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changeset 20:de7fbcb1348c draft

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planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/small_rna_maps commit 44599c93586bc909f405ac6b745230563b290ee2
author artbio
date Sun, 25 Nov 2018 06:56:40 -0500
parents f33afecac67a
children b585cb347a26
files newtests/bed1.bed newtests/bed2.bed newtests/bed3.bed newtests/clustering.pdf newtests/clustering.tab newtests/clustering_unstranded.pdf newtests/clustering_unstranded.tab newtests/global_merge.pdf newtests/global_nomerge.pdf newtests/input1__single_plot_mean.pdf newtests/input1_counts_yminneg5_5.tab newtests/input1_input2_counts.tab newtests/input1_input2_double_plot_counts_size_ylimneg5_5.pdf newtests/input1_input2_norm_1_2_counts.tab newtests/input1_input2_norm_1_2_single_plot_counts.pdf newtests/input1_input2_size.tab newtests/input1_mean.tab newtests/input1_median.tab newtests/input1_min20_max30_single_plot_size.pdf newtests/input1_min20_max30_size.tab newtests/input1_single_plot_median.pdf newtests/input1_yminneg5_5_single_plot_counts.pdf newtests/input_single_chr_x_6_single_plot_coverage.pdf newtests/input_single_chr_x_6_single_plot_coverage.tab newtests/size.tab small_rna_maps.py small_rna_maps.xml test-data/bed1.bed test-data/bed2.bed test-data/bed3.bed test-data/bed4.bed test-data/bed5.bed
diffstat 32 files changed, 343 insertions(+), 5777 deletions(-) [+]
line wrap: on
line diff
--- a/newtests/bed1.bed	Thu Nov 22 20:05:32 2018 -0500
+++ /dev/null	Thu Jan 01 00:00:00 1970 +0000
@@ -1,118 +0,0 @@
-FBtr0070001	0	1	cluster	1	+
-FBtr0070001	6	18	cluster	14	+
-FBtr0070001	26	34	cluster	42	+
-FBtr0070001	71	72	cluster	0	+
-FBtr0070533	0	1	cluster	1	+
-FBtr0070533	11	38	cluster	23	+
-FBtr0070533	71	72	cluster	0	+
-FBtr0070603	0	42	cluster	68	+
-FBtr0070603	50	56	cluster	2	+
-FBtr0070603	71	72	cluster	0	+
-FBtr0070604	0	1	cluster	1	+
-FBtr0070604	17	22	cluster	2	+
-FBtr0070604	29	32	cluster	36	+
-FBtr0070604	56	57	cluster	1	+
-FBtr0070604	71	72	cluster	0	+
-FBtr0070911	0	1	cluster	0	+
-FBtr0070911	14	15	cluster	1	+
-FBtr0070911	37	38	cluster	1	+
-FBtr0070911	72	73	cluster	0	+
-FBtr0078490	0	1	cluster	0	+
-FBtr0078490	12	18	cluster	4	+
-FBtr0078490	24	28	cluster	3	+
-FBtr0078490	37	38	cluster	1	+
-FBtr0078490	71	72	cluster	0	+
-FBtr0078580	0	31	cluster	1102	+
-FBtr0078580	51	52	cluster	2	+
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-FBtr0078790	0	1	cluster	1	+
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-FBtr0078790	68	69	cluster	1	-
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-FBtr0080609	0	20	cluster	60	+
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-FBtr0080660	0	7	cluster	7	+
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-FBtr0080663	0	17	cluster	102	+
-FBtr0080663	25	26	cluster	1	+
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-FBtr0080664	0	21	cluster	108	+
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-FBtr0080664	49	56	cluster	11	+
-FBtr0080664	70	71	cluster	0	+
--- a/newtests/bed2.bed	Thu Nov 22 20:05:32 2018 -0500
+++ /dev/null	Thu Jan 01 00:00:00 1970 +0000
@@ -1,116 +0,0 @@
-FBtr0070001	0	1	cluster	1	.
-FBtr0070001	6	18	cluster	14	.
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-FBtr0070911	37	38	cluster	1	.
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-FBtr0078490	0	1	cluster	0	.
-FBtr0078490	12	18	cluster	4	.
-FBtr0078490	24	28	cluster	3	.
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--- a/newtests/bed3.bed	Thu Nov 22 20:05:32 2018 -0500
+++ /dev/null	Thu Jan 01 00:00:00 1970 +0000
@@ -1,35 +0,0 @@
-FBtr0070001	6	18	cluster	14	+
-FBtr0070001	26	34	cluster	42	+
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-FBtr0070603	0	42	cluster	68	+
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Binary file newtests/clustering.pdf has changed
--- a/newtests/clustering.tab	Thu Nov 22 20:05:32 2018 -0500
+++ /dev/null	Thu Jan 01 00:00:00 1970 +0000
@@ -1,119 +0,0 @@
-Dataset	Chromosome	Chrom_length	Coordinate	Polarity	Counts	Start-End	Cluster Size	density
-input1.bam	FBtr0070001	72	1	F	1	1-1	1	1.0
-input1.bam	FBtr0070001	72	12	F	14	7-18	12	1.16666666667
-input1.bam	FBtr0070001	72	30	F	42	27-34	8	5.25
-input1.bam	FBtr0070001	72	72	F	0	72-72	1	0.0
-input1.bam	FBtr0070533	72	1	F	1	1-1	1	1.0
-input1.bam	FBtr0070533	72	25	F	23	12-38	27	0.851851851852
-input1.bam	FBtr0070533	72	72	F	0	72-72	1	0.0
-input1.bam	FBtr0070603	72	21	F	68	1-42	42	1.61904761905
-input1.bam	FBtr0070603	72	53	F	2	51-56	6	0.333333333333
-input1.bam	FBtr0070603	72	72	F	0	72-72	1	0.0
-input1.bam	FBtr0070604	72	1	F	1	1-1	1	1.0
-input1.bam	FBtr0070604	72	20	F	2	18-22	5	0.4
-input1.bam	FBtr0070604	72	31	F	36	30-32	3	12.0
-input1.bam	FBtr0070604	72	57	F	1	57-57	1	1.0
-input1.bam	FBtr0070604	72	72	F	0	72-72	1	0.0
-input1.bam	FBtr0070911	73	1	F	0	1-1	1	0.0
-input1.bam	FBtr0070911	73	15	F	1	15-15	1	1.0
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-input1.bam	FBtr0070911	73	73	F	0	73-73	1	0.0
-input1.bam	FBtr0078490	72	1	F	0	1-1	1	0.0
-input1.bam	FBtr0078490	72	15	F	4	13-18	6	0.666666666667
-input1.bam	FBtr0078490	72	26	F	3	25-28	4	0.75
-input1.bam	FBtr0078490	72	38	F	1	38-38	1	1.0
-input1.bam	FBtr0078490	72	72	F	0	72-72	1	0.0
-input1.bam	FBtr0078580	72	16	F	1102	1-31	31	35.5483870968
-input1.bam	FBtr0078580	72	52	F	2	52-52	1	2.0
-input1.bam	FBtr0078580	72	72	F	0	72-72	1	0.0
-input1.bam	FBtr0078790	73	1	F	1	1-1	1	1.0
-input1.bam	FBtr0078790	73	17	F	2	17-17	1	2.0
-input1.bam	FBtr0078790	73	33	F	1	33-33	1	1.0
-input1.bam	FBtr0078790	73	47	F	9	42-52	11	0.818181818182
-input1.bam	FBtr0078790	73	69	R	1	69-69	1	1.0
-input1.bam	FBtr0078790	73	73	F	0	73-73	1	0.0
-input1.bam	FBtr0079064	72	2	F	2	1-3	3	0.666666666667
-input1.bam	FBtr0079064	72	33	F	1	33-33	1	1.0
-input1.bam	FBtr0079064	72	52	F	1	52-52	1	1.0
-input1.bam	FBtr0079064	72	72	F	0	72-72	1	0.0
-input1.bam	FBtr0079090	72	1	F	2	1-1	1	2.0
-input1.bam	FBtr0079090	72	26	F	1	26-26	1	1.0
-input1.bam	FBtr0079090	72	33	F	1	33-33	1	1.0
-input1.bam	FBtr0079090	72	53	F	1	53-53	1	1.0
-input1.bam	FBtr0079090	72	56	R	1	56-56	1	1.0
-input1.bam	FBtr0079090	72	72	F	0	72-72	1	0.0
-input1.bam	FBtr0079338	73	1	F	0	1-1	1	0.0
-input1.bam	FBtr0079338	73	14	F	5	12-17	6	0.833333333333
-input1.bam	FBtr0079338	73	25	F	1	25-25	1	1.0
-input1.bam	FBtr0079338	73	44	F	10	42-46	5	2.0
-input1.bam	FBtr0079338	73	73	F	0	73-73	1	0.0
-input1.bam	FBtr0079528	71	9	F	97	1-18	18	5.38888888889
-input1.bam	FBtr0079528	71	28	F	1	28-28	1	1.0
-input1.bam	FBtr0079528	71	36	F	3	35-37	3	1.0
-input1.bam	FBtr0079528	71	51	F	5	51-51	1	5.0
-input1.bam	FBtr0079528	71	71	F	0	71-71	1	0.0
-input1.bam	FBtr0079596	73	10	F	148	1-19	19	7.78947368421
-input1.bam	FBtr0079596	73	53	F	4	53-54	2	2.0
-input1.bam	FBtr0079596	73	73	F	0	73-73	1	0.0
-input1.bam	FBtr0079677	72	3	F	2	1-5	5	0.4
-input1.bam	FBtr0079677	72	52	F	2	52-53	2	1.0
-input1.bam	FBtr0079677	72	72	F	0	72-72	1	0.0
-input1.bam	FBtr0079690	72	1	F	1	1-1	1	1.0
-input1.bam	FBtr0079690	72	24	F	2	22-27	6	0.333333333333
-input1.bam	FBtr0079690	72	33	F	2	33-33	1	2.0
-input1.bam	FBtr0079690	72	72	F	0	72-72	1	0.0
-input1.bam	FBtr0079692	73	1	F	3	1-1	1	3.0
-input1.bam	FBtr0079692	73	18	F	1	18-18	1	1.0
-input1.bam	FBtr0079692	73	25	F	1	25-25	1	1.0
-input1.bam	FBtr0079692	73	32	F	1	32-32	1	1.0
-input1.bam	FBtr0079692	73	73	F	0	73-73	1	0.0
-input1.bam	FBtr0079693	72	1	F	5	1-1	1	5.0
-input1.bam	FBtr0079693	72	25	F	1	25-25	1	1.0
-input1.bam	FBtr0079693	72	72	F	0	72-72	1	0.0
-input1.bam	FBtr0079694	72	1	F	5	1-1	1	5.0
-input1.bam	FBtr0079694	72	18	F	1	18-18	1	1.0
-input1.bam	FBtr0079694	72	52	F	1	52-52	1	1.0
-input1.bam	FBtr0079694	72	72	F	0	72-72	1	0.0
-input1.bam	FBtr0079702	72	1	F	1	1-1	1	1.0
-input1.bam	FBtr0079702	72	19	F	2	19-19	1	2.0
-input1.bam	FBtr0079702	72	56	F	1	56-56	1	1.0
-input1.bam	FBtr0079702	72	72	F	0	72-72	1	0.0
-input1.bam	FBtr0079728	72	1	F	2	1-1	1	2.0
-input1.bam	FBtr0079728	72	8	F	1	8-8	1	1.0
-input1.bam	FBtr0079728	72	19	F	1	19-19	1	1.0
-input1.bam	FBtr0079728	72	33	F	3	33-33	1	3.0
-input1.bam	FBtr0079728	72	56	F	1	56-56	1	1.0
-input1.bam	FBtr0079728	72	72	F	0	72-72	1	0.0
-input1.bam	FBtr0079729	72	1	F	1	1-1	1	1.0
-input1.bam	FBtr0079729	72	13	F	1	13-13	1	1.0
-input1.bam	FBtr0079729	72	54	F	2	52-57	6	0.333333333333
-input1.bam	FBtr0079729	72	72	F	0	72-72	1	0.0
-input1.bam	FBtr0079752	72	1	F	2	1-1	1	2.0
-input1.bam	FBtr0079752	72	9	F	2	7-12	6	0.333333333333
-input1.bam	FBtr0079752	72	33	F	2	33-33	1	2.0
-input1.bam	FBtr0079752	72	52	F	2	52-52	1	2.0
-input1.bam	FBtr0079752	72	72	F	0	72-72	1	0.0
-input1.bam	FBtr0079820	74	1	F	0	1-1	1	0.0
-input1.bam	FBtr0079820	74	50	F	13	45-56	12	1.08333333333
-input1.bam	FBtr0079820	74	74	F	0	74-74	1	0.0
-input1.bam	FBtr0080609	72	10	F	60	1-20	20	3.0
-input1.bam	FBtr0080609	72	42	F	1	42-42	1	1.0
-input1.bam	FBtr0080609	72	51	F	2	51-52	2	1.0
-input1.bam	FBtr0080609	72	72	F	0	72-72	1	0.0
-input1.bam	FBtr0080644	72	6	F	6	1-12	12	0.5
-input1.bam	FBtr0080644	72	72	F	0	72-72	1	0.0
-input1.bam	FBtr0080646	72	4	F	3	1-7	7	0.428571428571
-input1.bam	FBtr0080646	72	72	F	0	72-72	1	0.0
-input1.bam	FBtr0080647	72	6	F	10	1-12	12	0.833333333333
-input1.bam	FBtr0080647	72	72	F	0	72-72	1	0.0
-input1.bam	FBtr0080660	72	4	F	7	1-7	7	1.0
-input1.bam	FBtr0080660	72	72	F	0	72-72	1	0.0
-input1.bam	FBtr0080663	71	9	F	102	1-17	17	6.0
-input1.bam	FBtr0080663	71	26	F	1	26-26	1	1.0
-input1.bam	FBtr0080663	71	32	F	2	32-32	1	2.0
-input1.bam	FBtr0080663	71	50	F	10	50-51	2	5.0
-input1.bam	FBtr0080663	71	71	F	0	71-71	1	0.0
-input1.bam	FBtr0080664	71	11	F	108	1-21	21	5.14285714286
-input1.bam	FBtr0080664	71	33	F	9	28-38	11	0.818181818182
-input1.bam	FBtr0080664	71	53	F	11	50-56	7	1.57142857143
-input1.bam	FBtr0080664	71	71	F	0	71-71	1	0.0
Binary file newtests/clustering_unstranded.pdf has changed
--- a/newtests/clustering_unstranded.tab	Thu Nov 22 20:05:32 2018 -0500
+++ /dev/null	Thu Jan 01 00:00:00 1970 +0000
@@ -1,117 +0,0 @@
-Dataset	Chromosome	Chrom_length	Coordinate	Polarity	Counts	Start-End	Cluster Size	density
-input1.bam	FBtr0070001	72	1	F	1	1-1	1	1.0
-input1.bam	FBtr0070001	72	12	F	14	7-18	12	1.16666666667
-input1.bam	FBtr0070001	72	30	F	42	27-34	8	5.25
-input1.bam	FBtr0070001	72	72	F	0	72-72	1	0.0
-input1.bam	FBtr0070533	72	1	F	1	1-1	1	1.0
-input1.bam	FBtr0070533	72	25	F	23	12-38	27	0.851851851852
-input1.bam	FBtr0070533	72	72	F	0	72-72	1	0.0
-input1.bam	FBtr0070603	72	21	F	68	1-42	42	1.61904761905
-input1.bam	FBtr0070603	72	53	F	2	51-56	6	0.333333333333
-input1.bam	FBtr0070603	72	72	F	0	72-72	1	0.0
-input1.bam	FBtr0070604	72	1	F	1	1-1	1	1.0
-input1.bam	FBtr0070604	72	20	F	2	18-22	5	0.4
-input1.bam	FBtr0070604	72	31	F	36	30-32	3	12.0
-input1.bam	FBtr0070604	72	57	F	1	57-57	1	1.0
-input1.bam	FBtr0070604	72	72	F	0	72-72	1	0.0
-input1.bam	FBtr0070911	73	1	F	0	1-1	1	0.0
-input1.bam	FBtr0070911	73	15	F	1	15-15	1	1.0
-input1.bam	FBtr0070911	73	38	F	1	38-38	1	1.0
-input1.bam	FBtr0070911	73	73	F	0	73-73	1	0.0
-input1.bam	FBtr0078490	72	1	F	0	1-1	1	0.0
-input1.bam	FBtr0078490	72	15	F	4	13-18	6	0.666666666667
-input1.bam	FBtr0078490	72	26	F	3	25-28	4	0.75
-input1.bam	FBtr0078490	72	38	F	1	38-38	1	1.0
-input1.bam	FBtr0078490	72	72	F	0	72-72	1	0.0
-input1.bam	FBtr0078580	72	16	F	1102	1-31	31	35.5483870968
-input1.bam	FBtr0078580	72	52	F	2	52-52	1	2.0
-input1.bam	FBtr0078580	72	72	F	0	72-72	1	0.0
-input1.bam	FBtr0078790	73	1	F	1	1-1	1	1.0
-input1.bam	FBtr0078790	73	17	F	2	17-17	1	2.0
-input1.bam	FBtr0078790	73	33	F	1	33-33	1	1.0
-input1.bam	FBtr0078790	73	47	F	9	42-52	11	0.818181818182
-input1.bam	FBtr0078790	73	71	F	1	69-73	5	0.2
-input1.bam	FBtr0079064	72	2	F	2	1-3	3	0.666666666667
-input1.bam	FBtr0079064	72	33	F	1	33-33	1	1.0
-input1.bam	FBtr0079064	72	52	F	1	52-52	1	1.0
-input1.bam	FBtr0079064	72	72	F	0	72-72	1	0.0
-input1.bam	FBtr0079090	72	1	F	2	1-1	1	2.0
-input1.bam	FBtr0079090	72	26	F	1	26-26	1	1.0
-input1.bam	FBtr0079090	72	33	F	1	33-33	1	1.0
-input1.bam	FBtr0079090	72	54	F	2	53-56	4	0.5
-input1.bam	FBtr0079090	72	72	F	0	72-72	1	0.0
-input1.bam	FBtr0079338	73	1	F	0	1-1	1	0.0
-input1.bam	FBtr0079338	73	14	F	5	12-17	6	0.833333333333
-input1.bam	FBtr0079338	73	25	F	1	25-25	1	1.0
-input1.bam	FBtr0079338	73	44	F	10	42-46	5	2.0
-input1.bam	FBtr0079338	73	73	F	0	73-73	1	0.0
-input1.bam	FBtr0079528	71	9	F	97	1-18	18	5.38888888889
-input1.bam	FBtr0079528	71	28	F	1	28-28	1	1.0
-input1.bam	FBtr0079528	71	36	F	3	35-37	3	1.0
-input1.bam	FBtr0079528	71	51	F	5	51-51	1	5.0
-input1.bam	FBtr0079528	71	71	F	0	71-71	1	0.0
-input1.bam	FBtr0079596	73	10	F	148	1-19	19	7.78947368421
-input1.bam	FBtr0079596	73	53	F	4	53-54	2	2.0
-input1.bam	FBtr0079596	73	73	F	0	73-73	1	0.0
-input1.bam	FBtr0079677	72	3	F	2	1-5	5	0.4
-input1.bam	FBtr0079677	72	52	F	2	52-53	2	1.0
-input1.bam	FBtr0079677	72	72	F	0	72-72	1	0.0
-input1.bam	FBtr0079690	72	1	F	1	1-1	1	1.0
-input1.bam	FBtr0079690	72	24	F	2	22-27	6	0.333333333333
-input1.bam	FBtr0079690	72	33	F	2	33-33	1	2.0
-input1.bam	FBtr0079690	72	72	F	0	72-72	1	0.0
-input1.bam	FBtr0079692	73	1	F	3	1-1	1	3.0
-input1.bam	FBtr0079692	73	18	F	1	18-18	1	1.0
-input1.bam	FBtr0079692	73	25	F	1	25-25	1	1.0
-input1.bam	FBtr0079692	73	32	F	1	32-32	1	1.0
-input1.bam	FBtr0079692	73	73	F	0	73-73	1	0.0
-input1.bam	FBtr0079693	72	1	F	5	1-1	1	5.0
-input1.bam	FBtr0079693	72	25	F	1	25-25	1	1.0
-input1.bam	FBtr0079693	72	72	F	0	72-72	1	0.0
-input1.bam	FBtr0079694	72	1	F	5	1-1	1	5.0
-input1.bam	FBtr0079694	72	18	F	1	18-18	1	1.0
-input1.bam	FBtr0079694	72	52	F	1	52-52	1	1.0
-input1.bam	FBtr0079694	72	72	F	0	72-72	1	0.0
-input1.bam	FBtr0079702	72	1	F	1	1-1	1	1.0
-input1.bam	FBtr0079702	72	19	F	2	19-19	1	2.0
-input1.bam	FBtr0079702	72	56	F	1	56-56	1	1.0
-input1.bam	FBtr0079702	72	72	F	0	72-72	1	0.0
-input1.bam	FBtr0079728	72	1	F	2	1-1	1	2.0
-input1.bam	FBtr0079728	72	8	F	1	8-8	1	1.0
-input1.bam	FBtr0079728	72	19	F	1	19-19	1	1.0
-input1.bam	FBtr0079728	72	33	F	3	33-33	1	3.0
-input1.bam	FBtr0079728	72	56	F	1	56-56	1	1.0
-input1.bam	FBtr0079728	72	72	F	0	72-72	1	0.0
-input1.bam	FBtr0079729	72	1	F	1	1-1	1	1.0
-input1.bam	FBtr0079729	72	13	F	1	13-13	1	1.0
-input1.bam	FBtr0079729	72	54	F	2	52-57	6	0.333333333333
-input1.bam	FBtr0079729	72	72	F	0	72-72	1	0.0
-input1.bam	FBtr0079752	72	1	F	2	1-1	1	2.0
-input1.bam	FBtr0079752	72	9	F	2	7-12	6	0.333333333333
-input1.bam	FBtr0079752	72	33	F	2	33-33	1	2.0
-input1.bam	FBtr0079752	72	52	F	2	52-52	1	2.0
-input1.bam	FBtr0079752	72	72	F	0	72-72	1	0.0
-input1.bam	FBtr0079820	74	1	F	0	1-1	1	0.0
-input1.bam	FBtr0079820	74	50	F	13	45-56	12	1.08333333333
-input1.bam	FBtr0079820	74	74	F	0	74-74	1	0.0
-input1.bam	FBtr0080609	72	10	F	60	1-20	20	3.0
-input1.bam	FBtr0080609	72	42	F	1	42-42	1	1.0
-input1.bam	FBtr0080609	72	51	F	2	51-52	2	1.0
-input1.bam	FBtr0080609	72	72	F	0	72-72	1	0.0
-input1.bam	FBtr0080644	72	6	F	6	1-12	12	0.5
-input1.bam	FBtr0080644	72	72	F	0	72-72	1	0.0
-input1.bam	FBtr0080646	72	4	F	3	1-7	7	0.428571428571
-input1.bam	FBtr0080646	72	72	F	0	72-72	1	0.0
-input1.bam	FBtr0080647	72	6	F	10	1-12	12	0.833333333333
-input1.bam	FBtr0080647	72	72	F	0	72-72	1	0.0
-input1.bam	FBtr0080660	72	4	F	7	1-7	7	1.0
-input1.bam	FBtr0080660	72	72	F	0	72-72	1	0.0
-input1.bam	FBtr0080663	71	9	F	102	1-17	17	6.0
-input1.bam	FBtr0080663	71	26	F	1	26-26	1	1.0
-input1.bam	FBtr0080663	71	32	F	2	32-32	1	2.0
-input1.bam	FBtr0080663	71	50	F	10	50-51	2	5.0
-input1.bam	FBtr0080663	71	71	F	0	71-71	1	0.0
-input1.bam	FBtr0080664	71	11	F	108	1-21	21	5.14285714286
-input1.bam	FBtr0080664	71	33	F	9	28-38	11	0.818181818182
-input1.bam	FBtr0080664	71	53	F	11	50-56	7	1.57142857143
-input1.bam	FBtr0080664	71	71	F	0	71-71	1	0.0
Binary file newtests/global_merge.pdf has changed
Binary file newtests/global_nomerge.pdf has changed
Binary file newtests/input1__single_plot_mean.pdf has changed
--- a/newtests/input1_counts_yminneg5_5.tab	Thu Nov 22 20:05:32 2018 -0500
+++ /dev/null	Thu Jan 01 00:00:00 1970 +0000
@@ -1,300 +0,0 @@
-Dataset	Chromosome	Chrom_length	Coordinate	Polarity	Counts
