chr1	+	134021	134041	572.0
-chr1	+	29864	29884	570.0
-chr1	+	70953	70973	555.0
-chr1	+	87002	87022	550.0
-chr1	+	129555	129575	536.0
-chr1	+	119754	119774	515.0
-chr1	+	43523	43543	505.0
-chr1	+	97898	97918	501.0
-chr1	+	40830	40850	491.0
-chr1	+	153095	153115	490.0
-chr1	+	7303	7323	484.0
-chr1	+	115866	115886	480.0
-chr1	+	129680	129700	464.0
-chr1	+	187155	187175	455.0
-chr1	+	192271	192291	453.0
-chr1	+	150449	150469	436.0
-chr1	+	9367	9387	425.0
-chr1	+	93793	93813	415.0
-chr1	+	87572	87592	407.0
-chr1	+	124845	124865	383.0
-chr1	+	4053	4073	381.0
-chr1	+	136072	136092	380.0
-chr1	+	39942	39962	375.0
-chr1	+	61977	61997	368.0
-chr1	+	2976	2996	356.0
-chr1	+	27978	27998	354.0
-chr1	+	195756	195776	348.0
-chr1	+	172223	172243	338.0
-chr1	+	143657	143677	328.0
-chr1	+	45409	45429	307.0
-chr1	+	45248	45268	305.0
-chr1	+	68564	68584	303.0
-chr1	+	119953	119973	295.0
-chr1	+	48319	48339	290.0
-chr1	+	48772	48792	284.0
-chr1	+	126369	126389	284.0
-chr1	+	116432	116452	267.0
-chr1	+	199649	199669	264.0
-chr1	+	204126	204146	261.0
-chr1	+	130514	130534	243.0
-chr1	+	55692	55712	228.0
-chr1	+	117198	117218	228.0
-chr1	+	42843	42863	218.0
-chr1	+	59583	59603	204.0
-chr1	+	124669	124689	203.0
-chr1	+	2613	2633	202.0
-chr1	+	40264	40284	199.0
-chr1	+	21406	21426	177.0
-chr1	+	20391	20411	173.0
-chr1	+	20626	20646	171.0
-chr1	+	198594	198614	170.0
-chr1	+	149343	149363	159.0
-chr1	+	121016	121036	155.0
+chrom	strand	start	end	value
+chr1	+	100364	100384	2695.0
+chr1	+	30	50	2140.0
+chr1	+	5379	5399	1572.0
+chr1	+	52440	52460	1562.0
+chr1	+	73234	73254	1492.0
+chr1	+	31096	31116	1481.0
+chr1	+	145253	145273	1394.0
+chr1	+	10641	10661	1359.0
+chr1	+	200580	200600	1298.0
+chr1	+	64772	64792	1292.0
+chr1	+	86886	86906	1253.0
+chr1	+	103207	103227	1229.0
+chr1	+	43835	43855	1173.0
+chr1	+	29570	29590	1130.0
+chr1	+	83774	83794	1125.0
+chr1	+	165827	165847	1109.0
+chr1	+	92775	92795	1105.0
+chr1	+	4748	4768	1077.0
+chr1	+	126733	126753	952.0
+chr1	+	71041	71061	881.0
+chr1	+	35773	35793	866.0
+chr1	+	53097	53117	835.0
+chr1	+	71556	71576	835.0
+chr1	+	30964	30984	829.0
+chr1	+	31019	31039	810.0
+chr1	+	55349	55369	794.0
+chr1	+	203193	203213	789.0
+chr1	+	39794	39814	780.0
+chr1	+	153928	153948	768.0
+chr1	+	179472	179492	696.0
+chr1	+	178117	178137	686.0
+chr1	+	1298	1318	684.0
+chr1	+	87085	87105	676.0
+chr1	+	192754	192774	668.0
+chr1	+	89611	89631	640.0
+chr1	+	20205	20225	634.0
+chr1	+	118428	118448	633.0
+chr1	+	110736	110756	621.0
+chr1	+	48642	48662	610.0
+chr1	+	159372	159392	605.0
+chr1	+	6453	6473	601.0
+chr1	+	112137	112157	601.0
+chr1	+	142905	142925	599.0
+chr1	+	167443	167463	597.0
+chr1	+	126073	126093	590.0
+chr1	+	6233	6253	589.0
+chr1	+	43657	43677	586.0
+chr1	+	134021	134041	572.0
+chr1	+	29864	29884	570.0
+chr1	+	70953	70973	555.0
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--- a/test-data/statistics1.tabular	Mon Nov 06 23:19:50 2017 -0500
+++ b/test-data/statistics1.tabular	Thu May 02 08:30:22 2019 -0400
@@ -1,4 +1,4 @@
-fname	final_mode	preview_mode	perc95	paired	orphans
-mode: data 1	-3.5	16.5	1437.0	112	386
-closest: data 1	-3.5	NA	1437.0	112	386
-largest: data 1	-3.5	NA	1437.0	110	388
+fname	final_mode	preview_mode	perc95	paired	orphans
+mode: data 1	63.5	63.5	1437.0	114	385
+closest: data 1	8.5	NA	1437.0	112	387
+largest: data 1	63.5	NA	1437.0	110	389
--- a/test-data/statistics2.tabular	Mon Nov 06 23:19:50 2017 -0500
+++ b/test-data/statistics2.tabular	Thu May 02 08:30:22 2019 -0400
@@ -1,4 +1,4 @@
-fname	final_mode	preview_mode	perc95	paired	orphans
-mode: data 1	-3.5	16.5	1437.0	132	366
-closest: data 1	-3.5	NA	1437.0	132	366
-largest: data 1	-24.5	NA	1437.0	128	370
+fname	final_mode	preview_mode	perc95	paired	orphans
+mode: data 1	8.5	16.5	1437.0	132	367
+closest: data 1	8.5	NA	1437.0	132	367
+largest: data 1	-3.5	NA	1437.0	128	371