-input1.bam	FBtr0070001	72	1	F	1
-input1.bam	FBtr0070001	72	7	F	6
-input1.bam	FBtr0070001	72	8	F	3
-input1.bam	FBtr0070001	72	11	F	2
-input1.bam	FBtr0070001	72	16	F	1
-input1.bam	FBtr0070001	72	17	F	1
-input1.bam	FBtr0070001	72	18	F	1
-input1.bam	FBtr0070001	72	27	F	2
-input1.bam	FBtr0070001	72	30	F	1
-input1.bam	FBtr0070001	72	31	F	11
-input1.bam	FBtr0070001	72	32	F	27
-input1.bam	FBtr0070001	72	34	F	1
-input1.bam	FBtr0070001	72	72	F	0
-input1.bam	FBtr0070533	72	1	F	1
-input1.bam	FBtr0070533	72	12	F	2
-input1.bam	FBtr0070533	72	15	F	1
-input1.bam	FBtr0070533	72	19	F	5
-input1.bam	FBtr0070533	72	20	F	1
-input1.bam	FBtr0070533	72	21	F	1
-input1.bam	FBtr0070533	72	22	F	1
-input1.bam	FBtr0070533	72	25	F	1
-input1.bam	FBtr0070533	72	26	F	1
-input1.bam	FBtr0070533	72	28	F	1
-input1.bam	FBtr0070533	72	32	F	4
-input1.bam	FBtr0070533	72	35	F	1
-input1.bam	FBtr0070533	72	37	F	2
-input1.bam	FBtr0070533	72	38	F	2
-input1.bam	FBtr0070533	72	72	F	0
-input1.bam	FBtr0070603	72	1	F	2
-input1.bam	FBtr0070603	72	3	F	1
-input1.bam	FBtr0070603	72	4	F	1
-input1.bam	FBtr0070603	72	6	F	1
-input1.bam	FBtr0070603	72	7	F	7
-input1.bam	FBtr0070603	72	8	F	4
-input1.bam	FBtr0070603	72	9	F	7
-input1.bam	FBtr0070603	72	12	F	2
-input1.bam	FBtr0070603	72	13	F	1
-input1.bam	FBtr0070603	72	15	F	2
-input1.bam	FBtr0070603	72	16	F	2
-input1.bam	FBtr0070603	72	17	F	3
-input1.bam	FBtr0070603	72	18	F	1
-input1.bam	FBtr0070603	72	19	F	9
-input1.bam	FBtr0070603	72	20	F	3
-input1.bam	FBtr0070603	72	21	F	1
-input1.bam	FBtr0070603	72	22	F	3
-input1.bam	FBtr0070603	72	24	F	2
-input1.bam	FBtr0070603	72	25	F	1
-input1.bam	FBtr0070603	72	26	F	6
-input1.bam	FBtr0070603	72	27	F	3
-input1.bam	FBtr0070603	72	32	F	1
-input1.bam	FBtr0070603	72	34	F	3
-input1.bam	FBtr0070603	72	38	F	1
-input1.bam	FBtr0070603	72	42	F	1
-input1.bam	FBtr0070603	72	51	F	1
-input1.bam	FBtr0070603	72	56	F	1
-input1.bam	FBtr0070603	72	72	F	0
-input1.bam	FBtr0070604	72	1	F	1
-input1.bam	FBtr0070604	72	18	F	1
-input1.bam	FBtr0070604	72	22	F	1
-input1.bam	FBtr0070604	72	30	F	2
-input1.bam	FBtr0070604	72	31	F	10
-input1.bam	FBtr0070604	72	32	F	24
-input1.bam	FBtr0070604	72	57	F	1
-input1.bam	FBtr0070604	72	72	F	0
-input1.bam	FBtr0070911	73	1	F	0
-input1.bam	FBtr0070911	73	15	F	1
-input1.bam	FBtr0070911	73	38	F	1
-input1.bam	FBtr0070911	73	73	F	0
-input1.bam	FBtr0078490	72	1	F	0
-input1.bam	FBtr0078490	72	13	F	2
-input1.bam	FBtr0078490	72	17	F	1
-input1.bam	FBtr0078490	72	18	F	1
-input1.bam	FBtr0078490	72	25	F	1
-input1.bam	FBtr0078490	72	28	F	2
-input1.bam	FBtr0078490	72	38	F	1
-input1.bam	FBtr0078490	72	72	F	0
-input1.bam	FBtr0078580	72	1	F	1041
-input1.bam	FBtr0078580	72	3	F	3
-input1.bam	FBtr0078580	72	4	F	4
-input1.bam	FBtr0078580	72	5	F	5
-input1.bam	FBtr0078580	72	6	F	4
-input1.bam	FBtr0078580	72	7	F	1
-input1.bam	FBtr0078580	72	8	F	2
-input1.bam	FBtr0078580	72	11	F	1
-input1.bam	FBtr0078580	72	12	F	13
-input1.bam	FBtr0078580	72	14	F	7
-input1.bam	FBtr0078580	72	15	F	1
-input1.bam	FBtr0078580	72	16	F	4
-input1.bam	FBtr0078580	72	17	F	1
-input1.bam	FBtr0078580	72	19	F	1
-input1.bam	FBtr0078580	72	20	F	2
-input1.bam	FBtr0078580	72	21	F	5
-input1.bam	FBtr0078580	72	24	F	3
-input1.bam	FBtr0078580	72	25	F	2
-input1.bam	FBtr0078580	72	29	F	1
-input1.bam	FBtr0078580	72	31	F	1
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-input1.bam	FBtr0079090	72	1	F	2
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-input1.bam	FBtr0079090	72	33	F	1
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-input1.bam	FBtr0079090	72	56	R	1
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-input1.bam	FBtr0079338	73	1	F	0
-input1.bam	FBtr0079338	73	12	F	1
-input1.bam	FBtr0079338	73	13	F	2
-input1.bam	FBtr0079338	73	14	F	1
-input1.bam	FBtr0079338	73	17	F	1
-input1.bam	FBtr0079338	73	25	F	1
-input1.bam	FBtr0079338	73	42	F	8
-input1.bam	FBtr0079338	73	43	F	1
-input1.bam	FBtr0079338	73	46	F	1
-input1.bam	FBtr0079338	73	73	F	0
-input1.bam	FBtr0079528	71	1	F	19
-input1.bam	FBtr0079528	71	3	F	55
-input1.bam	FBtr0079528	71	4	F	2
-input1.bam	FBtr0079528	71	8	F	4
-input1.bam	FBtr0079528	71	10	F	1
-input1.bam	FBtr0079528	71	11	F	2
-input1.bam	FBtr0079528	71	13	F	1
-input1.bam	FBtr0079528	71	14	F	4
-input1.bam	FBtr0079528	71	16	F	1
-input1.bam	FBtr0079528	71	17	F	4
-input1.bam	FBtr0079528	71	18	F	4
-input1.bam	FBtr0079528	71	28	F	1
-input1.bam	FBtr0079528	71	35	F	1
-input1.bam	FBtr0079528	71	36	F	1
-input1.bam	FBtr0079528	71	37	F	1
-input1.bam	FBtr0079528	71	51	F	5
-input1.bam	FBtr0079528	71	71	F	0
-input1.bam	FBtr0079596	73	1	F	13
-input1.bam	FBtr0079596	73	3	F	13
-input1.bam	FBtr0079596	73	4	F	31
-input1.bam	FBtr0079596	73	5	F	2
-input1.bam	FBtr0079596	73	6	F	11
-input1.bam	FBtr0079596	73	8	F	9
-input1.bam	FBtr0079596	73	9	F	12
-input1.bam	FBtr0079596	73	10	F	3
-input1.bam	FBtr0079596	73	11	F	19
-input1.bam	FBtr0079596	73	12	F	1
-input1.bam	FBtr0079596	73	13	F	20
-input1.bam	FBtr0079596	73	14	F	6
-input1.bam	FBtr0079596	73	15	F	1
-input1.bam	FBtr0079596	73	16	F	3
-input1.bam	FBtr0079596	73	17	F	2
-input1.bam	FBtr0079596	73	18	F	1
-input1.bam	FBtr0079596	73	19	F	1
-input1.bam	FBtr0079596	73	53	F	2
-input1.bam	FBtr0079596	73	54	F	2
-input1.bam	FBtr0079596	73	73	F	0
-input1.bam	FBtr0079677	72	1	F	1
-input1.bam	FBtr0079677	72	5	F	1
-input1.bam	FBtr0079677	72	52	F	1
-input1.bam	FBtr0079677	72	53	F	1
-input1.bam	FBtr0079677	72	72	F	0
-input1.bam	FBtr0079690	72	1	F	1
-input1.bam	FBtr0079690	72	22	F	1
-input1.bam	FBtr0079690	72	27	F	1
-input1.bam	FBtr0079690	72	33	F	2
-input1.bam	FBtr0079690	72	72	F	0
-input1.bam	FBtr0079692	73	1	F	3
-input1.bam	FBtr0079692	73	18	F	1
-input1.bam	FBtr0079692	73	25	F	1
-input1.bam	FBtr0079692	73	32	F	1
-input1.bam	FBtr0079692	73	73	F	0
-input1.bam	FBtr0079693	72	1	F	5
-input1.bam	FBtr0079693	72	25	F	1
-input1.bam	FBtr0079693	72	72	F	0
-input1.bam	FBtr0079694	72	1	F	5
-input1.bam	FBtr0079694	72	18	F	1
-input1.bam	FBtr0079694	72	52	F	1
-input1.bam	FBtr0079694	72	72	F	0
-input1.bam	FBtr0079702	72	1	F	1
-input1.bam	FBtr0079702	72	19	F	2
-input1.bam	FBtr0079702	72	56	F	1
-input1.bam	FBtr0079702	72	72	F	0
-input1.bam	FBtr0079728	72	1	F	2
-input1.bam	FBtr0079728	72	8	F	1
-input1.bam	FBtr0079728	72	19	F	1
-input1.bam	FBtr0079728	72	33	F	3
-input1.bam	FBtr0079728	72	56	F	1
-input1.bam	FBtr0079728	72	72	F	0
-input1.bam	FBtr0079729	72	1	F	1
-input1.bam	FBtr0079729	72	13	F	1
-input1.bam	FBtr0079729	72	52	F	1
-input1.bam	FBtr0079729	72	57	F	1
-input1.bam	FBtr0079729	72	72	F	0
-input1.bam	FBtr0079752	72	1	F	2
-input1.bam	FBtr0079752	72	7	F	1
-input1.bam	FBtr0079752	72	12	F	1
-input1.bam	FBtr0079752	72	33	F	2
-input1.bam	FBtr0079752	72	52	F	2
-input1.bam	FBtr0079752	72	72	F	0
-input1.bam	FBtr0079820	74	1	F	0
-input1.bam	FBtr0079820	74	45	F	1
-input1.bam	FBtr0079820	74	46	F	2
-input1.bam	FBtr0079820	74	48	F	1
-input1.bam	FBtr0079820	74	49	F	1
-input1.bam	FBtr0079820	74	51	F	1
-input1.bam	FBtr0079820	74	54	F	4
-input1.bam	FBtr0079820	74	55	F	1
-input1.bam	FBtr0079820	74	56	F	2
-input1.bam	FBtr0079820	74	74	F	0
-input1.bam	FBtr0080609	72	1	F	13
-input1.bam	FBtr0080609	72	3	F	2
-input1.bam	FBtr0080609	72	4	F	10
-input1.bam	FBtr0080609	72	5	F	2
-input1.bam	FBtr0080609	72	7	F	19
-input1.bam	FBtr0080609	72	8	F	4
-input1.bam	FBtr0080609	72	9	F	3
-input1.bam	FBtr0080609	72	12	F	1
-input1.bam	FBtr0080609	72	15	F	1
-input1.bam	FBtr0080609	72	16	F	1
-input1.bam	FBtr0080609	72	17	F	2
-input1.bam	FBtr0080609	72	19	F	1
-input1.bam	FBtr0080609	72	20	F	1
-input1.bam	FBtr0080609	72	42	F	1
-input1.bam	FBtr0080609	72	51	F	1
-input1.bam	FBtr0080609	72	52	F	1
-input1.bam	FBtr0080609	72	72	F	0
-input1.bam	FBtr0080644	72	1	F	1
-input1.bam	FBtr0080644	72	4	F	2
-input1.bam	FBtr0080644	72	7	F	1
-input1.bam	FBtr0080644	72	12	F	2
-input1.bam	FBtr0080644	72	72	F	0
-input1.bam	FBtr0080646	72	1	F	1
-input1.bam	FBtr0080646	72	6	F	1
-input1.bam	FBtr0080646	72	7	F	1
-input1.bam	FBtr0080646	72	72	F	0
-input1.bam	FBtr0080647	72	1	F	3
-input1.bam	FBtr0080647	72	3	F	1
-input1.bam	FBtr0080647	72	6	F	2
-input1.bam	FBtr0080647	72	8	F	1
-input1.bam	FBtr0080647	72	11	F	2
-input1.bam	FBtr0080647	72	12	F	1
-input1.bam	FBtr0080647	72	72	F	0
-input1.bam	FBtr0080660	72	1	F	0
-input1.bam	FBtr0080660	72	4	F	4
-input1.bam	FBtr0080660	72	7	F	3
-input1.bam	FBtr0080660	72	72	F	0
-input1.bam	FBtr0080663	71	1	F	22
-input1.bam	FBtr0080663	71	3	F	56
-input1.bam	FBtr0080663	71	4	F	4
-input1.bam	FBtr0080663	71	7	F	1
-input1.bam	FBtr0080663	71	8	F	4
-input1.bam	FBtr0080663	71	12	F	2
-input1.bam	FBtr0080663	71	14	F	2
-input1.bam	FBtr0080663	71	15	F	1
-input1.bam	FBtr0080663	71	16	F	3
-input1.bam	FBtr0080663	71	17	F	7
-input1.bam	FBtr0080663	71	26	F	1
-input1.bam	FBtr0080663	71	32	F	2
-input1.bam	FBtr0080663	71	50	F	1
-input1.bam	FBtr0080663	71	51	F	9
-input1.bam	FBtr0080663	71	71	F	0
-input1.bam	FBtr0080664	71	1	F	16
-input1.bam	FBtr0080664	71	3	F	56
-input1.bam	FBtr0080664	71	4	F	4
-input1.bam	FBtr0080664	71	6	F	1
-input1.bam	FBtr0080664	71	7	F	1
-input1.bam	FBtr0080664	71	8	F	4
-input1.bam	FBtr0080664	71	9	F	1
-input1.bam	FBtr0080664	71	11	F	3
-input1.bam	FBtr0080664	71	12	F	3
-input1.bam	FBtr0080664	71	13	F	2
-input1.bam	FBtr0080664	71	14	F	3
-input1.bam	FBtr0080664	71	16	F	2
-input1.bam	FBtr0080664	71	17	F	10
-input1.bam	FBtr0080664	71	18	F	1
-input1.bam	FBtr0080664	71	21	F	1
-input1.bam	FBtr0080664	71	28	F	2
-input1.bam	FBtr0080664	71	32	F	1
-input1.bam	FBtr0080664	71	33	F	1
-input1.bam	FBtr0080664	71	34	F	1
-input1.bam	FBtr0080664	71	35	F	1
-input1.bam	FBtr0080664	71	36	F	1
-input1.bam	FBtr0080664	71	37	F	1
-input1.bam	FBtr0080664	71	38	F	1
-input1.bam	FBtr0080664	71	50	F	2
-input1.bam	FBtr0080664	71	51	F	7
-input1.bam	FBtr0080664	71	52	F	1
-input1.bam	FBtr0080664	71	56	F	1
-input1.bam	FBtr0080664	71	71	F	0
--- a/newtests/input1_input2_counts.tab	Thu Nov 22 20:05:32 2018 -0500
+++ /dev/null	Thu Jan 01 00:00:00 1970 +0000
@@ -1,617 +0,0 @@
-Dataset	Chromosome	Chrom_length	Coordinate	Polarity	Counts
-input1.bam	FBtr0070001	72	1	F	1
-input1.bam	FBtr0070001	72	7	F	6
-input1.bam	FBtr0070001	72	8	F	3
-input1.bam	FBtr0070001	72	11	F	2
-input1.bam	FBtr0070001	72	16	F	1
-input1.bam	FBtr0070001	72	17	F	1
-input1.bam	FBtr0070001	72	18	F	1
-input1.bam	FBtr0070001	72	27	F	2
-input1.bam	FBtr0070001	72	30	F	1
-input1.bam	FBtr0070001	72	31	F	11
-input1.bam	FBtr0070001	72	32	F	27
-input1.bam	FBtr0070001	72	34	F	1
-input1.bam	FBtr0070001	72	72	F	0
-input1.bam	FBtr0070533	72	1	F	1
-input1.bam	FBtr0070533	72	12	F	2
-input1.bam	FBtr0070533	72	15	F	1
-input1.bam	FBtr0070533	72	19	F	5
-input1.bam	FBtr0070533	72	20	F	1
-input1.bam	FBtr0070533	72	21	F	1
-input1.bam	FBtr0070533	72	22	F	1
-input1.bam	FBtr0070533	72	25	F	1
-input1.bam	FBtr0070533	72	26	F	1
-input1.bam	FBtr0070533	72	28	F	1
-input1.bam	FBtr0070533	72	32	F	4
-input1.bam	FBtr0070533	72	35	F	1
-input1.bam	FBtr0070533	72	37	F	2
-input1.bam	FBtr0070533	72	38	F	2
-input1.bam	FBtr0070533	72	72	F	0
-input1.bam	FBtr0070603	72	1	F	2
-input1.bam	FBtr0070603	72	3	F	1
-input1.bam	FBtr0070603	72	4	F	1
-input1.bam	FBtr0070603	72	6	F	1
-input1.bam	FBtr0070603	72	7	F	7
-input1.bam	FBtr0070603	72	8	F	4
-input1.bam	FBtr0070603	72	9	F	7
-input1.bam	FBtr0070603	72	12	F	2
-input1.bam	FBtr0070603	72	13	F	1
-input1.bam	FBtr0070603	72	15	F	2
-input1.bam	FBtr0070603	72	16	F	2
-input1.bam	FBtr0070603	72	17	F	3
-input1.bam	FBtr0070603	72	18	F	1
-input1.bam	FBtr0070603	72	19	F	9
-input1.bam	FBtr0070603	72	20	F	3
-input1.bam	FBtr0070603	72	21	F	1
-input1.bam	FBtr0070603	72	22	F	3
-input1.bam	FBtr0070603	72	24	F	2
-input1.bam	FBtr0070603	72	25	F	1
-input1.bam	FBtr0070603	72	26	F	6
-input1.bam	FBtr0070603	72	27	F	3
-input1.bam	FBtr0070603	72	32	F	1
-input1.bam	FBtr0070603	72	34	F	3
-input1.bam	FBtr0070603	72	38	F	1
-input1.bam	FBtr0070603	72	42	F	1
-input1.bam	FBtr0070603	72	51	F	1
-input1.bam	FBtr0070603	72	56	F	1
-input1.bam	FBtr0070603	72	72	F	0
-input1.bam	FBtr0070604	72	1	F	1
-input1.bam	FBtr0070604	72	18	F	1
-input1.bam	FBtr0070604	72	22	F	1
-input1.bam	FBtr0070604	72	30	F	2
-input1.bam	FBtr0070604	72	31	F	10
-input1.bam	FBtr0070604	72	32	F	24
-input1.bam	FBtr0070604	72	57	F	1
-input1.bam	FBtr0070604	72	72	F	0
-input1.bam	FBtr0070911	73	1	F	0
-input1.bam	FBtr0070911	73	15	F	1
-input1.bam	FBtr0070911	73	38	F	1
-input1.bam	FBtr0070911	73	73	F	0
-input1.bam	FBtr0078490	72	1	F	0
-input1.bam	FBtr0078490	72	13	F	2
-input1.bam	FBtr0078490	72	17	F	1
-input1.bam	FBtr0078490	72	18	F	1
-input1.bam	FBtr0078490	72	25	F	1
-input1.bam	FBtr0078490	72	28	F	2
-input1.bam	FBtr0078490	72	38	F	1
-input1.bam	FBtr0078490	72	72	F	0
-input1.bam	FBtr0078580	72	1	F	1041
-input1.bam	FBtr0078580	72	3	F	3
-input1.bam	FBtr0078580	72	4	F	4
-input1.bam	FBtr0078580	72	5	F	5
-input1.bam	FBtr0078580	72	6	F	4
-input1.bam	FBtr0078580	72	7	F	1
-input1.bam	FBtr0078580	72	8	F	2
-input1.bam	FBtr0078580	72	11	F	1
-input1.bam	FBtr0078580	72	12	F	13
-input1.bam	FBtr0078580	72	14	F	7
-input1.bam	FBtr0078580	72	15	F	1
-input1.bam	FBtr0078580	72	16	F	4
-input1.bam	FBtr0078580	72	17	F	1
-input1.bam	FBtr0078580	72	19	F	1
-input1.bam	FBtr0078580	72	20	F	2
-input1.bam	FBtr0078580	72	21	F	5
-input1.bam	FBtr0078580	72	24	F	3
-input1.bam	FBtr0078580	72	25	F	2
-input1.bam	FBtr0078580	72	29	F	1
-input1.bam	FBtr0078580	72	31	F	1
-input1.bam	FBtr0078580	72	52	F	2
-input1.bam	FBtr0078580	72	72	F	0
-input1.bam	FBtr0078790	73	1	F	1
-input1.bam	FBtr0078790	73	17	F	2
-input1.bam	FBtr0078790	73	33	F	1
-input1.bam	FBtr0078790	73	42	F	4
-input1.bam	FBtr0078790	73	44	F	2
-input1.bam	FBtr0078790	73	46	F	1
-input1.bam	FBtr0078790	73	47	F	1
-input1.bam	FBtr0078790	73	52	F	1
-input1.bam	FBtr0078790	73	69	R	1
-input1.bam	FBtr0078790	73	73	F	0
-input1.bam	FBtr0079064	72	1	F	1
-input1.bam	FBtr0079064	72	3	F	1
-input1.bam	FBtr0079064	72	33	F	1
-input1.bam	FBtr0079064	72	52	F	1
-input1.bam	FBtr0079064	72	72	F	0
-input1.bam	FBtr0079090	72	1	F	2
-input1.bam	FBtr0079090	72	26	F	1
-input1.bam	FBtr0079090	72	33	F	1
-input1.bam	FBtr0079090	72	53	F	1
-input1.bam	FBtr0079090	72	56	R	1
-input1.bam	FBtr0079090	72	72	F	0
-input1.bam	FBtr0079338	73	1	F	0
-input1.bam	FBtr0079338	73	12	F	1
-input1.bam	FBtr0079338	73	13	F	2
-input1.bam	FBtr0079338	73	14	F	1
-input1.bam	FBtr0079338	73	17	F	1
-input1.bam	FBtr0079338	73	25	F	1
-input1.bam	FBtr0079338	73	42	F	8
-input1.bam	FBtr0079338	73	43	F	1
-input1.bam	FBtr0079338	73	46	F	1
-input1.bam	FBtr0079338	73	73	F	0
-input1.bam	FBtr0079528	71	1	F	19
-input1.bam	FBtr0079528	71	3	F	55
-input1.bam	FBtr0079528	71	4	F	2
-input1.bam	FBtr0079528	71	8	F	4
-input1.bam	FBtr0079528	71	10	F	1
-input1.bam	FBtr0079528	71	11	F	2
-input1.bam	FBtr0079528	71	13	F	1
-input1.bam	FBtr0079528	71	14	F	4
-input1.bam	FBtr0079528	71	16	F	1
-input1.bam	FBtr0079528	71	17	F	4
-input1.bam	FBtr0079528	71	18	F	4
-input1.bam	FBtr0079528	71	28	F	1
-input1.bam	FBtr0079528	71	35	F	1
-input1.bam	FBtr0079528	71	36	F	1
-input1.bam	FBtr0079528	71	37	F	1
-input1.bam	FBtr0079528	71	51	F	5
-input1.bam	FBtr0079528	71	71	F	0
-input1.bam	FBtr0079596	73	1	F	13
-input1.bam	FBtr0079596	73	3	F	13
-input1.bam	FBtr0079596	73	4	F	31
-input1.bam	FBtr0079596	73	5	F	2
-input1.bam	FBtr0079596	73	6	F	11
-input1.bam	FBtr0079596	73	8	F	9
-input1.bam	FBtr0079596	73	9	F	12
-input1.bam	FBtr0079596	73	10	F	3
-input1.bam	FBtr0079596	73	11	F	19
-input1.bam	FBtr0079596	73	12	F	1
-input1.bam	FBtr0079596	73	13	F	20
-input1.bam	FBtr0079596	73	14	F	6
-input1.bam	FBtr0079596	73	15	F	1
-input1.bam	FBtr0079596	73	16	F	3
-input1.bam	FBtr0079596	73	17	F	2
-input1.bam	FBtr0079596	73	18	F	1
-input1.bam	FBtr0079596	73	19	F	1
-input1.bam	FBtr0079596	73	53	F	2
-input1.bam	FBtr0079596	73	54	F	2
-input1.bam	FBtr0079596	73	73	F	0
-input1.bam	FBtr0079677	72	1	F	1
-input1.bam	FBtr0079677	72	5	F	1
-input1.bam	FBtr0079677	72	52	F	1
-input1.bam	FBtr0079677	72	53	F	1
-input1.bam	FBtr0079677	72	72	F	0
-input1.bam	FBtr0079690	72	1	F	1
-input1.bam	FBtr0079690	72	22	F	1
-input1.bam	FBtr0079690	72	27	F	1
-input1.bam	FBtr0079690	72	33	F	2
-input1.bam	FBtr0079690	72	72	F	0
-input1.bam	FBtr0079692	73	1	F	3
-input1.bam	FBtr0079692	73	18	F	1
-input1.bam	FBtr0079692	73	25	F	1
-input1.bam	FBtr0079692	73	32	F	1
-input1.bam	FBtr0079692	73	73	F	0
-input1.bam	FBtr0079693	72	1	F	5
-input1.bam	FBtr0079693	72	25	F	1
-input1.bam	FBtr0079693	72	72	F	0
-input1.bam	FBtr0079694	72	1	F	5
-input1.bam	FBtr0079694	72	18	F	1
-input1.bam	FBtr0079694	72	52	F	1
-input1.bam	FBtr0079694	72	72	F	0
-input1.bam	FBtr0079702	72	1	F	1
-input1.bam	FBtr0079702	72	19	F	2
-input1.bam	FBtr0079702	72	56	F	1
-input1.bam	FBtr0079702	72	72	F	0
-input1.bam	FBtr0079728	72	1	F	2
-input1.bam	FBtr0079728	72	8	F	1
-input1.bam	FBtr0079728	72	19	F	1
-input1.bam	FBtr0079728	72	33	F	3
-input1.bam	FBtr0079728	72	56	F	1
-input1.bam	FBtr0079728	72	72	F	0
-input1.bam	FBtr0079729	72	1	F	1
-input1.bam	FBtr0079729	72	13	F	1
-input1.bam	FBtr0079729	72	52	F	1
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-input2.bam	FBtr0080663	71	71	F	0
-input2.bam	FBtr0080664	71	1	F	1
-input2.bam	FBtr0080664	71	3	F	2
-input2.bam	FBtr0080664	71	10	F	1
-input2.bam	FBtr0080664	71	11	F	2
-input2.bam	FBtr0080664	71	12	F	3
-input2.bam	FBtr0080664	71	13	F	11
-input2.bam	FBtr0080664	71	14	F	11
-input2.bam	FBtr0080664	71	15	F	17
-input2.bam	FBtr0080664	71	16	F	15
-input2.bam	FBtr0080664	71	17	F	13
-input2.bam	FBtr0080664	71	18	F	10
-input2.bam	FBtr0080664	71	19	F	8
-input2.bam	FBtr0080664	71	20	F	1
-input2.bam	FBtr0080664	71	21	F	15
-input2.bam	FBtr0080664	71	22	F	6
-input2.bam	FBtr0080664	71	24	F	1
-input2.bam	FBtr0080664	71	30	F	1
-input2.bam	FBtr0080664	71	31	F	3
-input2.bam	FBtr0080664	71	32	F	39
-input2.bam	FBtr0080664	71	33	F	4
-input2.bam	FBtr0080664	71	34	F	37
-input2.bam	FBtr0080664	71	35	F	135
-input2.bam	FBtr0080664	71	36	F	8
-input2.bam	FBtr0080664	71	37	F	25
-input2.bam	FBtr0080664	71	38	F	8
-input2.bam	FBtr0080664	71	39	F	1
-input2.bam	FBtr0080664	71	42	F	1
-input2.bam	FBtr0080664	71	47	F	1
-input2.bam	FBtr0080664	71	50	F	2
-input2.bam	FBtr0080664	71	52	F	1
-input2.bam	FBtr0080664	71	53	F	1
-input2.bam	FBtr0080664	71	56	F	1
-input2.bam	FBtr0080664	71	57	F	2
-input2.bam	FBtr0080664	71	62	R	1
-input2.bam	FBtr0080664	71	71	F	0
-input2.bam	FBtr0080664	71	71	R	1
Binary file newtests/input1_input2_double_plot_counts_size_ylimneg5_5.pdf has changed
--- a/newtests/input1_input2_norm_1_2_counts.tab	Thu Nov 22 20:05:32 2018 -0500
+++ /dev/null	Thu Jan 01 00:00:00 1970 +0000
@@ -1,617 +0,0 @@
-Dataset	Chromosome	Chrom_length	Coordinate	Polarity	Counts
-input1.bam	FBtr0070001	72	1	F	1
-input1.bam	FBtr0070001	72	7	F	6
-input1.bam	FBtr0070001	72	8	F	3
-input1.bam	FBtr0070001	72	11	F	2
-input1.bam	FBtr0070001	72	16	F	1
-input1.bam	FBtr0070001	72	17	F	1
-input1.bam	FBtr0070001	72	18	F	1
-input1.bam	FBtr0070001	72	27	F	2
-input1.bam	FBtr0070001	72	30	F	1
-input1.bam	FBtr0070001	72	31	F	11
-input1.bam	FBtr0070001	72	32	F	27
-input1.bam	FBtr0070001	72	34	F	1
-input1.bam	FBtr0070001	72	72	F	0
-input1.bam	FBtr0070533	72	1	F	1
-input1.bam	FBtr0070533	72	12	F	2
-input1.bam	FBtr0070533	72	15	F	1
-input1.bam	FBtr0070533	72	19	F	5
-input1.bam	FBtr0070533	72	20	F	1
-input1.bam	FBtr0070533	72	21	F	1
-input1.bam	FBtr0070533	72	22	F	1
-input1.bam	FBtr0070533	72	25	F	1
-input1.bam	FBtr0070533	72	26	F	1
-input1.bam	FBtr0070533	72	28	F	1
-input1.bam	FBtr0070533	72	32	F	4
-input1.bam	FBtr0070533	72	35	F	1
-input1.bam	FBtr0070533	72	37	F	2
-input1.bam	FBtr0070533	72	38	F	2
-input1.bam	FBtr0070533	72	72	F	0
-input1.bam	FBtr0070603	72	1	F	2
-input1.bam	FBtr0070603	72	3	F	1
-input1.bam	FBtr0070603	72	4	F	1
-input1.bam	FBtr0070603	72	6	F	1
-input1.bam	FBtr0070603	72	7	F	7
-input1.bam	FBtr0070603	72	8	F	4
-input1.bam	FBtr0070603	72	9	F	7
-input1.bam	FBtr0070603	72	12	F	2
-input1.bam	FBtr0070603	72	13	F	1
-input1.bam	FBtr0070603	72	15	F	2
-input1.bam	FBtr0070603	72	16	F	2
-input1.bam	FBtr0070603	72	17	F	3
-input1.bam	FBtr0070603	72	18	F	1
-input1.bam	FBtr0070603	72	19	F	9
-input1.bam	FBtr0070603	72	20	F	3
-input1.bam	FBtr0070603	72	21	F	1
-input1.bam	FBtr0070603	72	22	F	3
-input1.bam	FBtr0070603	72	24	F	2
-input1.bam	FBtr0070603	72	25	F	1
-input1.bam	FBtr0070603	72	26	F	6
-input1.bam	FBtr0070603	72	27	F	3
-input1.bam	FBtr0070603	72	32	F	1
-input1.bam	FBtr0070603	72	34	F	3
-input1.bam	FBtr0070603	72	38	F	1
-input1.bam	FBtr0070603	72	42	F	1
-input1.bam	FBtr0070603	72	51	F	1
-input1.bam	FBtr0070603	72	56	F	1
-input1.bam	FBtr0070603	72	72	F	0
-input1.bam	FBtr0070604	72	1	F	1
-input1.bam	FBtr0070604	72	18	F	1
-input1.bam	FBtr0070604	72	22	F	1
-input1.bam	FBtr0070604	72	30	F	2
-input1.bam	FBtr0070604	72	31	F	10
-input1.bam	FBtr0070604	72	32	F	24
-input1.bam	FBtr0070604	72	57	F	1
-input1.bam	FBtr0070604	72	72	F	0
-input1.bam	FBtr0070911	73	1	F	0
-input1.bam	FBtr0070911	73	15	F	1
-input1.bam	FBtr0070911	73	38	F	1
-input1.bam	FBtr0070911	73	73	F	0
-input1.bam	FBtr0078490	72	1	F	0
-input1.bam	FBtr0078490	72	13	F	2
-input1.bam	FBtr0078490	72	17	F	1
-input1.bam	FBtr0078490	72	18	F	1
-input1.bam	FBtr0078490	72	25	F	1
-input1.bam	FBtr0078490	72	28	F	2
-input1.bam	FBtr0078490	72	38	F	1
-input1.bam	FBtr0078490	72	72	F	0
-input1.bam	FBtr0078580	72	1	F	1041
-input1.bam	FBtr0078580	72	3	F	3
-input1.bam	FBtr0078580	72	4	F	4
-input1.bam	FBtr0078580	72	5	F	5
-input1.bam	FBtr0078580	72	6	F	4
-input1.bam	FBtr0078580	72	7	F	1
-input1.bam	FBtr0078580	72	8	F	2
-input1.bam	FBtr0078580	72	11	F	1
-input1.bam	FBtr0078580	72	12	F	13
-input1.bam	FBtr0078580	72	14	F	7
-input1.bam	FBtr0078580	72	15	F	1
-input1.bam	FBtr0078580	72	16	F	4
-input1.bam	FBtr0078580	72	17	F	1
-input1.bam	FBtr0078580	72	19	F	1
-input1.bam	FBtr0078580	72	20	F	2
-input1.bam	FBtr0078580	72	21	F	5
-input1.bam	FBtr0078580	72	24	F	3
-input1.bam	FBtr0078580	72	25	F	2
-input1.bam	FBtr0078580	72	29	F	1
-input1.bam	FBtr0078580	72	31	F	1
-input1.bam	FBtr0078580	72	52	F	2
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-input1.bam	FBtr0078790	73	42	F	4
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-input1.bam	FBtr0078790	73	47	F	1
-input1.bam	FBtr0078790	73	52	F	1
-input1.bam	FBtr0078790	73	69	R	1
-input1.bam	FBtr0078790	73	73	F	0
-input1.bam	FBtr0079064	72	1	F	1
-input1.bam	FBtr0079064	72	3	F	1
-input1.bam	FBtr0079064	72	33	F	1
-input1.bam	FBtr0079064	72	52	F	1
-input1.bam	FBtr0079064	72	72	F	0
-input1.bam	FBtr0079090	72	1	F	2
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-input1.bam	FBtr0079090	72	33	F	1
-input1.bam	FBtr0079090	72	53	F	1
-input1.bam	FBtr0079090	72	56	R	1
-input1.bam	FBtr0079090	72	72	F	0
-input1.bam	FBtr0079338	73	1	F	0
-input1.bam	FBtr0079338	73	12	F	1
-input1.bam	FBtr0079338	73	13	F	2
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-input1.bam	FBtr0079338	73	17	F	1
-input1.bam	FBtr0079338	73	25	F	1
-input1.bam	FBtr0079338	73	42	F	8
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-input1.bam	FBtr0079338	73	46	F	1
-input1.bam	FBtr0079338	73	73	F	0
-input1.bam	FBtr0079528	71	1	F	19
-input1.bam	FBtr0079528	71	3	F	55
-input1.bam	FBtr0079528	71	4	F	2
-input1.bam	FBtr0079528	71	8	F	4
-input1.bam	FBtr0079528	71	10	F	1
-input1.bam	FBtr0079528	71	11	F	2
-input1.bam	FBtr0079528	71	13	F	1
-input1.bam	FBtr0079528	71	14	F	4
-input1.bam	FBtr0079528	71	16	F	1
-input1.bam	FBtr0079528	71	17	F	4
-input1.bam	FBtr0079528	71	18	F	4
-input1.bam	FBtr0079528	71	28	F	1
-input1.bam	FBtr0079528	71	35	F	1
-input1.bam	FBtr0079528	71	36	F	1
-input1.bam	FBtr0079528	71	37	F	1
-input1.bam	FBtr0079528	71	51	F	5
-input1.bam	FBtr0079528	71	71	F	0
-input1.bam	FBtr0079596	73	1	F	13
-input1.bam	FBtr0079596	73	3	F	13
-input1.bam	FBtr0079596	73	4	F	31
-input1.bam	FBtr0079596	73	5	F	2
-input1.bam	FBtr0079596	73	6	F	11
-input1.bam	FBtr0079596	73	8	F	9
-input1.bam	FBtr0079596	73	9	F	12
-input1.bam	FBtr0079596	73	10	F	3
-input1.bam	FBtr0079596	73	11	F	19
-input1.bam	FBtr0079596	73	12	F	1
-input1.bam	FBtr0079596	73	13	F	20
-input1.bam	FBtr0079596	73	14	F	6
-input1.bam	FBtr0079596	73	15	F	1
-input1.bam	FBtr0079596	73	16	F	3
-input1.bam	FBtr0079596	73	17	F	2
-input1.bam	FBtr0079596	73	18	F	1
-input1.bam	FBtr0079596	73	19	F	1
-input1.bam	FBtr0079596	73	53	F	2
-input1.bam	FBtr0079596	73	54	F	2
-input1.bam	FBtr0079596	73	73	F	0
-input1.bam	FBtr0079677	72	1	F	1
-input1.bam	FBtr0079677	72	5	F	1
-input1.bam	FBtr0079677	72	52	F	1
-input1.bam	FBtr0079677	72	53	F	1
-input1.bam	FBtr0079677	72	72	F	0
-input1.bam	FBtr0079690	72	1	F	1
-input1.bam	FBtr0079690	72	22	F	1
-input1.bam	FBtr0079690	72	27	F	1
-input1.bam	FBtr0079690	72	33	F	2
-input1.bam	FBtr0079690	72	72	F	0
-input1.bam	FBtr0079692	73	1	F	3
-input1.bam	FBtr0079692	73	18	F	1
-input1.bam	FBtr0079692	73	25	F	1
-input1.bam	FBtr0079692	73	32	F	1
-input1.bam	FBtr0079692	73	73	F	0
-input1.bam	FBtr0079693	72	1	F	5
-input1.bam	FBtr0079693	72	25	F	1
-input1.bam	FBtr0079693	72	72	F	0
-input1.bam	FBtr0079694	72	1	F	5
-input1.bam	FBtr0079694	72	18	F	1
-input1.bam	FBtr0079694	72	52	F	1
-input1.bam	FBtr0079694	72	72	F	0
-input1.bam	FBtr0079702	72	1	F	1
-input1.bam	FBtr0079702	72	19	F	2
-input1.bam	FBtr0079702	72	56	F	1
-input1.bam	FBtr0079702	72	72	F	0
-input1.bam	FBtr0079728	72	1	F	2
-input1.bam	FBtr0079728	72	8	F	1
-input1.bam	FBtr0079728	72	19	F	1
-input1.bam	FBtr0079728	72	33	F	3
-input1.bam	FBtr0079728	72	56	F	1
-input1.bam	FBtr0079728	72	72	F	0
-input1.bam	FBtr0079729	72	1	F	1
-input1.bam	FBtr0079729	72	13	F	1
-input1.bam	FBtr0079729	72	52	F	1
-input1.bam	FBtr0079729	72	57	F	1
-input1.bam	FBtr0079729	72	72	F	0
-input1.bam	FBtr0079752	72	1	F	2
-input1.bam	FBtr0079752	72	7	F	1
-input1.bam	FBtr0079752	72	12	F	1
-input1.bam	FBtr0079752	72	33	F	2
-input1.bam	FBtr0079752	72	52	F	2
-input1.bam	FBtr0079752	72	72	F	0
-input1.bam	FBtr0079820	74	1	F	0
-input1.bam	FBtr0079820	74	45	F	1
-input1.bam	FBtr0079820	74	46	F	2
-input1.bam	FBtr0079820	74	48	F	1
-input1.bam	FBtr0079820	74	49	F	1
-input1.bam	FBtr0079820	74	51	F	1
-input1.bam	FBtr0079820	74	54	F	4
-input1.bam	FBtr0079820	74	55	F	1
-input1.bam	FBtr0079820	74	56	F	2
-input1.bam	FBtr0079820	74	74	F	0
-input1.bam	FBtr0080609	72	1	F	13
-input1.bam	FBtr0080609	72	3	F	2
-input1.bam	FBtr0080609	72	4	F	10
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-input1.bam	FBtr0080609	72	9	F	3
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-input2.bam	FBtr0070603	72	22	F	21
-input2.bam	FBtr0070603	72	25	F	1
-input2.bam	FBtr0070603	72	27	F	2
-input2.bam	FBtr0070603	72	28	F	2
-input2.bam	FBtr0070603	72	30	F	2
-input2.bam	FBtr0070603	72	31	F	2
-input2.bam	FBtr0070603	72	34	F	4
-input2.bam	FBtr0070603	72	35	F	2
-input2.bam	FBtr0070603	72	37	F	2
-input2.bam	FBtr0070603	72	38	F	2
-input2.bam	FBtr0070603	72	41	F	3
-input2.bam	FBtr0070603	72	51	F	2
-input2.bam	FBtr0070603	72	53	F	2
-input2.bam	FBtr0070603	72	72	F	0
-input2.bam	FBtr0070604	72	1	F	0
-input2.bam	FBtr0070604	72	3	F	1
-input2.bam	FBtr0070604	72	31	F	1
-input2.bam	FBtr0070604	72	32	F	5
-input2.bam	FBtr0070604	72	40	F	1
-input2.bam	FBtr0070604	72	53	F	3
-input2.bam	FBtr0070604	72	56	F	4
-input2.bam	FBtr0070604	72	57	F	18
-input2.bam	FBtr0070604	72	58	F	22
-input2.bam	FBtr0070604	72	72	F	0
-input2.bam	FBtr0070911	73	1	F	0
-input2.bam	FBtr0070911	73	11	F	1
-input2.bam	FBtr0070911	73	32	F	1
-input2.bam	FBtr0070911	73	48	F	1
-input2.bam	FBtr0070911	73	73	F	0
-input2.bam	FBtr0078490	72	1	F	3
-input2.bam	FBtr0078490	72	13	F	2
-input2.bam	FBtr0078490	72	14	F	4
-input2.bam	FBtr0078490	72	20	F	1
-input2.bam	FBtr0078490	72	30	F	1
-input2.bam	FBtr0078490	72	38	F	2
-input2.bam	FBtr0078490	72	41	F	1
-input2.bam	FBtr0078490	72	72	F	0
-input2.bam	FBtr0078580	72	1	F	146
-input2.bam	FBtr0078580	72	11	F	1
-input2.bam	FBtr0078580	72	13	F	1
-input2.bam	FBtr0078580	72	15	F	3
-input2.bam	FBtr0078580	72	16	F	5
-input2.bam	FBtr0078580	72	17	F	2
-input2.bam	FBtr0078580	72	18	F	9
-input2.bam	FBtr0078580	72	19	F	20
-input2.bam	FBtr0078580	72	20	F	21
-input2.bam	FBtr0078580	72	21	F	55
-input2.bam	FBtr0078580	72	22	F	1
-input2.bam	FBtr0078580	72	23	F	11
-input2.bam	FBtr0078580	72	24	F	24
-input2.bam	FBtr0078580	72	25	F	20
-input2.bam	FBtr0078580	72	26	F	19
-input2.bam	FBtr0078580	72	27	F	9
-input2.bam	FBtr0078580	72	28	F	2
-input2.bam	FBtr0078580	72	29	F	9
-input2.bam	FBtr0078580	72	30	F	2
-input2.bam	FBtr0078580	72	31	F	1
-input2.bam	FBtr0078580	72	40	F	5
-input2.bam	FBtr0078580	72	43	F	1
-input2.bam	FBtr0078580	72	52	F	3
-input2.bam	FBtr0078580	72	72	F	0
-input2.bam	FBtr0078790	73	1	F	0
-input2.bam	FBtr0078790	73	17	F	1
-input2.bam	FBtr0078790	73	41	F	2
-input2.bam	FBtr0078790	73	42	F	1
-input2.bam	FBtr0078790	73	46	F	1
-input2.bam	FBtr0078790	73	51	F	1
-input2.bam	FBtr0078790	73	52	F	2
-input2.bam	FBtr0078790	73	54	F	2
-input2.bam	FBtr0078790	73	73	F	0
-input2.bam	FBtr0079064	72	1	F	3
-input2.bam	FBtr0079064	72	52	F	2
-input2.bam	FBtr0079064	72	72	F	0
-input2.bam	FBtr0079090	72	1	F	1
-input2.bam	FBtr0079090	72	16	F	1
-input2.bam	FBtr0079090	72	20	F	1
-input2.bam	FBtr0079090	72	33	F	1
-input2.bam	FBtr0079090	72	35	F	1
-input2.bam	FBtr0079090	72	52	F	2
-input2.bam	FBtr0079090	72	72	F	0
-input2.bam	FBtr0079338	73	1	F	0
-input2.bam	FBtr0079338	73	12	F	2
-input2.bam	FBtr0079338	73	13	F	4
-input2.bam	FBtr0079338	73	14	F	6
-input2.bam	FBtr0079338	73	16	F	4
-input2.bam	FBtr0079338	73	17	F	2
-input2.bam	FBtr0079338	73	18	F	1
-input2.bam	FBtr0079338	73	39	F	1
-input2.bam	FBtr0079338	73	41	F	2
-input2.bam	FBtr0079338	73	42	F	1
-input2.bam	FBtr0079338	73	73	F	0
-input2.bam	FBtr0079528	71	1	F	2
-input2.bam	FBtr0079528	71	3	F	1
-input2.bam	FBtr0079528	71	10	F	4
-input2.bam	FBtr0079528	71	11	F	3
-input2.bam	FBtr0079528	71	13	F	4
-input2.bam	FBtr0079528	71	14	F	17
-input2.bam	FBtr0079528	71	15	F	19
-input2.bam	FBtr0079528	71	16	F	10
-input2.bam	FBtr0079528	71	17	F	12
-input2.bam	FBtr0079528	71	18	F	13
-input2.bam	FBtr0079528	71	19	F	6
-input2.bam	FBtr0079528	71	20	F	7
-input2.bam	FBtr0079528	71	21	F	13
-input2.bam	FBtr0079528	71	22	F	5
-input2.bam	FBtr0079528	71	23	F	1
-input2.bam	FBtr0079528	71	30	F	1
-input2.bam	FBtr0079528	71	31	F	2
-input2.bam	FBtr0079528	71	32	F	39
-input2.bam	FBtr0079528	71	33	F	4
-input2.bam	FBtr0079528	71	34	F	27
-input2.bam	FBtr0079528	71	35	F	122
-input2.bam	FBtr0079528	71	36	F	6
-input2.bam	FBtr0079528	71	37	F	21
-input2.bam	FBtr0079528	71	38	F	12
-input2.bam	FBtr0079528	71	43	F	1
-input2.bam	FBtr0079528	71	46	F	1
-input2.bam	FBtr0079528	71	50	F	2
-input2.bam	FBtr0079528	71	51	F	4
-input2.bam	FBtr0079528	71	53	F	1
-input2.bam	FBtr0079528	71	56	F	2
-input2.bam	FBtr0079528	71	57	F	3
-input2.bam	FBtr0079528	71	71	F	0
-input2.bam	FBtr0079596	73	1	F	22
-input2.bam	FBtr0079596	73	2	F	1
-input2.bam	FBtr0079596	73	3	F	8
-input2.bam	FBtr0079596	73	4	F	5
-input2.bam	FBtr0079596	73	5	F	9
-input2.bam	FBtr0079596	73	6	F	1
-input2.bam	FBtr0079596	73	8	F	2
-input2.bam	FBtr0079596	73	9	F	2
-input2.bam	FBtr0079596	73	11	F	18
-input2.bam	FBtr0079596	73	12	F	44
-input2.bam	FBtr0079596	73	13	F	40
-input2.bam	FBtr0079596	73	14	F	36
-input2.bam	FBtr0079596	73	15	F	81
-input2.bam	FBtr0079596	73	16	F	13
-input2.bam	FBtr0079596	73	17	F	11
-input2.bam	FBtr0079596	73	18	F	12
-input2.bam	FBtr0079596	73	19	F	4
-input2.bam	FBtr0079596	73	22	F	2
-input2.bam	FBtr0079596	73	42	F	1
-input2.bam	FBtr0079596	73	53	F	3
-input2.bam	FBtr0079596	73	59	R	1
-input2.bam	FBtr0079596	73	73	F	0
-input2.bam	FBtr0079677	72	1	F	2
-input2.bam	FBtr0079677	72	15	F	1
-input2.bam	FBtr0079677	72	24	F	1
-input2.bam	FBtr0079677	72	43	F	1
-input2.bam	FBtr0079677	72	52	F	1
-input2.bam	FBtr0079677	72	54	F	1
-input2.bam	FBtr0079677	72	72	F	0
-input2.bam	FBtr0079690	72	1	F	1
-input2.bam	FBtr0079690	72	15	F	1
-input2.bam	FBtr0079690	72	17	F	1
-input2.bam	FBtr0079690	72	19	F	1
-input2.bam	FBtr0079690	72	21	F	1
-input2.bam	FBtr0079690	72	72	F	0
-input2.bam	FBtr0079692	73	1	F	0
-input2.bam	FBtr0079692	73	4	F	1
-input2.bam	FBtr0079692	73	7	F	1
-input2.bam	FBtr0079692	73	12	F	1
-input2.bam	FBtr0079692	73	15	F	1
-input2.bam	FBtr0079692	73	73	F	0
-input2.bam	FBtr0079693	72	1	F	3
-input2.bam	FBtr0079693	72	17	F	2
-input2.bam	FBtr0079693	72	20	F	1
-input2.bam	FBtr0079693	72	45	F	1
-input2.bam	FBtr0079693	72	52	F	1
-input2.bam	FBtr0079693	72	54	F	1
-input2.bam	FBtr0079693	72	72	F	0
-input2.bam	FBtr0079694	72	1	F	2
-input2.bam	FBtr0079694	72	16	F	1
-input2.bam	FBtr0079694	72	17	F	1
-input2.bam	FBtr0079694	72	18	F	1
-input2.bam	FBtr0079694	72	52	F	1
-input2.bam	FBtr0079694	72	72	F	0
-input2.bam	FBtr0079702	72	1	F	2
-input2.bam	FBtr0079702	72	52	F	2
-input2.bam	FBtr0079702	72	72	F	0
-input2.bam	FBtr0079728	72	1	F	3
-input2.bam	FBtr0079728	72	20	F	1
-input2.bam	FBtr0079728	72	52	F	2
-input2.bam	FBtr0079728	72	72	F	0
-input2.bam	FBtr0079729	72	1	F	1
-input2.bam	FBtr0079729	72	19	F	1
-input2.bam	FBtr0079729	72	33	F	1
-input2.bam	FBtr0079729	72	53	F	1
-input2.bam	FBtr0079729	72	72	F	0
-input2.bam	FBtr0079752	72	1	F	0
-input2.bam	FBtr0079752	72	49	F	1
-input2.bam	FBtr0079752	72	52	F	1
-input2.bam	FBtr0079752	72	72	F	0
-input2.bam	FBtr0079820	74	1	F	0
-input2.bam	FBtr0079820	74	39	F	1
-input2.bam	FBtr0079820	74	52	F	1
-input2.bam	FBtr0079820	74	53	F	28
-input2.bam	FBtr0079820	74	54	F	26
-input2.bam	FBtr0079820	74	55	F	10
-input2.bam	FBtr0079820	74	56	F	2
-input2.bam	FBtr0079820	74	57	F	6
-input2.bam	FBtr0079820	74	58	F	5
-input2.bam	FBtr0079820	74	59	F	11
-input2.bam	FBtr0079820	74	60	F	19
-input2.bam	FBtr0079820	74	74	F	0
-input2.bam	FBtr0080609	72	1	F	0
-input2.bam	FBtr0080609	72	20	F	1
-input2.bam	FBtr0080609	72	21	F	2
-input2.bam	FBtr0080609	72	22	F	1
-input2.bam	FBtr0080609	72	33	F	1
-input2.bam	FBtr0080609	72	39	F	1
-input2.bam	FBtr0080609	72	52	F	1
-input2.bam	FBtr0080609	72	53	F	1
-input2.bam	FBtr0080609	72	72	F	0
-input2.bam	FBtr0080644	72	1	F	0
-input2.bam	FBtr0080644	72	57	F	1
-input2.bam	FBtr0080644	72	58	F	7
-input2.bam	FBtr0080644	72	72	F	0
-input2.bam	FBtr0080646	72	1	F	0
-input2.bam	FBtr0080646	72	51	F	1
-input2.bam	FBtr0080646	72	57	F	2
-input2.bam	FBtr0080646	72	58	F	9
-input2.bam	FBtr0080646	72	72	F	0
-input2.bam	FBtr0080647	72	1	F	1
-input2.bam	FBtr0080647	72	57	F	4
-input2.bam	FBtr0080647	72	58	F	7
-input2.bam	FBtr0080647	72	72	F	0
-input2.bam	FBtr0080660	72	1	F	0
-input2.bam	FBtr0080660	72	58	F	11
-input2.bam	FBtr0080660	72	72	F	0
-input2.bam	FBtr0080663	71	1	F	2
-input2.bam	FBtr0080663	71	11	F	1
-input2.bam	FBtr0080663	71	12	F	4
-input2.bam	FBtr0080663	71	13	F	4
-input2.bam	FBtr0080663	71	14	F	22
-input2.bam	FBtr0080663	71	15	F	14
-input2.bam	FBtr0080663	71	16	F	5
-input2.bam	FBtr0080663	71	17	F	12
-input2.bam	FBtr0080663	71	18	F	5
-input2.bam	FBtr0080663	71	19	F	6
-input2.bam	FBtr0080663	71	20	F	6
-input2.bam	FBtr0080663	71	21	F	13
-input2.bam	FBtr0080663	71	22	F	3
-input2.bam	FBtr0080663	71	31	F	1
-input2.bam	FBtr0080663	71	50	F	2
-input2.bam	FBtr0080663	71	51	F	1
-input2.bam	FBtr0080663	71	52	F	2
-input2.bam	FBtr0080663	71	57	F	3
-input2.bam	FBtr0080663	71	71	F	0
-input2.bam	FBtr0080664	71	1	F	1
-input2.bam	FBtr0080664	71	3	F	2
-input2.bam	FBtr0080664	71	10	F	1
-input2.bam	FBtr0080664	71	11	F	2
-input2.bam	FBtr0080664	71	12	F	3
-input2.bam	FBtr0080664	71	13	F	11
-input2.bam	FBtr0080664	71	14	F	11
-input2.bam	FBtr0080664	71	15	F	17
-input2.bam	FBtr0080664	71	16	F	15
-input2.bam	FBtr0080664	71	17	F	13
-input2.bam	FBtr0080664	71	18	F	10
-input2.bam	FBtr0080664	71	19	F	8
-input2.bam	FBtr0080664	71	20	F	1
-input2.bam	FBtr0080664	71	21	F	15
-input2.bam	FBtr0080664	71	22	F	6
-input2.bam	FBtr0080664	71	24	F	1
-input2.bam	FBtr0080664	71	30	F	1
-input2.bam	FBtr0080664	71	31	F	3
-input2.bam	FBtr0080664	71	32	F	39
-input2.bam	FBtr0080664	71	33	F	4
-input2.bam	FBtr0080664	71	34	F	37
-input2.bam	FBtr0080664	71	35	F	135
-input2.bam	FBtr0080664	71	36	F	8
-input2.bam	FBtr0080664	71	37	F	25
-input2.bam	FBtr0080664	71	38	F	8
-input2.bam	FBtr0080664	71	39	F	1
-input2.bam	FBtr0080664	71	42	F	1
-input2.bam	FBtr0080664	71	47	F	1
-input2.bam	FBtr0080664	71	50	F	2
-input2.bam	FBtr0080664	71	52	F	1
-input2.bam	FBtr0080664	71	53	F	1
-input2.bam	FBtr0080664	71	56	F	1
-input2.bam	FBtr0080664	71	57	F	2
-input2.bam	FBtr0080664	71	62	R	1
-input2.bam	FBtr0080664	71	71	F	0
-input2.bam	FBtr0080664	71	71	R	1
Binary file newtests/input1_input2_norm_1_2_single_plot_counts.pdf has changed
--- a/newtests/input1_input2_size.tab	Thu Nov 22 20:05:32 2018 -0500
+++ /dev/null	Thu Jan 01 00:00:00 1970 +0000
@@ -1,1045 +0,0 @@
-Dataset	Chromosome	Polarity	Size	Counts
-input1.bam	FBtr0070001	F	16	2
-input1.bam	FBtr0070001	F	17	1
-input1.bam	FBtr0070001	F	18	0
-input1.bam	FBtr0070001	F	19	1
-input1.bam	FBtr0070001	F	20	4
-input1.bam	FBtr0070001	F	21	4
-input1.bam	FBtr0070001	F	22	29
-input1.bam	FBtr0070001	F	23	15
-input1.bam	FBtr0070001	F	24	1
-input1.bam	FBtr0070001	R	16	0
-input1.bam	FBtr0070001	R	17	0
-input1.bam	FBtr0070001	R	18	0
-input1.bam	FBtr0070001	R	19	0
-input1.bam	FBtr0070001	R	20	0
-input1.bam	FBtr0070001	R	21	0
-input1.bam	FBtr0070001	R	22	0
-input1.bam	FBtr0070001	R	23	0
-input1.bam	FBtr0070001	R	24	0
-input1.bam	FBtr0070533	F	15	2
-input1.bam	FBtr0070533	F	16	1
-input1.bam	FBtr0070533	F	17	1
-input1.bam	FBtr0070533	F	18	6
-input1.bam	FBtr0070533	F	19	3
-input1.bam	FBtr0070533	F	20	2
-input1.bam	FBtr0070533	F	21	2
-input1.bam	FBtr0070533	F	22	4
-input1.bam	FBtr0070533	F	23	2
-input1.bam	FBtr0070533	F	24	0
-input1.bam	FBtr0070533	F	25	1
-input1.bam	FBtr0070533	R	15	0
-input1.bam	FBtr0070533	R	16	0
-input1.bam	FBtr0070533	R	17	0
-input1.bam	FBtr0070533	R	18	0
-input1.bam	FBtr0070533	R	19	0
-input1.bam	FBtr0070533	R	20	0
-input1.bam	FBtr0070533	R	21	0
-input1.bam	FBtr0070533	R	22	0
-input1.bam	FBtr0070533	R	23	0
-input1.bam	FBtr0070533	R	24	0
-input1.bam	FBtr0070533	R	25	0
-input1.bam	FBtr0070603	F	15	9
-input1.bam	FBtr0070603	F	16	6
-input1.bam	FBtr0070603	F	17	10
-input1.bam	FBtr0070603	F	18	7
-input1.bam	FBtr0070603	F	19	1
-input1.bam	FBtr0070603	F	20	6
-input1.bam	FBtr0070603	F	21	3
-input1.bam	FBtr0070603	F	22	3
-input1.bam	FBtr0070603	F	23	10
-input1.bam	FBtr0070603	F	24	2
-input1.bam	FBtr0070603	F	25	5
-input1.bam	FBtr0070603	F	26	5
-input1.bam	FBtr0070603	F	27	3
-input1.bam	FBtr0070603	R	15	0
-input1.bam	FBtr0070603	R	16	0
-input1.bam	FBtr0070603	R	17	0
-input1.bam	FBtr0070603	R	18	0
-input1.bam	FBtr0070603	R	19	0
-input1.bam	FBtr0070603	R	20	0
-input1.bam	FBtr0070603	R	21	0
-input1.bam	FBtr0070603	R	22	0
-input1.bam	FBtr0070603	R	23	0
-input1.bam	FBtr0070603	R	24	0
-input1.bam	FBtr0070603	R	25	0
-input1.bam	FBtr0070603	R	26	0
-input1.bam	FBtr0070603	R	27	0
-input1.bam	FBtr0070604	F	15	2
-input1.bam	FBtr0070604	F	16	0
-input1.bam	FBtr0070604	F	17	0
-input1.bam	FBtr0070604	F	18	2
-input1.bam	FBtr0070604	F	19	2
-input1.bam	FBtr0070604	F	20	0
-input1.bam	FBtr0070604	F	21	1
-input1.bam	FBtr0070604	F	22	23
-input1.bam	FBtr0070604	F	23	10
-input1.bam	FBtr0070604	R	15	0
-input1.bam	FBtr0070604	R	16	0
-input1.bam	FBtr0070604	R	17	0
-input1.bam	FBtr0070604	R	18	0
-input1.bam	FBtr0070604	R	19	0
-input1.bam	FBtr0070604	R	20	0
-input1.bam	FBtr0070604	R	21	0
-input1.bam	FBtr0070604	R	22	0
-input1.bam	FBtr0070604	R	23	0
-input1.bam	FBtr0070911	F	15	1
-input1.bam	FBtr0070911	F	16	0
-input1.bam	FBtr0070911	F	17	0
-input1.bam	FBtr0070911	F	18	0
-input1.bam	FBtr0070911	F	19	0
-input1.bam	FBtr0070911	F	20	0
-input1.bam	FBtr0070911	F	21	1
-input1.bam	FBtr0070911	R	15	0
-input1.bam	FBtr0070911	R	16	0
-input1.bam	FBtr0070911	R	17	0
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-input2.bam	FBtr0079729	F	16	2
-input2.bam	FBtr0079729	F	17	1
-input2.bam	FBtr0079729	R	15	0
-input2.bam	FBtr0079729	R	16	0
-input2.bam	FBtr0079729	R	17	0
-input2.bam	FBtr0079752	F	17	1
-input2.bam	FBtr0079752	F	18	0
-input2.bam	FBtr0079752	F	19	0
-input2.bam	FBtr0079752	F	20	0
-input2.bam	FBtr0079752	F	21	0
-input2.bam	FBtr0079752	F	22	0
-input2.bam	FBtr0079752	F	23	0
-input2.bam	FBtr0079752	F	24	1
-input2.bam	FBtr0079752	R	17	0
-input2.bam	FBtr0079752	R	18	0
-input2.bam	FBtr0079752	R	19	0
-input2.bam	FBtr0079752	R	20	0
-input2.bam	FBtr0079752	R	21	0
-input2.bam	FBtr0079752	R	22	0
-input2.bam	FBtr0079752	R	23	0
-input2.bam	FBtr0079752	R	24	0
-input2.bam	FBtr0079820	F	15	27
-input2.bam	FBtr0079820	F	16	10
-input2.bam	FBtr0079820	F	17	7
-input2.bam	FBtr0079820	F	18	8
-input2.bam	FBtr0079820	F	19	25
-input2.bam	FBtr0079820	F	20	24
-input2.bam	FBtr0079820	F	21	7
-input2.bam	FBtr0079820	F	22	1
-input2.bam	FBtr0079820	R	15	0
-input2.bam	FBtr0079820	R	16	0
-input2.bam	FBtr0079820	R	17	0
-input2.bam	FBtr0079820	R	18	0
-input2.bam	FBtr0079820	R	19	0
-input2.bam	FBtr0079820	R	20	0
-input2.bam	FBtr0079820	R	21	0
-input2.bam	FBtr0079820	R	22	0
-input2.bam	FBtr0080609	F	17	2
-input2.bam	FBtr0080609	F	18	1
-input2.bam	FBtr0080609	F	19	2
-input2.bam	FBtr0080609	F	20	0
-input2.bam	FBtr0080609	F	21	0
-input2.bam	FBtr0080609	F	22	1
-input2.bam	FBtr0080609	F	23	1
-input2.bam	FBtr0080609	F	24	0
-input2.bam	FBtr0080609	F	25	1
-input2.bam	FBtr0080609	R	17	0
-input2.bam	FBtr0080609	R	18	0
-input2.bam	FBtr0080609	R	19	0
-input2.bam	FBtr0080609	R	20	0
-input2.bam	FBtr0080609	R	21	0
-input2.bam	FBtr0080609	R	22	0
-input2.bam	FBtr0080609	R	23	0
-input2.bam	FBtr0080609	R	24	0
-input2.bam	FBtr0080609	R	25	0
-input2.bam	FBtr0080644	F	15	8
-input2.bam	FBtr0080644	R	15	0
-input2.bam	FBtr0080646	F	15	10
-input2.bam	FBtr0080646	F	16	1
-input2.bam	FBtr0080646	F	17	0
-input2.bam	FBtr0080646	F	18	0
-input2.bam	FBtr0080646	F	19	0
-input2.bam	FBtr0080646	F	20	0
-input2.bam	FBtr0080646	F	21	1
-input2.bam	FBtr0080646	R	15	0
-input2.bam	FBtr0080646	R	16	0
-input2.bam	FBtr0080646	R	17	0
-input2.bam	FBtr0080646	R	18	0
-input2.bam	FBtr0080646	R	19	0
-input2.bam	FBtr0080646	R	20	0
-input2.bam	FBtr0080646	R	21	0
-input2.bam	FBtr0080647	F	15	9
-input2.bam	FBtr0080647	F	16	2
-input2.bam	FBtr0080647	F	17	0
-input2.bam	FBtr0080647	F	18	1
-input2.bam	FBtr0080647	R	15	0
-input2.bam	FBtr0080647	R	16	0
-input2.bam	FBtr0080647	R	17	0
-input2.bam	FBtr0080647	R	18	0
-input2.bam	FBtr0080660	F	15	11
-input2.bam	FBtr0080660	R	15	0
-input2.bam	FBtr0080663	F	15	26
-input2.bam	FBtr0080663	F	16	14
-input2.bam	FBtr0080663	F	17	14
-input2.bam	FBtr0080663	F	18	26
-input2.bam	FBtr0080663	F	19	9
-input2.bam	FBtr0080663	F	20	7
-input2.bam	FBtr0080663	F	21	4
-input2.bam	FBtr0080663	F	22	5
-input2.bam	FBtr0080663	F	23	0
-input2.bam	FBtr0080663	F	24	1
-input2.bam	FBtr0080663	R	15	0
-input2.bam	FBtr0080663	R	16	0
-input2.bam	FBtr0080663	R	17	0
-input2.bam	FBtr0080663	R	18	0
-input2.bam	FBtr0080663	R	19	0
-input2.bam	FBtr0080663	R	20	0
-input2.bam	FBtr0080663	R	21	0
-input2.bam	FBtr0080663	R	22	0
-input2.bam	FBtr0080663	R	23	0
-input2.bam	FBtr0080663	R	24	0
-input2.bam	FBtr0080664	F	15	165
-input2.bam	FBtr0080664	F	16	59
-input2.bam	FBtr0080664	F	17	20
-input2.bam	FBtr0080664	F	18	75
-input2.bam	FBtr0080664	F	19	24
-input2.bam	FBtr0080664	F	20	21
-input2.bam	FBtr0080664	F	21	8
-input2.bam	FBtr0080664	F	22	4
-input2.bam	FBtr0080664	F	23	4
-input2.bam	FBtr0080664	F	24	0
-input2.bam	FBtr0080664	F	25	3
-input2.bam	FBtr0080664	F	26	4
-input2.bam	FBtr0080664	R	15	0
-input2.bam	FBtr0080664	R	16	0
-input2.bam	FBtr0080664	R	17	0
-input2.bam	FBtr0080664	R	18	0
-input2.bam	FBtr0080664	R	19	0
-input2.bam	FBtr0080664	R	20	0
-input2.bam	FBtr0080664	R	21	0
-input2.bam	FBtr0080664	R	22	1
-input2.bam	FBtr0080664	R	23	1
-input2.bam	FBtr0080664	R	24	0
-input2.bam	FBtr0080664	R	25	0
-input2.bam	FBtr0080664	R	26	0
--- a/newtests/input1_mean.tab	Thu Nov 22 20:05:32 2018 -0500
+++ /dev/null	Thu Jan 01 00:00:00 1970 +0000
@@ -1,300 +0,0 @@
-Dataset	Chromosome	Chrom_length	Coordinate	Polarity	Mean
-input1.bam	FBtr0070001	72	1	F	17.0
-input1.bam	FBtr0070001	72	7	F	20.3
-input1.bam	FBtr0070001	72	8	F	21.3
-input1.bam	FBtr0070001	72	11	F	20.5
-input1.bam	FBtr0070001	72	16	F	19.0
-input1.bam	FBtr0070001	72	17	F	23.0
-input1.bam	FBtr0070001	72	18	F	16.0
-input1.bam	FBtr0070001	72	27	F	23.5
-input1.bam	FBtr0070001	72	30	F	23.0
-input1.bam	FBtr0070001	72	31	F	23.0
-input1.bam	FBtr0070001	72	32	F	22.0
-input1.bam	FBtr0070001	72	34	F	20.0
-input1.bam	FBtr0070001	72	72	F	0
-input1.bam	FBtr0070533	72	1	F	15.0
-input1.bam	FBtr0070533	72	12	F	18.0
-input1.bam	FBtr0070533	72	15	F	15.0
-input1.bam	FBtr0070533	72	19	F	21.8
-input1.bam	FBtr0070533	72	20	F	23.0
-input1.bam	FBtr0070533	72	21	F	18.0
-input1.bam	FBtr0070533	72	22	F	20.0
-input1.bam	FBtr0070533	72	25	F	17.0
-input1.bam	FBtr0070533	72	26	F	16.0
-input1.bam	FBtr0070533	72	28	F	25.0
-input1.bam	FBtr0070533	72	32	F	20.5
-input1.bam	FBtr0070533	72	35	F	19.0
-input1.bam	FBtr0070533	72	37	F	19.0
-input1.bam	FBtr0070533	72	38	F	18.0
-input1.bam	FBtr0070533	72	72	F	0
-input1.bam	FBtr0070603	72	1	F	16.5
-input1.bam	FBtr0070603	72	3	F	21.0
-input1.bam	FBtr0070603	72	4	F	20.0
-input1.bam	FBtr0070603	72	6	F	18.0
-input1.bam	FBtr0070603	72	7	F	17.1
-input1.bam	FBtr0070603	72	8	F	16.0
-input1.bam	FBtr0070603	72	9	F	15.0
-input1.bam	FBtr0070603	72	12	F	20.0
-input1.bam	FBtr0070603	72	13	F	22.0
-input1.bam	FBtr0070603	72	15	F	18.5
-input1.bam	FBtr0070603	72	16	F	20.5
-input1.bam	FBtr0070603	72	17	F	24.0
-input1.bam	FBtr0070603	72	18	F	16.0
-input1.bam	FBtr0070603	72	19	F	22.6
-input1.bam	FBtr0070603	72	20	F	21.0
-input1.bam	FBtr0070603	72	21	F	25.0
-input1.bam	FBtr0070603	72	22	F	20.7
-input1.bam	FBtr0070603	72	24	F	19.5
-input1.bam	FBtr0070603	72	25	F	23.0
-input1.bam	FBtr0070603	72	26	F	25.8
-input1.bam	FBtr0070603	72	27	F	26.3
-input1.bam	FBtr0070603	72	32	F	20.0
-input1.bam	FBtr0070603	72	34	F	19.3
-input1.bam	FBtr0070603	72	38	F	18.0
-input1.bam	FBtr0070603	72	42	F	21.0
-input1.bam	FBtr0070603	72	51	F	18.0
-input1.bam	FBtr0070603	72	56	F	16.0
-input1.bam	FBtr0070603	72	72	F	0
-input1.bam	FBtr0070604	72	1	F	15.0
-input1.bam	FBtr0070604	72	18	F	23.0
-input1.bam	FBtr0070604	72	22	F	19.0
-input1.bam	FBtr0070604	72	30	F	18.0
-input1.bam	FBtr0070604	72	31	F	22.6
-input1.bam	FBtr0070604	72	32	F	22.0
-input1.bam	FBtr0070604	72	57	F	15.0
-input1.bam	FBtr0070604	72	72	F	0
-input1.bam	FBtr0070911	73	1	F	0
-input1.bam	FBtr0070911	73	15	F	21.0
-input1.bam	FBtr0070911	73	38	F	15.0
-input1.bam	FBtr0070911	73	73	F	0
-input1.bam	FBtr0078490	72	1	F	0
-input1.bam	FBtr0078490	72	13	F	16.0
-input1.bam	FBtr0078490	72	17	F	16.0
-input1.bam	FBtr0078490	72	18	F	15.0
-input1.bam	FBtr0078490	72	25	F	15.0
-input1.bam	FBtr0078490	72	28	F	19.0
-input1.bam	FBtr0078490	72	38	F	18.0
-input1.bam	FBtr0078490	72	72	F	0
-input1.bam	FBtr0078580	72	1	F	18.9
-input1.bam	FBtr0078580	72	3	F	22.0
-input1.bam	FBtr0078580	72	4	F	25.3
-input1.bam	FBtr0078580	72	5	F	21.0
-input1.bam	FBtr0078580	72	6	F	19.0
-input1.bam	FBtr0078580	72	7	F	22.0
-input1.bam	FBtr0078580	72	8	F	18.0
-input1.bam	FBtr0078580	72	11	F	23.0
-input1.bam	FBtr0078580	72	12	F	18.0
-input1.bam	FBtr0078580	72	14	F	15.3
-input1.bam	FBtr0078580	72	15	F	16.0
-input1.bam	FBtr0078580	72	16	F	19.0
-input1.bam	FBtr0078580	72	17	F	17.0
-input1.bam	FBtr0078580	72	19	F	24.0
-input1.bam	FBtr0078580	72	20	F	21.0
-input1.bam	FBtr0078580	72	21	F	19.4
-input1.bam	FBtr0078580	72	24	F	17.0
-input1.bam	FBtr0078580	72	25	F	27.5
-input1.bam	FBtr0078580	72	29	F	17.0
-input1.bam	FBtr0078580	72	31	F	17.0
-input1.bam	FBtr0078580	72	52	F	16.0
-input1.bam	FBtr0078580	72	72	F	0
-input1.bam	FBtr0078790	73	1	F	19.0
-input1.bam	FBtr0078790	73	17	F	16.0
-input1.bam	FBtr0078790	73	33	F	23.0
-input1.bam	FBtr0078790	73	42	F	18.5
-input1.bam	FBtr0078790	73	44	F	19.5
-input1.bam	FBtr0078790	73	46	F	17.0
-input1.bam	FBtr0078790	73	47	F	18.0
-input1.bam	FBtr0078790	73	52	F	20.0
-input1.bam	FBtr0078790	73	69	R	15.0
-input1.bam	FBtr0078790	73	73	F	0
-input1.bam	FBtr0079064	72	1	F	15.0
-input1.bam	FBtr0079064	72	3	F	21.0
-input1.bam	FBtr0079064	72	33	F	15.0
-input1.bam	FBtr0079064	72	52	F	17.0
-input1.bam	FBtr0079064	72	72	F	0
-input1.bam	FBtr0079090	72	1	F	21.5
-input1.bam	FBtr0079090	72	26	F	24.0
-input1.bam	FBtr0079090	72	33	F	16.0
-input1.bam	FBtr0079090	72	53	F	18.0
-input1.bam	FBtr0079090	72	56	R	21.0
-input1.bam	FBtr0079090	72	72	F	0
-input1.bam	FBtr0079338	73	1	F	0
-input1.bam	FBtr0079338	73	12	F	17.0
-input1.bam	FBtr0079338	73	13	F	17.5
-input1.bam	FBtr0079338	73	14	F	15.0
-input1.bam	FBtr0079338	73	17	F	15.0
-input1.bam	FBtr0079338	73	25	F	16.0
-input1.bam	FBtr0079338	73	42	F	21.8
-input1.bam	FBtr0079338	73	43	F	21.0
-input1.bam	FBtr0079338	73	46	F	18.0
-input1.bam	FBtr0079338	73	73	F	0
-input1.bam	FBtr0079528	71	1	F	20.8
-input1.bam	FBtr0079528	71	3	F	23.6
-input1.bam	FBtr0079528	71	4	F	24.0
-input1.bam	FBtr0079528	71	8	F	20.3
-input1.bam	FBtr0079528	71	10	F	21.0
-input1.bam	FBtr0079528	71	11	F	19.0
-input1.bam	FBtr0079528	71	13	F	16.0
-input1.bam	FBtr0079528	71	14	F	18.5
-input1.bam	FBtr0079528	71	16	F	15.0
-input1.bam	FBtr0079528	71	17	F	15.3
-input1.bam	FBtr0079528	71	18	F	19.8
-input1.bam	FBtr0079528	71	28	F	16.0
-input1.bam	FBtr0079528	71	35	F	15.0
-input1.bam	FBtr0079528	71	36	F	20.0
-input1.bam	FBtr0079528	71	37	F	18.0
-input1.bam	FBtr0079528	71	51	F	15.0
-input1.bam	FBtr0079528	71	71	F	0
-input1.bam	FBtr0079596	73	1	F	16.2
-input1.bam	FBtr0079596	73	3	F	21.8
-input1.bam	FBtr0079596	73	4	F	21.5
-input1.bam	FBtr0079596	73	5	F	18.5
-input1.bam	FBtr0079596	73	6	F	17.5
-input1.bam	FBtr0079596	73	8	F	16.6
-input1.bam	FBtr0079596	73	9	F	16.1
-input1.bam	FBtr0079596	73	10	F	15.3
-input1.bam	FBtr0079596	73	11	F	15.2
-input1.bam	FBtr0079596	73	12	F	17.0
-input1.bam	FBtr0079596	73	13	F	16.1
-input1.bam	FBtr0079596	73	14	F	15.0
-input1.bam	FBtr0079596	73	15	F	18.0
-input1.bam	FBtr0079596	73	16	F	16.7
-input1.bam	FBtr0079596	73	17	F	16.0
-input1.bam	FBtr0079596	73	18	F	15.0
-input1.bam	FBtr0079596	73	19	F	15.0
-input1.bam	FBtr0079596	73	53	F	18.5
-input1.bam	FBtr0079596	73	54	F	19.5
-input1.bam	FBtr0079596	73	73	F	0
-input1.bam	FBtr0079677	72	1	F	23.0
-input1.bam	FBtr0079677	72	5	F	19.0
-input1.bam	FBtr0079677	72	52	F	19.0
-input1.bam	FBtr0079677	72	53	F	18.0
-input1.bam	FBtr0079677	72	72	F	0
-input1.bam	FBtr0079690	72	1	F	15.0
-input1.bam	FBtr0079690	72	22	F	15.0
-input1.bam	FBtr0079690	72	27	F	25.0
-input1.bam	FBtr0079690	72	33	F	16.0
-input1.bam	FBtr0079690	72	72	F	0
-input1.bam	FBtr0079692	73	1	F	19.3
-input1.bam	FBtr0079692	73	18	F	18.0
-input1.bam	FBtr0079692	73	25	F	17.0
-input1.bam	FBtr0079692	73	32	F	20.0
-input1.bam	FBtr0079692	73	73	F	0
-input1.bam	FBtr0079693	72	1	F	17.2
-input1.bam	FBtr0079693	72	25	F	23.0
-input1.bam	FBtr0079693	72	72	F	0
-input1.bam	FBtr0079694	72	1	F	20.4
-input1.bam	FBtr0079694	72	18	F	19.0
-input1.bam	FBtr0079694	72	52	F	17.0
-input1.bam	FBtr0079694	72	72	F	0
-input1.bam	FBtr0079702	72	1	F	15.0
-input1.bam	FBtr0079702	72	19	F	18.0
-input1.bam	FBtr0079702	72	56	F	15.0
-input1.bam	FBtr0079702	72	72	F	0
-input1.bam	FBtr0079728	72	1	F	16.0
-input1.bam	FBtr0079728	72	8	F	20.0
-input1.bam	FBtr0079728	72	19	F	24.0
-input1.bam	FBtr0079728	72	33	F	15.7
-input1.bam	FBtr0079728	72	56	F	15.0
-input1.bam	FBtr0079728	72	72	F	0
-input1.bam	FBtr0079729	72	1	F	15.0
-input1.bam	FBtr0079729	72	13	F	22.0
-input1.bam	FBtr0079729	72	52	F	18.0
-input1.bam	FBtr0079729	72	57	F	16.0
-input1.bam	FBtr0079729	72	72	F	0
-input1.bam	FBtr0079752	72	1	F	19.5
-input1.bam	FBtr0079752	72	7	F	20.0
-input1.bam	FBtr0079752	72	12	F	16.0
-input1.bam	FBtr0079752	72	33	F	16.0
-input1.bam	FBtr0079752	72	52	F	19.5
-input1.bam	FBtr0079752	72	72	F	0
-input1.bam	FBtr0079820	74	1	F	0
-input1.bam	FBtr0079820	74	45	F	20.0
-input1.bam	FBtr0079820	74	46	F	17.0
-input1.bam	FBtr0079820	74	48	F	18.0
-input1.bam	FBtr0079820	74	49	F	24.0
-input1.bam	FBtr0079820	74	51	F	20.0
-input1.bam	FBtr0079820	74	54	F	17.0
-input1.bam	FBtr0079820	74	55	F	18.0
-input1.bam	FBtr0079820	74	56	F	18.5
-input1.bam	FBtr0079820	74	74	F	0
-input1.bam	FBtr0080609	72	1	F	18.8
-input1.bam	FBtr0080609	72	3	F	21.0
-input1.bam	FBtr0080609	72	4	F	20.0
-input1.bam	FBtr0080609	72	5	F	19.0
-input1.bam	FBtr0080609	72	7	F	17.1
-input1.bam	FBtr0080609	72	8	F	16.0
-input1.bam	FBtr0080609	72	9	F	15.0
-input1.bam	FBtr0080609	72	12	F	23.0
-input1.bam	FBtr0080609	72	15	F	19.0
-input1.bam	FBtr0080609	72	16	F	23.0
-input1.bam	FBtr0080609	72	17	F	20.5
-input1.bam	FBtr0080609	72	19	F	26.0
-input1.bam	FBtr0080609	72	20	F	25.0
-input1.bam	FBtr0080609	72	42	F	21.0
-input1.bam	FBtr0080609	72	51	F	18.0
-input1.bam	FBtr0080609	72	52	F	15.0
-input1.bam	FBtr0080609	72	72	F	0
-input1.bam	FBtr0080644	72	1	F	27.0
-input1.bam	FBtr0080644	72	4	F	20.5
-input1.bam	FBtr0080644	72	7	F	16.0
-input1.bam	FBtr0080644	72	12	F	16.0
-input1.bam	FBtr0080644	72	72	F	0
-input1.bam	FBtr0080646	72	1	F	16.0
-input1.bam	FBtr0080646	72	6	F	22.0
-input1.bam	FBtr0080646	72	7	F	21.0
-input1.bam	FBtr0080646	72	72	F	0
-input1.bam	FBtr0080647	72	1	F	16.3
-input1.bam	FBtr0080647	72	3	F	16.0
-input1.bam	FBtr0080647	72	6	F	19.0
-input1.bam	FBtr0080647	72	8	F	20.0
-input1.bam	FBtr0080647	72	11	F	17.0
-input1.bam	FBtr0080647	72	12	F	16.0
-input1.bam	FBtr0080647	72	72	F	0
-input1.bam	FBtr0080660	72	1	F	0
-input1.bam	FBtr0080660	72	4	F	24.0
-input1.bam	FBtr0080660	72	7	F	19.3
-input1.bam	FBtr0080660	72	72	F	0
-input1.bam	FBtr0080663	71	1	F	18.8
-input1.bam	FBtr0080663	71	3	F	23.7
-input1.bam	FBtr0080663	71	4	F	23.3
-input1.bam	FBtr0080663	71	7	F	16.0
-input1.bam	FBtr0080663	71	8	F	19.3
-input1.bam	FBtr0080663	71	12	F	16.0
-input1.bam	FBtr0080663	71	14	F	19.0
-input1.bam	FBtr0080663	71	15	F	17.0
-input1.bam	FBtr0080663	71	16	F	15.7
-input1.bam	FBtr0080663	71	17	F	15.6
-input1.bam	FBtr0080663	71	26	F	18.0
-input1.bam	FBtr0080663	71	32	F	15.5
-input1.bam	FBtr0080663	71	50	F	17.0
-input1.bam	FBtr0080663	71	51	F	15.6
-input1.bam	FBtr0080663	71	71	F	0
-input1.bam	FBtr0080664	71	1	F	19.5
-input1.bam	FBtr0080664	71	3	F	23.8
-input1.bam	FBtr0080664	71	4	F	23.5
-input1.bam	FBtr0080664	71	6	F	23.0
-input1.bam	FBtr0080664	71	7	F	21.0
-input1.bam	FBtr0080664	71	8	F	20.5
-input1.bam	FBtr0080664	71	9	F	20.0
-input1.bam	FBtr0080664	71	11	F	16.7
-input1.bam	FBtr0080664	71	12	F	18.0
-input1.bam	FBtr0080664	71	13	F	20.0
-input1.bam	FBtr0080664	71	14	F	18.3
-input1.bam	FBtr0080664	71	16	F	15.0
-input1.bam	FBtr0080664	71	17	F	15.8
-input1.bam	FBtr0080664	71	18	F	15.0
-input1.bam	FBtr0080664	71	21	F	15.0
-input1.bam	FBtr0080664	71	28	F	16.0
-input1.bam	FBtr0080664	71	32	F	15.0
-input1.bam	FBtr0080664	71	33	F	20.0
-input1.bam	FBtr0080664	71	34	F	16.0
-input1.bam	FBtr0080664	71	35	F	15.0
-input1.bam	FBtr0080664	71	36	F	21.0
-input1.bam	FBtr0080664	71	37	F	18.0
-input1.bam	FBtr0080664	71	38	F	15.0
-input1.bam	FBtr0080664	71	50	F	16.0
-input1.bam	FBtr0080664	71	51	F	15.0
-input1.bam	FBtr0080664	71	52	F	15.0
-input1.bam	FBtr0080664	71	56	F	16.0
-input1.bam	FBtr0080664	71	71	F	0
--- a/newtests/input1_median.tab	Thu Nov 22 20:05:32 2018 -0500
+++ /dev/null	Thu Jan 01 00:00:00 1970 +0000
@@ -1,300 +0,0 @@
-Dataset	Chromosome	Chrom_length	Coordinate	Polarity	Median
-input1.bam	FBtr0070001	72	1	F	17.0
-input1.bam	FBtr0070001	72	7	F	21.0
-input1.bam	FBtr0070001	72	8	F	21.0
-input1.bam	FBtr0070001	72	11	F	20.5
-input1.bam	FBtr0070001	72	16	F	19.0
-input1.bam	FBtr0070001	72	17	F	23.0
-input1.bam	FBtr0070001	72	18	F	16.0
-input1.bam	FBtr0070001	72	27	F	23.5
-input1.bam	FBtr0070001	72	30	F	23.0
-input1.bam	FBtr0070001	72	31	F	23.0
-input1.bam	FBtr0070001	72	32	F	22.0
-input1.bam	FBtr0070001	72	34	F	20.0
-input1.bam	FBtr0070001	72	72	F	0
-input1.bam	FBtr0070533	72	1	F	15.0
-input1.bam	FBtr0070533	72	12	F	18.0
-input1.bam	FBtr0070533	72	15	F	15.0
-input1.bam	FBtr0070533	72	19	F	22.0
-input1.bam	FBtr0070533	72	20	F	23.0
-input1.bam	FBtr0070533	72	21	F	18.0
-input1.bam	FBtr0070533	72	22	F	20.0
-input1.bam	FBtr0070533	72	25	F	17.0
-input1.bam	FBtr0070533	72	26	F	16.0
-input1.bam	FBtr0070533	72	28	F	25.0
-input1.bam	FBtr0070533	72	32	F	21.0
-input1.bam	FBtr0070533	72	35	F	19.0
-input1.bam	FBtr0070533	72	37	F	19.0
-input1.bam	FBtr0070533	72	38	F	18.0
-input1.bam	FBtr0070533	72	72	F	0
-input1.bam	FBtr0070603	72	1	F	16.5
-input1.bam	FBtr0070603	72	3	F	21.0
-input1.bam	FBtr0070603	72	4	F	20.0
-input1.bam	FBtr0070603	72	6	F	18.0
-input1.bam	FBtr0070603	72	7	F	17.0
-input1.bam	FBtr0070603	72	8	F	16.0
-input1.bam	FBtr0070603	72	9	F	15.0
-input1.bam	FBtr0070603	72	12	F	20.0
-input1.bam	FBtr0070603	72	13	F	22.0
-input1.bam	FBtr0070603	72	15	F	18.5
-input1.bam	FBtr0070603	72	16	F	20.5
-input1.bam	FBtr0070603	72	17	F	25.0
-input1.bam	FBtr0070603	72	18	F	16.0
-input1.bam	FBtr0070603	72	19	F	23.0
-input1.bam	FBtr0070603	72	20	F	22.0
-input1.bam	FBtr0070603	72	21	F	25.0
-input1.bam	FBtr0070603	72	22	F	20.0
-input1.bam	FBtr0070603	72	24	F	19.5
-input1.bam	FBtr0070603	72	25	F	23.0
-input1.bam	FBtr0070603	72	26	F	26.0
-input1.bam	FBtr0070603	72	27	F	26.0
-input1.bam	FBtr0070603	72	32	F	20.0
-input1.bam	FBtr0070603	72	34	F	20.0
-input1.bam	FBtr0070603	72	38	F	18.0
-input1.bam	FBtr0070603	72	42	F	21.0
-input1.bam	FBtr0070603	72	51	F	18.0
-input1.bam	FBtr0070603	72	56	F	16.0
-input1.bam	FBtr0070603	72	72	F	0
-input1.bam	FBtr0070604	72	1	F	15.0
-input1.bam	FBtr0070604	72	18	F	23.0
-input1.bam	FBtr0070604	72	22	F	19.0
-input1.bam	FBtr0070604	72	30	F	18.0
-input1.bam	FBtr0070604	72	31	F	23.0
-input1.bam	FBtr0070604	72	32	F	22.0
-input1.bam	FBtr0070604	72	57	F	15.0
-input1.bam	FBtr0070604	72	72	F	0
-input1.bam	FBtr0070911	73	1	F	0
-input1.bam	FBtr0070911	73	15	F	21.0
-input1.bam	FBtr0070911	73	38	F	15.0
-input1.bam	FBtr0070911	73	73	F	0
-input1.bam	FBtr0078490	72	1	F	0
-input1.bam	FBtr0078490	72	13	F	16.0
-input1.bam	FBtr0078490	72	17	F	16.0
-input1.bam	FBtr0078490	72	18	F	15.0
-input1.bam	FBtr0078490	72	25	F	15.0
-input1.bam	FBtr0078490	72	28	F	19.0
-input1.bam	FBtr0078490	72	38	F	18.0
-input1.bam	FBtr0078490	72	72	F	0
-input1.bam	FBtr0078580	72	1	F	15.0
-input1.bam	FBtr0078580	72	3	F	22.0
-input1.bam	FBtr0078580	72	4	F	25.0
-input1.bam	FBtr0078580	72	5	F	20.0
-input1.bam	FBtr0078580	72	6	F	19.0
-input1.bam	FBtr0078580	72	7	F	22.0
-input1.bam	FBtr0078580	72	8	F	18.0
-input1.bam	FBtr0078580	72	11	F	23.0
-input1.bam	FBtr0078580	72	12	F	17.0
-input1.bam	FBtr0078580	72	14	F	15.0
-input1.bam	FBtr0078580	72	15	F	16.0
-input1.bam	FBtr0078580	72	16	F	19.0
-input1.bam	FBtr0078580	72	17	F	17.0
-input1.bam	FBtr0078580	72	19	F	24.0
-input1.bam	FBtr0078580	72	20	F	21.0
-input1.bam	FBtr0078580	72	21	F	20.0
-input1.bam	FBtr0078580	72	24	F	17.0
-input1.bam	FBtr0078580	72	25	F	27.5
-input1.bam	FBtr0078580	72	29	F	17.0
-input1.bam	FBtr0078580	72	31	F	17.0
-input1.bam	FBtr0078580	72	52	F	16.0
-input1.bam	FBtr0078580	72	72	F	0
-input1.bam	FBtr0078790	73	1	F	19.0
-input1.bam	FBtr0078790	73	17	F	16.0
-input1.bam	FBtr0078790	73	33	F	23.0
-input1.bam	FBtr0078790	73	42	F	18.5
-input1.bam	FBtr0078790	73	44	F	19.5
-input1.bam	FBtr0078790	73	46	F	17.0
-input1.bam	FBtr0078790	73	47	F	18.0
-input1.bam	FBtr0078790	73	52	F	20.0
-input1.bam	FBtr0078790	73	69	R	15.0
-input1.bam	FBtr0078790	73	73	F	0
-input1.bam	FBtr0079064	72	1	F	15.0
-input1.bam	FBtr0079064	72	3	F	21.0
-input1.bam	FBtr0079064	72	33	F	15.0
-input1.bam	FBtr0079064	72	52	F	17.0
-input1.bam	FBtr0079064	72	72	F	0
-input1.bam	FBtr0079090	72	1	F	21.5
-input1.bam	FBtr0079090	72	26	F	24.0
-input1.bam	FBtr0079090	72	33	F	16.0
-input1.bam	FBtr0079090	72	53	F	18.0
-input1.bam	FBtr0079090	72	56	R	21.0
-input1.bam	FBtr0079090	72	72	F	0
-input1.bam	FBtr0079338	73	1	F	0
-input1.bam	FBtr0079338	73	12	F	17.0
-input1.bam	FBtr0079338	73	13	F	17.5
-input1.bam	FBtr0079338	73	14	F	15.0
-input1.bam	FBtr0079338	73	17	F	15.0
-input1.bam	FBtr0079338	73	25	F	16.0
-input1.bam	FBtr0079338	73	42	F	22.0
-input1.bam	FBtr0079338	73	43	F	21.0
-input1.bam	FBtr0079338	73	46	F	18.0
-input1.bam	FBtr0079338	73	73	F	0
-input1.bam	FBtr0079528	71	1	F	20.0
-input1.bam	FBtr0079528	71	3	F	24.0
-input1.bam	FBtr0079528	71	4	F	24.0
-input1.bam	FBtr0079528	71	8	F	19.5
-input1.bam	FBtr0079528	71	10	F	21.0
-input1.bam	FBtr0079528	71	11	F	19.0
-input1.bam	FBtr0079528	71	13	F	16.0
-input1.bam	FBtr0079528	71	14	F	18.5
-input1.bam	FBtr0079528	71	16	F	15.0
-input1.bam	FBtr0079528	71	17	F	15.0
-input1.bam	FBtr0079528	71	18	F	20.0
-input1.bam	FBtr0079528	71	28	F	16.0
-input1.bam	FBtr0079528	71	35	F	15.0
-input1.bam	FBtr0079528	71	36	F	20.0
-input1.bam	FBtr0079528	71	37	F	18.0
-input1.bam	FBtr0079528	71	51	F	15.0
-input1.bam	FBtr0079528	71	71	F	0
-input1.bam	FBtr0079596	73	1	F	15.0
-input1.bam	FBtr0079596	73	3	F	23.0
-input1.bam	FBtr0079596	73	4	F	22.0
-input1.bam	FBtr0079596	73	5	F	18.5
-input1.bam	FBtr0079596	73	6	F	18.0
-input1.bam	FBtr0079596	73	8	F	17.0
-input1.bam	FBtr0079596	73	9	F	16.0
-input1.bam	FBtr0079596	73	10	F	15.0
-input1.bam	FBtr0079596	73	11	F	15.0
-input1.bam	FBtr0079596	73	12	F	17.0
-input1.bam	FBtr0079596	73	13	F	16.0
-input1.bam	FBtr0079596	73	14	F	15.0
-input1.bam	FBtr0079596	73	15	F	18.0
-input1.bam	FBtr0079596	73	16	F	17.0
-input1.bam	FBtr0079596	73	17	F	16.0
-input1.bam	FBtr0079596	73	18	F	15.0
-input1.bam	FBtr0079596	73	19	F	15.0
-input1.bam	FBtr0079596	73	53	F	18.5
-input1.bam	FBtr0079596	73	54	F	19.5
-input1.bam	FBtr0079596	73	73	F	0
-input1.bam	FBtr0079677	72	1	F	23.0
-input1.bam	FBtr0079677	72	5	F	19.0
-input1.bam	FBtr0079677	72	52	F	19.0
-input1.bam	FBtr0079677	72	53	F	18.0
-input1.bam	FBtr0079677	72	72	F	0
-input1.bam	FBtr0079690	72	1	F	15.0
-input1.bam	FBtr0079690	72	22	F	15.0
-input1.bam	FBtr0079690	72	27	F	25.0
-input1.bam	FBtr0079690	72	33	F	16.0
-input1.bam	FBtr0079690	72	72	F	0
-input1.bam	FBtr0079692	73	1	F	19.0
-input1.bam	FBtr0079692	73	18	F	18.0
-input1.bam	FBtr0079692	73	25	F	17.0
-input1.bam	FBtr0079692	73	32	F	20.0
-input1.bam	FBtr0079692	73	73	F	0
-input1.bam	FBtr0079693	72	1	F	15.0
-input1.bam	FBtr0079693	72	25	F	23.0
-input1.bam	FBtr0079693	72	72	F	0
-input1.bam	FBtr0079694	72	1	F	23.0
-input1.bam	FBtr0079694	72	18	F	19.0
-input1.bam	FBtr0079694	72	52	F	17.0
-input1.bam	FBtr0079694	72	72	F	0
-input1.bam	FBtr0079702	72	1	F	15.0
-input1.bam	FBtr0079702	72	19	F	18.0
-input1.bam	FBtr0079702	72	56	F	15.0
-input1.bam	FBtr0079702	72	72	F	0
-input1.bam	FBtr0079728	72	1	F	16.0
-input1.bam	FBtr0079728	72	8	F	20.0
-input1.bam	FBtr0079728	72	19	F	24.0
-input1.bam	FBtr0079728	72	33	F	15.0
-input1.bam	FBtr0079728	72	56	F	15.0
-input1.bam	FBtr0079728	72	72	F	0
-input1.bam	FBtr0079729	72	1	F	15.0
-input1.bam	FBtr0079729	72	13	F	22.0
-input1.bam	FBtr0079729	72	52	F	18.0
-input1.bam	FBtr0079729	72	57	F	16.0
-input1.bam	FBtr0079729	72	72	F	0
-input1.bam	FBtr0079752	72	1	F	19.5
-input1.bam	FBtr0079752	72	7	F	20.0
-input1.bam	FBtr0079752	72	12	F	16.0
-input1.bam	FBtr0079752	72	33	F	16.0
-input1.bam	FBtr0079752	72	52	F	19.5
-input1.bam	FBtr0079752	72	72	F	0
-input1.bam	FBtr0079820	74	1	F	0
-input1.bam	FBtr0079820	74	45	F	20.0
-input1.bam	FBtr0079820	74	46	F	17.0
-input1.bam	FBtr0079820	74	48	F	18.0
-input1.bam	FBtr0079820	74	49	F	24.0
-input1.bam	FBtr0079820	74	51	F	20.0
-input1.bam	FBtr0079820	74	54	F	17.0
-input1.bam	FBtr0079820	74	55	F	18.0
-input1.bam	FBtr0079820	74	56	F	18.5
-input1.bam	FBtr0079820	74	74	F	0
-input1.bam	FBtr0080609	72	1	F	18.0
-input1.bam	FBtr0080609	72	3	F	21.0
-input1.bam	FBtr0080609	72	4	F	20.0
-input1.bam	FBtr0080609	72	5	F	19.0
-input1.bam	FBtr0080609	72	7	F	17.0
-input1.bam	FBtr0080609	72	8	F	16.0
-input1.bam	FBtr0080609	72	9	F	15.0
-input1.bam	FBtr0080609	72	12	F	23.0
-input1.bam	FBtr0080609	72	15	F	19.0
-input1.bam	FBtr0080609	72	16	F	23.0
-input1.bam	FBtr0080609	72	17	F	20.5
-input1.bam	FBtr0080609	72	19	F	26.0
-input1.bam	FBtr0080609	72	20	F	25.0
-input1.bam	FBtr0080609	72	42	F	21.0
-input1.bam	FBtr0080609	72	51	F	18.0
-input1.bam	FBtr0080609	72	52	F	15.0
-input1.bam	FBtr0080609	72	72	F	0
-input1.bam	FBtr0080644	72	1	F	27.0
-input1.bam	FBtr0080644	72	4	F	20.5
-input1.bam	FBtr0080644	72	7	F	16.0
-input1.bam	FBtr0080644	72	12	F	16.0
-input1.bam	FBtr0080644	72	72	F	0
-input1.bam	FBtr0080646	72	1	F	16.0
-input1.bam	FBtr0080646	72	6	F	22.0
-input1.bam	FBtr0080646	72	7	F	21.0
-input1.bam	FBtr0080646	72	72	F	0
-input1.bam	FBtr0080647	72	1	F	16.0
-input1.bam	FBtr0080647	72	3	F	16.0
-input1.bam	FBtr0080647	72	6	F	19.0
-input1.bam	FBtr0080647	72	8	F	20.0
-input1.bam	FBtr0080647	72	11	F	17.0
-input1.bam	FBtr0080647	72	12	F	16.0
-input1.bam	FBtr0080647	72	72	F	0
-input1.bam	FBtr0080660	72	1	F	0
-input1.bam	FBtr0080660	72	4	F	24.0
-input1.bam	FBtr0080660	72	7	F	21.0
-input1.bam	FBtr0080660	72	72	F	0
-input1.bam	FBtr0080663	71	1	F	16.0
-input1.bam	FBtr0080663	71	3	F	24.0
-input1.bam	FBtr0080663	71	4	F	23.5
-input1.bam	FBtr0080663	71	7	F	16.0
-input1.bam	FBtr0080663	71	8	F	19.5
-input1.bam	FBtr0080663	71	12	F	16.0
-input1.bam	FBtr0080663	71	14	F	19.0
-input1.bam	FBtr0080663	71	15	F	17.0
-input1.bam	FBtr0080663	71	16	F	16.0
-input1.bam	FBtr0080663	71	17	F	15.0
-input1.bam	FBtr0080663	71	26	F	18.0
-input1.bam	FBtr0080663	71	32	F	15.5
-input1.bam	FBtr0080663	71	50	F	17.0
-input1.bam	FBtr0080663	71	51	F	15.0
-input1.bam	FBtr0080663	71	71	F	0
-input1.bam	FBtr0080664	71	1	F	17.0
-input1.bam	FBtr0080664	71	3	F	24.0
-input1.bam	FBtr0080664	71	4	F	23.5
-input1.bam	FBtr0080664	71	6	F	23.0
-input1.bam	FBtr0080664	71	7	F	21.0
-input1.bam	FBtr0080664	71	8	F	20.0
-input1.bam	FBtr0080664	71	9	F	20.0
-input1.bam	FBtr0080664	71	11	F	17.0
-input1.bam	FBtr0080664	71	12	F	17.0
-input1.bam	FBtr0080664	71	13	F	20.0
-input1.bam	FBtr0080664	71	14	F	18.0
-input1.bam	FBtr0080664	71	16	F	15.0
-input1.bam	FBtr0080664	71	17	F	15.5
-input1.bam	FBtr0080664	71	18	F	15.0
-input1.bam	FBtr0080664	71	21	F	15.0
-input1.bam	FBtr0080664	71	28	F	16.0
-input1.bam	FBtr0080664	71	32	F	15.0
-input1.bam	FBtr0080664	71	33	F	20.0
-input1.bam	FBtr0080664	71	34	F	16.0
-input1.bam	FBtr0080664	71	35	F	15.0
-input1.bam	FBtr0080664	71	36	F	21.0
-input1.bam	FBtr0080664	71	37	F	18.0
-input1.bam	FBtr0080664	71	38	F	15.0
-input1.bam	FBtr0080664	71	50	F	16.0
-input1.bam	FBtr0080664	71	51	F	15.0
-input1.bam	FBtr0080664	71	52	F	15.0
-input1.bam	FBtr0080664	71	56	F	16.0
-input1.bam	FBtr0080664	71	71	F	0
Binary file newtests/input1_min20_max30_single_plot_size.pdf has changed
--- a/newtests/input1_min20_max30_size.tab	Thu Nov 22 20:05:32 2018 -0500
+++ /dev/null	Thu Jan 01 00:00:00 1970 +0000
@@ -1,265 +0,0 @@
-Dataset	Chromosome	Polarity	Size	Counts
-input1.bam	FBtr0070001	F	20	4
-input1.bam	FBtr0070001	F	21	4
-input1.bam	FBtr0070001	F	22	29
-input1.bam	FBtr0070001	F	23	15
-input1.bam	FBtr0070001	F	24	1
-input1.bam	FBtr0070001	R	20	0
-input1.bam	FBtr0070001	R	21	0
-input1.bam	FBtr0070001	R	22	0
-input1.bam	FBtr0070001	R	23	0
-input1.bam	FBtr0070001	R	24	0
-input1.bam	FBtr0070533	F	20	2
-input1.bam	FBtr0070533	F	21	2
-input1.bam	FBtr0070533	F	22	4
-input1.bam	FBtr0070533	F	23	2
-input1.bam	FBtr0070533	F	24	0
-input1.bam	FBtr0070533	F	25	1
-input1.bam	FBtr0070533	R	20	0
-input1.bam	FBtr0070533	R	21	0
-input1.bam	FBtr0070533	R	22	0
-input1.bam	FBtr0070533	R	23	0
-input1.bam	FBtr0070533	R	24	0
-input1.bam	FBtr0070533	R	25	0
-input1.bam	FBtr0070603	F	20	6
-input1.bam	FBtr0070603	F	21	3
-input1.bam	FBtr0070603	F	22	3
-input1.bam	FBtr0070603	F	23	10
-input1.bam	FBtr0070603	F	24	2
-input1.bam	FBtr0070603	F	25	5
-input1.bam	FBtr0070603	F	26	5
-input1.bam	FBtr0070603	F	27	3
-input1.bam	FBtr0070603	R	20	0
-input1.bam	FBtr0070603	R	21	0
-input1.bam	FBtr0070603	R	22	0
-input1.bam	FBtr0070603	R	23	0
-input1.bam	FBtr0070603	R	24	0
-input1.bam	FBtr0070603	R	25	0
-input1.bam	FBtr0070603	R	26	0
-input1.bam	FBtr0070603	R	27	0
-input1.bam	FBtr0070604	F	21	1
-input1.bam	FBtr0070604	F	22	23
-input1.bam	FBtr0070604	F	23	10
-input1.bam	FBtr0070604	R	21	0
-input1.bam	FBtr0070604	R	22	0
-input1.bam	FBtr0070604	R	23	0
-input1.bam	FBtr0070911	F	21	1
-input1.bam	FBtr0070911	R	21	0
-input1.bam	FBtr0078490	F	23	1
-input1.bam	FBtr0078490	R	23	0
-input1.bam	FBtr0078580	F	20	9
-input1.bam	FBtr0078580	F	21	5
-input1.bam	FBtr0078580	F	22	13
-input1.bam	FBtr0078580	F	23	5
-input1.bam	FBtr0078580	F	24	180
-input1.bam	FBtr0078580	F	25	212
-input1.bam	FBtr0078580	F	26	1
-input1.bam	FBtr0078580	F	27	2
-input1.bam	FBtr0078580	F	28	17
-input1.bam	FBtr0078580	R	20	0
-input1.bam	FBtr0078580	R	21	0
-input1.bam	FBtr0078580	R	22	0
-input1.bam	FBtr0078580	R	23	0
-input1.bam	FBtr0078580	R	24	0
-input1.bam	FBtr0078580	R	25	0
-input1.bam	FBtr0078580	R	26	0
-input1.bam	FBtr0078580	R	27	0
-input1.bam	FBtr0078580	R	28	0
-input1.bam	FBtr0078790	F	20	2
-input1.bam	FBtr0078790	F	21	0
-input1.bam	FBtr0078790	F	22	2
-input1.bam	FBtr0078790	F	23	1
-input1.bam	FBtr0078790	R	20	0
-input1.bam	FBtr0078790	R	21	0
-input1.bam	FBtr0078790	R	22	0
-input1.bam	FBtr0078790	R	23	0
-input1.bam	FBtr0079064	F	21	1
-input1.bam	FBtr0079064	R	21	0
-input1.bam	FBtr0079090	F	21	0
-input1.bam	FBtr0079090	F	22	0
-input1.bam	FBtr0079090	F	23	0
-input1.bam	FBtr0079090	F	24	1
-input1.bam	FBtr0079090	F	25	0
-input1.bam	FBtr0079090	F	26	0
-input1.bam	FBtr0079090	F	27	0
-input1.bam	FBtr0079090	F	28	1
-input1.bam	FBtr0079090	R	21	1
-input1.bam	FBtr0079090	R	22	0
-input1.bam	FBtr0079090	R	23	0
-input1.bam	FBtr0079090	R	24	0
-input1.bam	FBtr0079090	R	25	0
-input1.bam	FBtr0079090	R	26	0
-input1.bam	FBtr0079090	R	27	0
-input1.bam	FBtr0079090	R	28	0
-input1.bam	FBtr0079338	F	21	3
-input1.bam	FBtr0079338	F	22	6
-input1.bam	FBtr0079338	R	21	0
-input1.bam	FBtr0079338	R	22	0
-input1.bam	FBtr0079528	F	20	12
-input1.bam	FBtr0079528	F	21	3
-input1.bam	FBtr0079528	F	22	2
-input1.bam	FBtr0079528	F	23	3
-input1.bam	FBtr0079528	F	24	36
-input1.bam	FBtr0079528	F	25	8
-input1.bam	FBtr0079528	F	26	5
-input1.bam	FBtr0079528	F	27	2
-input1.bam	FBtr0079528	F	28	2
-input1.bam	FBtr0079528	F	29	1
-input1.bam	FBtr0079528	R	20	0
-input1.bam	FBtr0079528	R	21	0
-input1.bam	FBtr0079528	R	22	0
-input1.bam	FBtr0079528	R	23	0
-input1.bam	FBtr0079528	R	24	0
-input1.bam	FBtr0079528	R	25	0
-input1.bam	FBtr0079528	R	26	0
-input1.bam	FBtr0079528	R	27	0
-input1.bam	FBtr0079528	R	28	0
-input1.bam	FBtr0079528	R	29	0
-input1.bam	FBtr0079596	F	20	13
-input1.bam	FBtr0079596	F	21	3
-input1.bam	FBtr0079596	F	22	16
-input1.bam	FBtr0079596	F	23	8
-input1.bam	FBtr0079596	F	24	0
-input1.bam	FBtr0079596	F	25	0
-input1.bam	FBtr0079596	F	26	3
-input1.bam	FBtr0079596	F	27	1
-input1.bam	FBtr0079596	R	20	0
-input1.bam	FBtr0079596	R	21	0
-input1.bam	FBtr0079596	R	22	0
-input1.bam	FBtr0079596	R	23	0
-input1.bam	FBtr0079596	R	24	0
-input1.bam	FBtr0079596	R	25	0
-input1.bam	FBtr0079596	R	26	0
-input1.bam	FBtr0079596	R	27	0
-input1.bam	FBtr0079677	F	23	1
-input1.bam	FBtr0079677	R	23	0
-input1.bam	FBtr0079690	F	25	1
-input1.bam	FBtr0079690	R	25	0
-input1.bam	FBtr0079692	F	20	1
-input1.bam	FBtr0079692	F	21	0
-input1.bam	FBtr0079692	F	22	0
-input1.bam	FBtr0079692	F	23	1
-input1.bam	FBtr0079692	R	20	0
-input1.bam	FBtr0079692	R	21	0
-input1.bam	FBtr0079692	R	22	0
-input1.bam	FBtr0079692	R	23	0
-input1.bam	FBtr0079693	F	23	1
-input1.bam	FBtr0079693	F	24	1
-input1.bam	FBtr0079693	R	23	0
-input1.bam	FBtr0079693	R	24	0
-input1.bam	FBtr0079694	F	23	1
-input1.bam	FBtr0079694	F	24	1
-input1.bam	FBtr0079694	F	25	1
-input1.bam	FBtr0079694	R	23	0
-input1.bam	FBtr0079694	R	24	0
-input1.bam	FBtr0079694	R	25	0
-input1.bam	FBtr0079702	F	10	0
-input1.bam	FBtr0079702	R	10	0
-input1.bam	FBtr0079728	F	20	1
-input1.bam	FBtr0079728	F	21	0
-input1.bam	FBtr0079728	F	22	0
-input1.bam	FBtr0079728	F	23	0
-input1.bam	FBtr0079728	F	24	1
-input1.bam	FBtr0079728	R	20	0
-input1.bam	FBtr0079728	R	21	0
-input1.bam	FBtr0079728	R	22	0
-input1.bam	FBtr0079728	R	23	0
-input1.bam	FBtr0079728	R	24	0
-input1.bam	FBtr0079729	F	22	1
-input1.bam	FBtr0079729	R	22	0
-input1.bam	FBtr0079752	F	20	2
-input1.bam	FBtr0079752	F	21	0
-input1.bam	FBtr0079752	F	22	0
-input1.bam	FBtr0079752	F	23	0
-input1.bam	FBtr0079752	F	24	1
-input1.bam	FBtr0079752	R	20	0
-input1.bam	FBtr0079752	R	21	0
-input1.bam	FBtr0079752	R	22	0
-input1.bam	FBtr0079752	R	23	0
-input1.bam	FBtr0079752	R	24	0
-input1.bam	FBtr0079820	F	20	2
-input1.bam	FBtr0079820	F	21	0
-input1.bam	FBtr0079820	F	22	0
-input1.bam	FBtr0079820	F	23	0
-input1.bam	FBtr0079820	F	24	1
-input1.bam	FBtr0079820	R	20	0
-input1.bam	FBtr0079820	R	21	0
-input1.bam	FBtr0079820	R	22	0
-input1.bam	FBtr0079820	R	23	0
-input1.bam	FBtr0079820	R	24	0
-input1.bam	FBtr0080609	F	20	10
-input1.bam	FBtr0080609	F	21	4
-input1.bam	FBtr0080609	F	22	0
-input1.bam	FBtr0080609	F	23	4
-input1.bam	FBtr0080609	F	24	1
-input1.bam	FBtr0080609	F	25	1
-input1.bam	FBtr0080609	F	26	1
-input1.bam	FBtr0080609	R	20	0
-input1.bam	FBtr0080609	R	21	0
-input1.bam	FBtr0080609	R	22	0
-input1.bam	FBtr0080609	R	23	0
-input1.bam	FBtr0080609	R	24	0
-input1.bam	FBtr0080609	R	25	0
-input1.bam	FBtr0080609	R	26	0
-input1.bam	FBtr0080644	F	24	1
-input1.bam	FBtr0080644	F	25	0
-input1.bam	FBtr0080644	F	26	0
-input1.bam	FBtr0080644	F	27	1
-input1.bam	FBtr0080644	R	24	0
-input1.bam	FBtr0080644	R	25	0
-input1.bam	FBtr0080644	R	26	0
-input1.bam	FBtr0080644	R	27	0
-input1.bam	FBtr0080646	F	21	1
-input1.bam	FBtr0080646	F	22	1
-input1.bam	FBtr0080646	R	21	0
-input1.bam	FBtr0080646	R	22	0
-input1.bam	FBtr0080647	F	20	1
-input1.bam	FBtr0080647	F	21	0
-input1.bam	FBtr0080647	F	22	1
-input1.bam	FBtr0080647	R	20	0
-input1.bam	FBtr0080647	R	21	0
-input1.bam	FBtr0080647	R	22	0
-input1.bam	FBtr0080660	F	21	2
-input1.bam	FBtr0080660	F	22	0
-input1.bam	FBtr0080660	F	23	0
-input1.bam	FBtr0080660	F	24	4
-input1.bam	FBtr0080660	R	21	0
-input1.bam	FBtr0080660	R	22	0
-input1.bam	FBtr0080660	R	23	0
-input1.bam	FBtr0080660	R	24	0
-input1.bam	FBtr0080663	F	20	10
-input1.bam	FBtr0080663	F	21	0
-input1.bam	FBtr0080663	F	22	1
-input1.bam	FBtr0080663	F	23	7
-input1.bam	FBtr0080663	F	24	33
-input1.bam	FBtr0080663	F	25	10
-input1.bam	FBtr0080663	F	26	6
-input1.bam	FBtr0080663	F	27	0
-input1.bam	FBtr0080663	F	28	2
-input1.bam	FBtr0080663	R	20	0
-input1.bam	FBtr0080663	R	21	0
-input1.bam	FBtr0080663	R	22	0
-input1.bam	FBtr0080663	R	23	0
-input1.bam	FBtr0080663	R	24	0
-input1.bam	FBtr0080663	R	25	0
-input1.bam	FBtr0080663	R	26	0
-input1.bam	FBtr0080663	R	27	0
-input1.bam	FBtr0080663	R	28	0
-input1.bam	FBtr0080664	F	20	12
-input1.bam	FBtr0080664	F	21	5
-input1.bam	FBtr0080664	F	22	0
-input1.bam	FBtr0080664	F	23	11
-input1.bam	FBtr0080664	F	24	33
-input1.bam	FBtr0080664	F	25	10
-input1.bam	FBtr0080664	F	26	4
-input1.bam	FBtr0080664	F	27	0
-input1.bam	FBtr0080664	F	28	2
-input1.bam	FBtr0080664	R	20	0
-input1.bam	FBtr0080664	R	21	0
-input1.bam	FBtr0080664	R	22	0
-input1.bam	FBtr0080664	R	23	0
-input1.bam	FBtr0080664	R	24	0
-input1.bam	FBtr0080664	R	25	0
-input1.bam	FBtr0080664	R	26	0
-input1.bam	FBtr0080664	R	27	0
-input1.bam	FBtr0080664	R	28	0
Binary file newtests/input1_single_plot_median.pdf has changed
Binary file newtests/input1_yminneg5_5_single_plot_counts.pdf has changed
Binary file newtests/input_single_chr_x_6_single_plot_coverage.pdf has changed
--- a/newtests/input_single_chr_x_6_single_plot_coverage.tab	Thu Nov 22 20:05:32 2018 -0500
+++ /dev/null	Thu Jan 01 00:00:00 1970 +0000
@@ -1,481 +0,0 @@
-Dataset	Chromosome	Chrom_length	Coordinate	Polarity	Coverage
-input_single_chr.bam_0	1	80	1	F	1
-input_single_chr.bam_0	1	80	2	F	1
-input_single_chr.bam_0	1	80	3	F	1
-input_single_chr.bam_0	1	80	4	F	1
-input_single_chr.bam_0	1	80	5	F	1
-input_single_chr.bam_0	1	80	6	F	1
-input_single_chr.bam_0	1	80	7	F	1
-input_single_chr.bam_0	1	80	8	F	1
-input_single_chr.bam_0	1	80	9	F	1
-input_single_chr.bam_0	1	80	10	F	1
-input_single_chr.bam_0	1	80	11	F	1
-input_single_chr.bam_0	1	80	12	F	1
-input_single_chr.bam_0	1	80	13	F	1
-input_single_chr.bam_0	1	80	14	F	1
-input_single_chr.bam_0	1	80	15	F	1
-input_single_chr.bam_0	1	80	16	F	1
-input_single_chr.bam_0	1	80	17	F	1
-input_single_chr.bam_0	1	80	18	F	1
-input_single_chr.bam_0	1	80	19	F	1
-input_single_chr.bam_0	1	80	20	F	1
-input_single_chr.bam_0	1	80	21	F	1
-input_single_chr.bam_0	1	80	22	F	1
-input_single_chr.bam_0	1	80	23	F	1
-input_single_chr.bam_0	1	80	24	F	1
-input_single_chr.bam_0	1	80	25	F	1
-input_single_chr.bam_0	1	80	26	F	1
-input_single_chr.bam_0	1	80	27	F	1
-input_single_chr.bam_0	1	80	28	F	1
-input_single_chr.bam_0	1	80	29	F	1
-input_single_chr.bam_0	1	80	30	F	1
-input_single_chr.bam_0	1	80	31	F	1
-input_single_chr.bam_0	1	80	32	F	1
-input_single_chr.bam_0	1	80	33	F	1
-input_single_chr.bam_0	1	80	34	F	1
-input_single_chr.bam_0	1	80	35	F	1
-input_single_chr.bam_0	1	80	36	F	1
-input_single_chr.bam_0	1	80	37	F	1
-input_single_chr.bam_0	1	80	38	F	1
-input_single_chr.bam_0	1	80	39	F	1
-input_single_chr.bam_0	1	80	40	F	1
-input_single_chr.bam_0	1	80	41	F	1
-input_single_chr.bam_0	1	80	42	F	1
-input_single_chr.bam_0	1	80	43	F	1
-input_single_chr.bam_0	1	80	44	F	1
-input_single_chr.bam_0	1	80	45	F	1
-input_single_chr.bam_0	1	80	46	F	1
-input_single_chr.bam_0	1	80	47	F	1
-input_single_chr.bam_0	1	80	48	F	1
-input_single_chr.bam_0	1	80	49	F	1
-input_single_chr.bam_0	1	80	50	F	1
-input_single_chr.bam_0	1	80	51	F	1
-input_single_chr.bam_0	1	80	52	F	1
-input_single_chr.bam_0	1	80	53	F	1
-input_single_chr.bam_0	1	80	54	F	1
-input_single_chr.bam_0	1	80	55	F	1
-input_single_chr.bam_0	1	80	56	F	1
-input_single_chr.bam_0	1	80	57	F	1
-input_single_chr.bam_0	1	80	58	F	1
-input_single_chr.bam_0	1	80	59	F	1
-input_single_chr.bam_0	1	80	60	F	1
-input_single_chr.bam_0	1	80	61	F	1
-input_single_chr.bam_0	1	80	62	F	1
-input_single_chr.bam_0	1	80	63	F	1
-input_single_chr.bam_0	1	80	64	F	1
-input_single_chr.bam_0	1	80	65	F	1
-input_single_chr.bam_0	1	80	66	F	1
-input_single_chr.bam_0	1	80	67	F	1
-input_single_chr.bam_0	1	80	68	F	1
-input_single_chr.bam_0	1	80	69	F	1
-input_single_chr.bam_0	1	80	70	F	1
-input_single_chr.bam_0	1	80	71	F	1
-input_single_chr.bam_0	1	80	72	F	1
-input_single_chr.bam_0	1	80	73	F	1
-input_single_chr.bam_0	1	80	74	F	1
-input_single_chr.bam_0	1	80	75	F	1
-input_single_chr.bam_0	1	80	76	F	1
-input_single_chr.bam_0	1	80	77	F	1
-input_single_chr.bam_0	1	80	78	F	1
-input_single_chr.bam_0	1	80	79	F	1
-input_single_chr.bam_0	1	80	80	F	1
-input_single_chr.bam_1	1	80	1	F	1
-input_single_chr.bam_1	1	80	2	F	1
-input_single_chr.bam_1	1	80	3	F	1
-input_single_chr.bam_1	1	80	4	F	1
-input_single_chr.bam_1	1	80	5	F	1
-input_single_chr.bam_1	1	80	6	F	1
-input_single_chr.bam_1	1	80	7	F	1
-input_single_chr.bam_1	1	80	8	F	1
-input_single_chr.bam_1	1	80	9	F	1
-input_single_chr.bam_1	1	80	10	F	1
-input_single_chr.bam_1	1	80	11	F	1
-input_single_chr.bam_1	1	80	12	F	1
-input_single_chr.bam_1	1	80	13	F	1
-input_single_chr.bam_1	1	80	14	F	1
-input_single_chr.bam_1	1	80	15	F	1
-input_single_chr.bam_1	1	80	16	F	1
-input_single_chr.bam_1	1	80	17	F	1
-input_single_chr.bam_1	1	80	18	F	1
-input_single_chr.bam_1	1	80	19	F	1
-input_single_chr.bam_1	1	80	20	F	1
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-input_single_chr.bam_5	1	80	53	F	1
-input_single_chr.bam_5	1	80	54	F	1
-input_single_chr.bam_5	1	80	55	F	1
-input_single_chr.bam_5	1	80	56	F	1
-input_single_chr.bam_5	1	80	57	F	1
-input_single_chr.bam_5	1	80	58	F	1
-input_single_chr.bam_5	1	80	59	F	1
-input_single_chr.bam_5	1	80	60	F	1
-input_single_chr.bam_5	1	80	61	F	1
-input_single_chr.bam_5	1	80	62	F	1
-input_single_chr.bam_5	1	80	63	F	1
-input_single_chr.bam_5	1	80	64	F	1
-input_single_chr.bam_5	1	80	65	F	1
-input_single_chr.bam_5	1	80	66	F	1
-input_single_chr.bam_5	1	80	67	F	1
-input_single_chr.bam_5	1	80	68	F	1
-input_single_chr.bam_5	1	80	69	F	1
-input_single_chr.bam_5	1	80	70	F	1
-input_single_chr.bam_5	1	80	71	F	1
-input_single_chr.bam_5	1	80	72	F	1
-input_single_chr.bam_5	1	80	73	F	1
-input_single_chr.bam_5	1	80	74	F	1
-input_single_chr.bam_5	1	80	75	F	1
-input_single_chr.bam_5	1	80	76	F	1
-input_single_chr.bam_5	1	80	77	F	1
-input_single_chr.bam_5	1	80	78	F	1
-input_single_chr.bam_5	1	80	79	F	1
-input_single_chr.bam_5	1	80	80	F	1
--- a/newtests/size.tab	Thu Nov 22 20:05:32 2018 -0500
+++ /dev/null	Thu Jan 01 00:00:00 1970 +0000
@@ -1,1045 +0,0 @@
-Dataset	Chromosome	Polarity	Size	Counts
-input1.bam	FBtr0070001	F	16	2
-input1.bam	FBtr0070001	F	17	1
-input1.bam	FBtr0070001	F	18	0
-input1.bam	FBtr0070001	F	19	1
-input1.bam	FBtr0070001	F	20	4
-input1.bam	FBtr0070001	F	21	4
-input1.bam	FBtr0070001	F	22	29
-input1.bam	FBtr0070001	F	23	15
-input1.bam	FBtr0070001	F	24	1
-input1.bam	FBtr0070001	R	16	0
-input1.bam	FBtr0070001	R	17	0
-input1.bam	FBtr0070001	R	18	0
-input1.bam	FBtr0070001	R	19	0
-input1.bam	FBtr0070001	R	20	0
-input1.bam	FBtr0070001	R	21	0
-input1.bam	FBtr0070001	R	22	0
-input1.bam	FBtr0070001	R	23	0
-input1.bam	FBtr0070001	R	24	0
-input1.bam	FBtr0070533	F	15	2
-input1.bam	FBtr0070533	F	16	1
-input1.bam	FBtr0070533	F	17	1
-input1.bam	FBtr0070533	F	18	6
-input1.bam	FBtr0070533	F	19	3
-input1.bam	FBtr0070533	F	20	2
-input1.bam	FBtr0070533	F	21	2
-input1.bam	FBtr0070533	F	22	4
-input1.bam	FBtr0070533	F	23	2
-input1.bam	FBtr0070533	F	24	0
-input1.bam	FBtr0070533	F	25	1
-input1.bam	FBtr0070533	R	15	0
-input1.bam	FBtr0070533	R	16	0
-input1.bam	FBtr0070533	R	17	0
-input1.bam	FBtr0070533	R	18	0
-input1.bam	FBtr0070533	R	19	0
-input1.bam	FBtr0070533	R	20	0
-input1.bam	FBtr0070533	R	21	0
-input1.bam	FBtr0070533	R	22	0
-input1.bam	FBtr0070533	R	23	0
-input1.bam	FBtr0070533	R	24	0
-input1.bam	FBtr0070533	R	25	0
-input1.bam	FBtr0070603	F	15	9
-input1.bam	FBtr0070603	F	16	6
-input1.bam	FBtr0070603	F	17	10
-input1.bam	FBtr0070603	F	18	7
-input1.bam	FBtr0070603	F	19	1
-input1.bam	FBtr0070603	F	20	6
-input1.bam	FBtr0070603	F	21	3
-input1.bam	FBtr0070603	F	22	3
-input1.bam	FBtr0070603	F	23	10
-input1.bam	FBtr0070603	F	24	2
-input1.bam	FBtr0070603	F	25	5
-input1.bam	FBtr0070603	F	26	5
-input1.bam	FBtr0070603	F	27	3
-input1.bam	FBtr0070603	R	15	0
-input1.bam	FBtr0070603	R	16	0
-input1.bam	FBtr0070603	R	17	0
-input1.bam	FBtr0070603	R	18	0
-input1.bam	FBtr0070603	R	19	0
-input1.bam	FBtr0070603	R	20	0
-input1.bam	FBtr0070603	R	21	0
-input1.bam	FBtr0070603	R	22	0
-input1.bam	FBtr0070603	R	23	0
-input1.bam	FBtr0070603	R	24	0
-input1.bam	FBtr0070603	R	25	0
-input1.bam	FBtr0070603	R	26	0
-input1.bam	FBtr0070603	R	27	0
-input1.bam	FBtr0070604	F	15	2
-input1.bam	FBtr0070604	F	16	0
-input1.bam	FBtr0070604	F	17	0
-input1.bam	FBtr0070604	F	18	2
-input1.bam	FBtr0070604	F	19	2
-input1.bam	FBtr0070604	F	20	0
-input1.bam	FBtr0070604	F	21	1
-input1.bam	FBtr0070604	F	22	23
-input1.bam	FBtr0070604	F	23	10
-input1.bam	FBtr0070604	R	15	0
-input1.bam	FBtr0070604	R	16	0
-input1.bam	FBtr0070604	R	17	0
-input1.bam	FBtr0070604	R	18	0
-input1.bam	FBtr0070604	R	19	0
-input1.bam	FBtr0070604	R	20	0
-input1.bam	FBtr0070604	R	21	0
-input1.bam	FBtr0070604	R	22	0
-input1.bam	FBtr0070604	R	23	0
-input1.bam	FBtr0070911	F	15	1
-input1.bam	FBtr0070911	F	16	0
-input1.bam	FBtr0070911	F	17	0
-input1.bam	FBtr0070911	F	18	0
-input1.bam	FBtr0070911	F	19	0
-input1.bam	FBtr0070911	F	20	0
-input1.bam	FBtr0070911	F	21	1
-input1.bam	FBtr0070911	R	15	0
-input1.bam	FBtr0070911	R	16	0
-input1.bam	FBtr0070911	R	17	0
-input1.bam	FBtr0070911	R	18	0
-input1.bam	FBtr0070911	R	19	0
-input1.bam	FBtr0070911	R	20	0
-input1.bam	FBtr0070911	R	21	0
-input1.bam	FBtr0078490	F	15	3
-input1.bam	FBtr0078490	F	16	3
-input1.bam	FBtr0078490	F	17	0
-input1.bam	FBtr0078490	F	18	1
-input1.bam	FBtr0078490	F	19	0
-input1.bam	FBtr0078490	F	20	0
-input1.bam	FBtr0078490	F	21	0
-input1.bam	FBtr0078490	F	22	0
-input1.bam	FBtr0078490	F	23	1
-input1.bam	FBtr0078490	R	15	0
-input1.bam	FBtr0078490	R	16	0
-input1.bam	FBtr0078490	R	17	0
-input1.bam	FBtr0078490	R	18	0
-input1.bam	FBtr0078490	R	19	0
-input1.bam	FBtr0078490	R	20	0
-input1.bam	FBtr0078490	R	21	0
-input1.bam	FBtr0078490	R	22	0
-input1.bam	FBtr0078490	R	23	0
-input1.bam	FBtr0078580	F	15	592
-input1.bam	FBtr0078580	F	16	20
-input1.bam	FBtr0078580	F	17	31
-input1.bam	FBtr0078580	F	18	9
-input1.bam	FBtr0078580	F	19	8
-input1.bam	FBtr0078580	F	20	9
-input1.bam	FBtr0078580	F	21	5
-input1.bam	FBtr0078580	F	22	13
-input1.bam	FBtr0078580	F	23	5
-input1.bam	FBtr0078580	F	24	180
-input1.bam	FBtr0078580	F	25	212
-input1.bam	FBtr0078580	F	26	1
-input1.bam	FBtr0078580	F	27	2
-input1.bam	FBtr0078580	F	28	17
-input1.bam	FBtr0078580	R	15	0
-input1.bam	FBtr0078580	R	16	0
-input1.bam	FBtr0078580	R	17	0
-input1.bam	FBtr0078580	R	18	0
-input1.bam	FBtr0078580	R	19	0
-input1.bam	FBtr0078580	R	20	0
-input1.bam	FBtr0078580	R	21	0
-input1.bam	FBtr0078580	R	22	0
-input1.bam	FBtr0078580	R	23	0
-input1.bam	FBtr0078580	R	24	0
-input1.bam	FBtr0078580	R	25	0
-input1.bam	FBtr0078580	R	26	0
-input1.bam	FBtr0078580	R	27	0
-input1.bam	FBtr0078580	R	28	0
-input1.bam	FBtr0078790	F	15	2
-input1.bam	FBtr0078790	F	16	2
-input1.bam	FBtr0078790	F	17	1
-input1.bam	FBtr0078790	F	18	1
-input1.bam	FBtr0078790	F	19	2
-input1.bam	FBtr0078790	F	20	2
-input1.bam	FBtr0078790	F	21	0
-input1.bam	FBtr0078790	F	22	2
-input1.bam	FBtr0078790	F	23	1
-input1.bam	FBtr0078790	R	15	1
-input1.bam	FBtr0078790	R	16	0
-input1.bam	FBtr0078790	R	17	0
-input1.bam	FBtr0078790	R	18	0
-input1.bam	FBtr0078790	R	19	0
-input1.bam	FBtr0078790	R	20	0
-input1.bam	FBtr0078790	R	21	0
-input1.bam	FBtr0078790	R	22	0
-input1.bam	FBtr0078790	R	23	0
-input1.bam	FBtr0079064	F	15	2
-input1.bam	FBtr0079064	F	16	0
-input1.bam	FBtr0079064	F	17	1
-input1.bam	FBtr0079064	F	18	0
-input1.bam	FBtr0079064	F	19	0
-input1.bam	FBtr0079064	F	20	0
-input1.bam	FBtr0079064	F	21	1
-input1.bam	FBtr0079064	R	15	0
-input1.bam	FBtr0079064	R	16	0
-input1.bam	FBtr0079064	R	17	0
-input1.bam	FBtr0079064	R	18	0
-input1.bam	FBtr0079064	R	19	0
-input1.bam	FBtr0079064	R	20	0
-input1.bam	FBtr0079064	R	21	0
-input1.bam	FBtr0079090	F	15	1
-input1.bam	FBtr0079090	F	16	1
-input1.bam	FBtr0079090	F	17	0
-input1.bam	FBtr0079090	F	18	1
-input1.bam	FBtr0079090	F	19	0
-input1.bam	FBtr0079090	F	20	0
-input1.bam	FBtr0079090	F	21	0
-input1.bam	FBtr0079090	F	22	0
-input1.bam	FBtr0079090	F	23	0
-input1.bam	FBtr0079090	F	24	1
-input1.bam	FBtr0079090	F	25	0
-input1.bam	FBtr0079090	F	26	0
-input1.bam	FBtr0079090	F	27	0
-input1.bam	FBtr0079090	F	28	1
-input1.bam	FBtr0079090	R	15	0
-input1.bam	FBtr0079090	R	16	0
-input1.bam	FBtr0079090	R	17	0
-input1.bam	FBtr0079090	R	18	0
-input1.bam	FBtr0079090	R	19	0
-input1.bam	FBtr0079090	R	20	0
-input1.bam	FBtr0079090	R	21	1
-input1.bam	FBtr0079090	R	22	0
-input1.bam	FBtr0079090	R	23	0
-input1.bam	FBtr0079090	R	24	0
-input1.bam	FBtr0079090	R	25	0
-input1.bam	FBtr0079090	R	26	0
-input1.bam	FBtr0079090	R	27	0
-input1.bam	FBtr0079090	R	28	0
-input1.bam	FBtr0079338	F	15	2
-input1.bam	FBtr0079338	F	16	2
-input1.bam	FBtr0079338	F	17	1
-input1.bam	FBtr0079338	F	18	1
-input1.bam	FBtr0079338	F	19	1
-input1.bam	FBtr0079338	F	20	0
-input1.bam	FBtr0079338	F	21	3
-input1.bam	FBtr0079338	F	22	6
-input1.bam	FBtr0079338	R	15	0
-input1.bam	FBtr0079338	R	16	0
-input1.bam	FBtr0079338	R	17	0
-input1.bam	FBtr0079338	R	18	0
-input1.bam	FBtr0079338	R	19	0
-input1.bam	FBtr0079338	R	20	0
-input1.bam	FBtr0079338	R	21	0
-input1.bam	FBtr0079338	R	22	0
-input1.bam	FBtr0079528	F	15	12
-input1.bam	FBtr0079528	F	16	11
-input1.bam	FBtr0079528	F	17	0
-input1.bam	FBtr0079528	F	18	5
-input1.bam	FBtr0079528	F	19	4
-input1.bam	FBtr0079528	F	20	12
-input1.bam	FBtr0079528	F	21	3
-input1.bam	FBtr0079528	F	22	2
-input1.bam	FBtr0079528	F	23	3
-input1.bam	FBtr0079528	F	24	36
-input1.bam	FBtr0079528	F	25	8
-input1.bam	FBtr0079528	F	26	5
-input1.bam	FBtr0079528	F	27	2
-input1.bam	FBtr0079528	F	28	2
-input1.bam	FBtr0079528	F	29	1
-input1.bam	FBtr0079528	R	15	0
-input1.bam	FBtr0079528	R	16	0
-input1.bam	FBtr0079528	R	17	0
-input1.bam	FBtr0079528	R	18	0
-input1.bam	FBtr0079528	R	19	0
-input1.bam	FBtr0079528	R	20	0
-input1.bam	FBtr0079528	R	21	0
-input1.bam	FBtr0079528	R	22	0
-input1.bam	FBtr0079528	R	23	0
-input1.bam	FBtr0079528	R	24	0
-input1.bam	FBtr0079528	R	25	0
-input1.bam	FBtr0079528	R	26	0
-input1.bam	FBtr0079528	R	27	0
-input1.bam	FBtr0079528	R	28	0
-input1.bam	FBtr0079528	R	29	0
-input1.bam	FBtr0079596	F	15	43
-input1.bam	FBtr0079596	F	16	34
-input1.bam	FBtr0079596	F	17	16
-input1.bam	FBtr0079596	F	18	5
-input1.bam	FBtr0079596	F	19	10
-input1.bam	FBtr0079596	F	20	13
-input1.bam	FBtr0079596	F	21	3
-input1.bam	FBtr0079596	F	22	16
-input1.bam	FBtr0079596	F	23	8
-input1.bam	FBtr0079596	F	24	0
-input1.bam	FBtr0079596	F	25	0
-input1.bam	FBtr0079596	F	26	3
-input1.bam	FBtr0079596	F	27	1
-input1.bam	FBtr0079596	R	15	0
-input1.bam	FBtr0079596	R	16	0
-input1.bam	FBtr0079596	R	17	0
-input1.bam	FBtr0079596	R	18	0
-input1.bam	FBtr0079596	R	19	0
-input1.bam	FBtr0079596	R	20	0
-input1.bam	FBtr0079596	R	21	0
-input1.bam	FBtr0079596	R	22	0
-input1.bam	FBtr0079596	R	23	0
-input1.bam	FBtr0079596	R	24	0
-input1.bam	FBtr0079596	R	25	0
-input1.bam	FBtr0079596	R	26	0
-input1.bam	FBtr0079596	R	27	0
-input1.bam	FBtr0079677	F	18	1
-input1.bam	FBtr0079677	F	19	2
-input1.bam	FBtr0079677	F	20	0
-input1.bam	FBtr0079677	F	21	0
-input1.bam	FBtr0079677	F	22	0
-input1.bam	FBtr0079677	F	23	1
-input1.bam	FBtr0079677	R	18	0
-input1.bam	FBtr0079677	R	19	0
-input1.bam	FBtr0079677	R	20	0
-input1.bam	FBtr0079677	R	21	0
-input1.bam	FBtr0079677	R	22	0
-input1.bam	FBtr0079677	R	23	0
-input1.bam	FBtr0079690	F	15	3
-input1.bam	FBtr0079690	F	16	0
-input1.bam	FBtr0079690	F	17	1
-input1.bam	FBtr0079690	F	18	0
-input1.bam	FBtr0079690	F	19	0
-input1.bam	FBtr0079690	F	20	0
-input1.bam	FBtr0079690	F	21	0
-input1.bam	FBtr0079690	F	22	0
-input1.bam	FBtr0079690	F	23	0
-input1.bam	FBtr0079690	F	24	0
-input1.bam	FBtr0079690	F	25	1
-input1.bam	FBtr0079690	R	15	0
-input1.bam	FBtr0079690	R	16	0
-input1.bam	FBtr0079690	R	17	0
-input1.bam	FBtr0079690	R	18	0
-input1.bam	FBtr0079690	R	19	0
-input1.bam	FBtr0079690	R	20	0
-input1.bam	FBtr0079690	R	21	0
-input1.bam	FBtr0079690	R	22	0
-input1.bam	FBtr0079690	R	23	0
-input1.bam	FBtr0079690	R	24	0
-input1.bam	FBtr0079690	R	25	0
-input1.bam	FBtr0079692	F	16	1
-input1.bam	FBtr0079692	F	17	1
-input1.bam	FBtr0079692	F	18	1
-input1.bam	FBtr0079692	F	19	1
-input1.bam	FBtr0079692	F	20	1
-input1.bam	FBtr0079692	F	21	0
-input1.bam	FBtr0079692	F	22	0
-input1.bam	FBtr0079692	F	23	1
-input1.bam	FBtr0079692	R	16	0
-input1.bam	FBtr0079692	R	17	0
-input1.bam	FBtr0079692	R	18	0
-input1.bam	FBtr0079692	R	19	0
-input1.bam	FBtr0079692	R	20	0
-input1.bam	FBtr0079692	R	21	0
-input1.bam	FBtr0079692	R	22	0
-input1.bam	FBtr0079692	R	23	0
-input1.bam	FBtr0079693	F	15	3
-input1.bam	FBtr0079693	F	16	0
-input1.bam	FBtr0079693	F	17	1
-input1.bam	FBtr0079693	F	18	0
-input1.bam	FBtr0079693	F	19	0
-input1.bam	FBtr0079693	F	20	0
-input1.bam	FBtr0079693	F	21	0
-input1.bam	FBtr0079693	F	22	0
-input1.bam	FBtr0079693	F	23	1
-input1.bam	FBtr0079693	F	24	1
-input1.bam	FBtr0079693	R	15	0
-input1.bam	FBtr0079693	R	16	0
-input1.bam	FBtr0079693	R	17	0
-input1.bam	FBtr0079693	R	18	0
-input1.bam	FBtr0079693	R	19	0
-input1.bam	FBtr0079693	R	20	0
-input1.bam	FBtr0079693	R	21	0
-input1.bam	FBtr0079693	R	22	0
-input1.bam	FBtr0079693	R	23	0
-input1.bam	FBtr0079693	R	24	0
-input1.bam	FBtr0079694	F	15	2
-input1.bam	FBtr0079694	F	16	0
-input1.bam	FBtr0079694	F	17	1
-input1.bam	FBtr0079694	F	18	0
-input1.bam	FBtr0079694	F	19	1
-input1.bam	FBtr0079694	F	20	0
-input1.bam	FBtr0079694	F	21	0
-input1.bam	FBtr0079694	F	22	0
-input1.bam	FBtr0079694	F	23	1
-input1.bam	FBtr0079694	F	24	1
-input1.bam	FBtr0079694	F	25	1
-input1.bam	FBtr0079694	R	15	0
-input1.bam	FBtr0079694	R	16	0
-input1.bam	FBtr0079694	R	17	0
-input1.bam	FBtr0079694	R	18	0
-input1.bam	FBtr0079694	R	19	0
-input1.bam	FBtr0079694	R	20	0
-input1.bam	FBtr0079694	R	21	0
-input1.bam	FBtr0079694	R	22	0
-input1.bam	FBtr0079694	R	23	0
-input1.bam	FBtr0079694	R	24	0
-input1.bam	FBtr0079694	R	25	0
-input1.bam	FBtr0079702	F	15	2
-input1.bam	FBtr0079702	F	16	0
-input1.bam	FBtr0079702	F	17	0
-input1.bam	FBtr0079702	F	18	2
-input1.bam	FBtr0079702	R	15	0
-input1.bam	FBtr0079702	R	16	0
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-input2.bam	FBtr0079338	R	21	0
-input2.bam	FBtr0079338	R	22	0
-input2.bam	FBtr0079338	R	23	0
-input2.bam	FBtr0079528	F	15	164
-input2.bam	FBtr0079528	F	16	46
-input2.bam	FBtr0079528	F	17	31
-input2.bam	FBtr0079528	F	18	56
-input2.bam	FBtr0079528	F	19	34
-input2.bam	FBtr0079528	F	20	8
-input2.bam	FBtr0079528	F	21	8
-input2.bam	FBtr0079528	F	22	8
-input2.bam	FBtr0079528	F	23	4
-input2.bam	FBtr0079528	F	24	1
-input2.bam	FBtr0079528	F	25	1
-input2.bam	FBtr0079528	F	26	4
-input2.bam	FBtr0079528	R	15	0
-input2.bam	FBtr0079528	R	16	0
-input2.bam	FBtr0079528	R	17	0
-input2.bam	FBtr0079528	R	18	0
-input2.bam	FBtr0079528	R	19	0
-input2.bam	FBtr0079528	R	20	0
-input2.bam	FBtr0079528	R	21	0
-input2.bam	FBtr0079528	R	22	0
-input2.bam	FBtr0079528	R	23	0
-input2.bam	FBtr0079528	R	24	0
-input2.bam	FBtr0079528	R	25	0
-input2.bam	FBtr0079528	R	26	0
-input2.bam	FBtr0079596	F	15	31
-input2.bam	FBtr0079596	F	16	21
-input2.bam	FBtr0079596	F	17	18
-input2.bam	FBtr0079596	F	18	79
-input2.bam	FBtr0079596	F	19	48
-input2.bam	FBtr0079596	F	20	49
-input2.bam	FBtr0079596	F	21	40
-input2.bam	FBtr0079596	F	22	26
-input2.bam	FBtr0079596	F	23	2
-input2.bam	FBtr0079596	F	24	1
-input2.bam	FBtr0079596	R	15	0
-input2.bam	FBtr0079596	R	16	0
-input2.bam	FBtr0079596	R	17	0
-input2.bam	FBtr0079596	R	18	0
-input2.bam	FBtr0079596	R	19	0
-input2.bam	FBtr0079596	R	20	0
-input2.bam	FBtr0079596	R	21	1
-input2.bam	FBtr0079596	R	22	0
-input2.bam	FBtr0079596	R	23	0
-input2.bam	FBtr0079596	R	24	0
-input2.bam	FBtr0079677	F	15	2
-input2.bam	FBtr0079677	F	16	1
-input2.bam	FBtr0079677	F	17	2
-input2.bam	FBtr0079677	F	18	0
-input2.bam	FBtr0079677	F	19	1
-input2.bam	FBtr0079677	F	20	1
-input2.bam	FBtr0079677	R	15	0
-input2.bam	FBtr0079677	R	16	0
-input2.bam	FBtr0079677	R	17	0
-input2.bam	FBtr0079677	R	18	0
-input2.bam	FBtr0079677	R	19	0
-input2.bam	FBtr0079677	R	20	0
-input2.bam	FBtr0079690	F	15	1
-input2.bam	FBtr0079690	F	16	1
-input2.bam	FBtr0079690	F	17	0
-input2.bam	FBtr0079690	F	18	0
-input2.bam	FBtr0079690	F	19	0
-input2.bam	FBtr0079690	F	20	2
-input2.bam	FBtr0079690	F	21	1
-input2.bam	FBtr0079690	R	15	0
-input2.bam	FBtr0079690	R	16	0
-input2.bam	FBtr0079690	R	17	0
-input2.bam	FBtr0079690	R	18	0
-input2.bam	FBtr0079690	R	19	0
-input2.bam	FBtr0079690	R	20	0
-input2.bam	FBtr0079690	R	21	0
-input2.bam	FBtr0079692	F	15	1
-input2.bam	FBtr0079692	F	16	0
-input2.bam	FBtr0079692	F	17	0
-input2.bam	FBtr0079692	F	18	1
-input2.bam	FBtr0079692	F	19	0
-input2.bam	FBtr0079692	F	20	0
-input2.bam	FBtr0079692	F	21	1
-input2.bam	FBtr0079692	F	22	1
-input2.bam	FBtr0079692	R	15	0
-input2.bam	FBtr0079692	R	16	0
-input2.bam	FBtr0079692	R	17	0
-input2.bam	FBtr0079692	R	18	0
-input2.bam	FBtr0079692	R	19	0
-input2.bam	FBtr0079692	R	20	0
-input2.bam	FBtr0079692	R	21	0
-input2.bam	FBtr0079692	R	22	0
-input2.bam	FBtr0079693	F	15	4
-input2.bam	FBtr0079693	F	16	2
-input2.bam	FBtr0079693	F	17	0
-input2.bam	FBtr0079693	F	18	1
-input2.bam	FBtr0079693	F	19	0
-input2.bam	FBtr0079693	F	20	2
-input2.bam	FBtr0079693	R	15	0
-input2.bam	FBtr0079693	R	16	0
-input2.bam	FBtr0079693	R	17	0
-input2.bam	FBtr0079693	R	18	0
-input2.bam	FBtr0079693	R	19	0
-input2.bam	FBtr0079693	R	20	0
-input2.bam	FBtr0079694	F	15	2
-input2.bam	FBtr0079694	F	16	0
-input2.bam	FBtr0079694	F	17	1
-input2.bam	FBtr0079694	F	18	2
-input2.bam	FBtr0079694	F	19	1
-input2.bam	FBtr0079694	R	15	0
-input2.bam	FBtr0079694	R	16	0
-input2.bam	FBtr0079694	R	17	0
-input2.bam	FBtr0079694	R	18	0
-input2.bam	FBtr0079694	R	19	0
-input2.bam	FBtr0079702	F	15	2
-input2.bam	FBtr0079702	F	16	0
-input2.bam	FBtr0079702	F	17	1
-input2.bam	FBtr0079702	F	18	1
-input2.bam	FBtr0079702	R	15	0
-input2.bam	FBtr0079702	R	16	0
-input2.bam	FBtr0079702	R	17	0
-input2.bam	FBtr0079702	R	18	0
-input2.bam	FBtr0079728	F	15	3
-input2.bam	FBtr0079728	F	16	1
-input2.bam	FBtr0079728	F	17	1
-input2.bam	FBtr0079728	F	18	1
-input2.bam	FBtr0079728	R	15	0
-input2.bam	FBtr0079728	R	16	0
-input2.bam	FBtr0079728	R	17	0
-input2.bam	FBtr0079728	R	18	0
-input2.bam	FBtr0079729	F	15	1
-input2.bam	FBtr0079729	F	16	2
-input2.bam	FBtr0079729	F	17	1
-input2.bam	FBtr0079729	R	15	0
-input2.bam	FBtr0079729	R	16	0
-input2.bam	FBtr0079729	R	17	0
-input2.bam	FBtr0079752	F	17	1
-input2.bam	FBtr0079752	F	18	0
-input2.bam	FBtr0079752	F	19	0
-input2.bam	FBtr0079752	F	20	0
-input2.bam	FBtr0079752	F	21	0
-input2.bam	FBtr0079752	F	22	0
-input2.bam	FBtr0079752	F	23	0
-input2.bam	FBtr0079752	F	24	1
-input2.bam	FBtr0079752	R	17	0
-input2.bam	FBtr0079752	R	18	0
-input2.bam	FBtr0079752	R	19	0
-input2.bam	FBtr0079752	R	20	0
-input2.bam	FBtr0079752	R	21	0
-input2.bam	FBtr0079752	R	22	0
-input2.bam	FBtr0079752	R	23	0
-input2.bam	FBtr0079752	R	24	0
-input2.bam	FBtr0079820	F	15	27
-input2.bam	FBtr0079820	F	16	10
-input2.bam	FBtr0079820	F	17	7
-input2.bam	FBtr0079820	F	18	8
-input2.bam	FBtr0079820	F	19	25
-input2.bam	FBtr0079820	F	20	24
-input2.bam	FBtr0079820	F	21	7
-input2.bam	FBtr0079820	F	22	1
-input2.bam	FBtr0079820	R	15	0
-input2.bam	FBtr0079820	R	16	0
-input2.bam	FBtr0079820	R	17	0
-input2.bam	FBtr0079820	R	18	0
-input2.bam	FBtr0079820	R	19	0
-input2.bam	FBtr0079820	R	20	0
-input2.bam	FBtr0079820	R	21	0
-input2.bam	FBtr0079820	R	22	0
-input2.bam	FBtr0080609	F	17	2
-input2.bam	FBtr0080609	F	18	1
-input2.bam	FBtr0080609	F	19	2
-input2.bam	FBtr0080609	F	20	0
-input2.bam	FBtr0080609	F	21	0
-input2.bam	FBtr0080609	F	22	1
-input2.bam	FBtr0080609	F	23	1
-input2.bam	FBtr0080609	F	24	0
-input2.bam	FBtr0080609	F	25	1
-input2.bam	FBtr0080609	R	17	0
-input2.bam	FBtr0080609	R	18	0
-input2.bam	FBtr0080609	R	19	0
-input2.bam	FBtr0080609	R	20	0
-input2.bam	FBtr0080609	R	21	0
-input2.bam	FBtr0080609	R	22	0
-input2.bam	FBtr0080609	R	23	0
-input2.bam	FBtr0080609	R	24	0
-input2.bam	FBtr0080609	R	25	0
-input2.bam	FBtr0080644	F	15	8
-input2.bam	FBtr0080644	R	15	0
-input2.bam	FBtr0080646	F	15	10
-input2.bam	FBtr0080646	F	16	1
-input2.bam	FBtr0080646	F	17	0
-input2.bam	FBtr0080646	F	18	0
-input2.bam	FBtr0080646	F	19	0
-input2.bam	FBtr0080646	F	20	0
-input2.bam	FBtr0080646	F	21	1
-input2.bam	FBtr0080646	R	15	0
-input2.bam	FBtr0080646	R	16	0
-input2.bam	FBtr0080646	R	17	0
-input2.bam	FBtr0080646	R	18	0
-input2.bam	FBtr0080646	R	19	0
-input2.bam	FBtr0080646	R	20	0
-input2.bam	FBtr0080646	R	21	0
-input2.bam	FBtr0080647	F	15	9
-input2.bam	FBtr0080647	F	16	2
-input2.bam	FBtr0080647	F	17	0
-input2.bam	FBtr0080647	F	18	1
-input2.bam	FBtr0080647	R	15	0
-input2.bam	FBtr0080647	R	16	0
-input2.bam	FBtr0080647	R	17	0
-input2.bam	FBtr0080647	R	18	0
-input2.bam	FBtr0080660	F	15	11
-input2.bam	FBtr0080660	R	15	0
-input2.bam	FBtr0080663	F	15	26
-input2.bam	FBtr0080663	F	16	14
-input2.bam	FBtr0080663	F	17	14
-input2.bam	FBtr0080663	F	18	26
-input2.bam	FBtr0080663	F	19	9
-input2.bam	FBtr0080663	F	20	7
-input2.bam	FBtr0080663	F	21	4
-input2.bam	FBtr0080663	F	22	5
-input2.bam	FBtr0080663	F	23	0
-input2.bam	FBtr0080663	F	24	1
-input2.bam	FBtr0080663	R	15	0
-input2.bam	FBtr0080663	R	16	0
-input2.bam	FBtr0080663	R	17	0
-input2.bam	FBtr0080663	R	18	0
-input2.bam	FBtr0080663	R	19	0
-input2.bam	FBtr0080663	R	20	0
-input2.bam	FBtr0080663	R	21	0
-input2.bam	FBtr0080663	R	22	0
-input2.bam	FBtr0080663	R	23	0
-input2.bam	FBtr0080663	R	24	0
-input2.bam	FBtr0080664	F	15	165
-input2.bam	FBtr0080664	F	16	59
-input2.bam	FBtr0080664	F	17	20
-input2.bam	FBtr0080664	F	18	75
-input2.bam	FBtr0080664	F	19	24
-input2.bam	FBtr0080664	F	20	21
-input2.bam	FBtr0080664	F	21	8
-input2.bam	FBtr0080664	F	22	4
-input2.bam	FBtr0080664	F	23	4
-input2.bam	FBtr0080664	F	24	0
-input2.bam	FBtr0080664	F	25	3
-input2.bam	FBtr0080664	F	26	4
-input2.bam	FBtr0080664	R	15	0
-input2.bam	FBtr0080664	R	16	0
-input2.bam	FBtr0080664	R	17	0
-input2.bam	FBtr0080664	R	18	0
-input2.bam	FBtr0080664	R	19	0
-input2.bam	FBtr0080664	R	20	0
-input2.bam	FBtr0080664	R	21	0
-input2.bam	FBtr0080664	R	22	1
-input2.bam	FBtr0080664	R	23	1
-input2.bam	FBtr0080664	R	24	0
-input2.bam	FBtr0080664	R	25	0
-input2.bam	FBtr0080664	R	26	0
--- a/small_rna_maps.py	Thu Nov 22 20:05:32 2018 -0500
+++ b/small_rna_maps.py	Sun Nov 25 06:56:40 2018 -0500
@@ -22,11 +22,21 @@
     the_parser.add_argument('--bed', dest='bed', required=False,
                             help='Name of bed output must be specified\
                             if --cluster option used')
-    the_parser.add_argument('--bed_skipcluster', dest='bed_skipcluster',
-                            required=False, type=int, default=0,
+    the_parser.add_argument('--bed_skipsize', dest='bed_skipsize',
+                            required=False, type=int, default=1,
                             help='Skip clusters of size equal or less than\
                             specified integer in the bed output. \
-                            Default = 1')
+                            Default = 0, not skipping')
+    the_parser.add_argument('--bed_skipdensity', dest='bed_skipdensity',
+                            required=False, type=float, default=0,
+                            help='Skip clusters of density equal or less than\
+                            specified float number in the bed output. \
+                            Default = 0, not skipping')
+    the_parser.add_argument('--bed_skipcounts', dest='bed_skipcounts',
+                            required=False, type=int, default=1,
+                            help='Skip clusters of size equal or less than\
+                            specified integer in the bed output. \
+                            Default = 0, not skipping')
     the_parser.add_argument('--outputs', nargs='+', action='store',
                             help='list of two output paths (only two)')
     the_parser.add_argument('-M', '--plot_methods', nargs='+', action='store',
@@ -107,7 +117,7 @@
                                     [read_length, ...]}
         and returns a map_dictionary with structure:
         {(chromosome,read_position,polarity):
-            ([read_length, ...], [start_clust, end_clust])}
+            [*counts*, [start_clust, end_clust]]}
         '''
         clustered_dic = defaultdict(list)
         for chrom in self.chromosomes:
@@ -277,7 +287,7 @@
                     line = [str(i) for i in line]
                     out.write('\t'.join(line) + '\n')
 
-    def write_cluster_table(self, clustered_dic, out, bedpath, skip):
+    def write_cluster_table(self, clustered_dic, out, bedpath):
         '''
         Writer of a tabular file
         Dataset, Chromosome, Chrom_length, Coordinate, Polarity,
@@ -285,32 +295,45 @@
         out is an *open* file handler
         bed is an a file handler internal to the function
         '''
+        def filterCluster(size, count, density):
+            if size < args.bed_skipsize:
+                return False
+            if count < args.bed_skipcounts:
+                return False
+            if density <= args.bed_skipdensity:
+                return False
+            return True
         bed = open(bedpath, 'w')
+        clusterid = 0
         for key in sorted(clustered_dic):
             start = clustered_dic[key][1][0]
             end = clustered_dic[key][1][1]
             size = end - start + 1
+            read_count = clustered_dic[key][0]
             if self.nostrand:
                 polarity = '.'
             elif key[2] == 'F':
                 polarity = '+'
             else:
                 polarity = '-'
-            density = float(clustered_dic[key][0]) / size
+            density = float(read_count) / size
             line = [self.sample_name, key[0], self.chromosomes[key[0]],
-                    key[1], key[2], clustered_dic[key][0],
+                    key[1], key[2], read_count,
                     str(start) + "-" + str(end), str(size), str(density)]
             line = [str(i) for i in line]
-            if size > skip:
-                bedline = [key[0], str(start-1), str(end), 'cluster',
-                           str(clustered_dic[key][0]), polarity]
+            out.write('\t'.join(line) + '\n')
+            if filterCluster(size, read_count, density):
+                clusterid += 1
+                name = 'cluster_' + str(clusterid)
+                bedline = [key[0], str(start-1), str(end), name,
+                           str(read_count), polarity, str(density)]
                 bed.write('\t'.join(bedline) + '\n')
-            out.write('\t'.join(line) + '\n')
+        print("number of reported clusters:", clusterid)
         bed.close()
 
 
 def main(inputs, samples, methods, outputs, minsize, maxsize, cluster,
-         nostrand, bedfile=None, bed_skipcluster=0):
+         nostrand, bedfile=None, bed_skipsize=0):
     for method, output in zip(methods, outputs):
         out = open(output, 'w')
         if method == 'Size':
@@ -333,8 +356,7 @@
                      "Size": mapobj.compute_size,
                      "cluster": mapobj.write_cluster_table}
             if cluster:
-                token["cluster"](mapobj.map_dict, out, bedfile,
-                                 bed_skipcluster)
+                token["cluster"](mapobj.map_dict, out, bedfile)
             else:
                 token[method](mapobj.map_dict, out)
         out.close()
@@ -347,5 +369,4 @@
         args.sample_names = [name + '_' + str(i) for
                              i, name in enumerate(args.sample_names)]
     main(args.inputs, args.sample_names, args.plot_methods, args.outputs,
-         args.minsize, args.maxsize, args.cluster, args.nostrand, args.bed,
-         args.bed_skipcluster)
+         args.minsize, args.maxsize, args.cluster, args.nostrand, args.bed)
--- a/small_rna_maps.xml	Thu Nov 22 20:05:32 2018 -0500
+++ b/small_rna_maps.xml	Sun Nov 25 06:56:40 2018 -0500
@@ -1,4 +1,4 @@
-<tool id="small_rna_maps" name="small_rna_maps" version="2.9.1">
+<tool id="small_rna_maps" name="small_rna_maps" version="2.10.0">
   <description></description>
   <requirements>
         <requirement type="package" version="1.11.2=py27_0">numpy</requirement>
@@ -39,7 +39,9 @@
                   --outputs '$output_tab'
                   --cluster ${plots_options.cluster}
                   --bed '$output_bed'
-                  --bed_skipcluster ${plots_options.skip_cluster}
+                  --bed_skipsize ${plots_options.skip_size}
+                  --bed_skipcounts ${plots_options.skip_counts}
+                  --bed_skipdensity ${plots_options.skip_density}
                   ${plots_options.strandness} &&
               #else:
                   --plot_methods '${plots_options.first_plot}'
@@ -127,12 +129,16 @@
         </when>
         <when value="cluster">
             <param name="first_plot" type="hidden" value="Counts"/>
-            <param name="cluster" type="integer" label="Aggregation distance in nucleotides" value="1"
+            <param name="cluster" type="integer" label="Clustering distance in nucleotides" value="1"
                    help="Sets the distance (in nt) below which reads are clustered to a single median position" />
             <param name="strandness" argument="--nostrand" type="boolean" truevalue="--nostrand" falsevalue="" checked="false"
                    label="Ignore polarity of reads ?" help="Set if you wish to cluster reads regardless of whether they are forward or reverse"/>
-            <param name="skip_cluster" type="integer" label="do not report cluster equal or less than the specified number of nucleotides" value="0"
-                   help="Set the number of nucleotides in the cluster for which and below which a cluster is not reported in the bed output. Set to 0 (default) reports all including singlets" />
+            <param name="skip_size" type="integer" label="do not report clusters whose size is less than the specified value" value="1"
+                   help="Cluster size threshod (in nucleotides) for reporting. Set to 1 (default) reports all clusters, including singlets" />
+            <param name="skip_counts" type="integer" label="do not report cluster with a number of reads lower than the specified value" value="1"
+                   help="Number-of-reads threshod (in nucleotides) for cluster reporting. Set to 1 (default) reports all clusters, irrespective of their counts" />
+             <param name="skip_density" type="float" label="do not report cluster with density equal or less than the specified value" value="0"
+                   help="Density threshod (in reads per nucleotides) for reporting. Set to 0 (default) reports all cluster densities" />
         </when>
     </conditional>
     <conditional name="ylimits_cond">
@@ -200,7 +206,7 @@
             <param name="plots_options_selector" value="cluster" />
             <param name="first_plot" value="Counts" />
             <param name="cluster" value="5" />
-            <param name="skip_cluster" value="0" />
+            <param name="skip_size" value="1" />
             <param name="strandness" value="false" />
             <output file="clustering.tab" name="output_tab" />
             <output file="clustering.pdf" name="output_pdf" />
@@ -216,13 +222,13 @@
             <param name="plots_options_selector" value="cluster" />
             <param name="first_plot" value="Counts" />
             <param name="cluster" value="5" />
-            <param name="skip_cluster" value="0" />
+            <param name="skip_size" value="1" />
             <param name="strandness" value="true" />
             <output file="clustering_unstranded.tab" name="output_tab" />
             <output file="clustering_unstranded.pdf" name="output_pdf" />
             <output file="bed2.bed" name="output_bed" />
         </test>
-        <test> <!-- 3.1 -->
+        <test> <!-- 4 -->
             <repeat name="series">
                 <param name="inputs" value="input1.bam" ftype="bam" />
                 <param name="normalization" value="1.0" />
@@ -232,13 +238,49 @@
             <param name="plots_options_selector" value="cluster" />
             <param name="first_plot" value="Counts" />
             <param name="cluster" value="5" />
-            <param name="skip_cluster" value="1" />
+            <param name="skip_size" value="2" />
             <param name="strandness" value="false" />
             <output file="clustering.tab" name="output_tab" />
             <output file="clustering.pdf" name="output_pdf" />
             <output file="bed3.bed" name="output_bed" />
         </test>
-        <test> <!-- 4 -->
+        <test> <!-- 5 -->
+            <repeat name="series">
+                <param name="inputs" value="input1.bam" ftype="bam" />
+                <param name="normalization" value="1.0" />
+            </repeat>
+            <param name="minsize" value="0" />
+            <param name="maxsize" value="10000" />
+            <param name="plots_options_selector" value="cluster" />
+            <param name="first_plot" value="Counts" />
+            <param name="cluster" value="5" />
+            <param name="skip_size" value="2" />
+            <param name="skip_counts" value="3" />
+            <param name="skip_density" value="1.0" />
+            <param name="strandness" value="false" />
+            <output file="clustering.tab" name="output_tab" />
+            <output file="clustering.pdf" name="output_pdf" />
+            <output file="bed4.bed" name="output_bed" />
+        </test>
+        <test> <!-- 6 -->
+            <repeat name="series">
+                <param name="inputs" value="input1.bam" ftype="bam" />
+                <param name="normalization" value="1.0" />
+            </repeat>
+            <param name="minsize" value="0" />
+            <param name="maxsize" value="10000" />
+            <param name="plots_options_selector" value="cluster" />
+            <param name="first_plot" value="Counts" />
+            <param name="cluster" value="5" />
+            <param name="skip_size" value="2" />
+            <param name="skip_counts" value="2" />
+            <param name="skip_density" value="0.4" />
+            <param name="strandness" value="true" />
+            <output file="clustering_unstranded.tab" name="output_tab" />
+            <output file="clustering_unstranded.pdf" name="output_pdf" />
+            <output file="bed5.bed" name="output_bed" />
+        </test>
+        <test> <!-- 7 -->
             <repeat name="series">
                 <param name="inputs" value="input1.bam" ftype="bam" />
                 <param name="normalization" value="1.0" />
@@ -250,7 +292,7 @@
             <output file="input1_min20_max30_size.tab" name="output_tab" />
             <output file="input1_min20_max30_single_plot_size.pdf" name="output_pdf" />
         </test>
-        <test> <!-- 5 -->
+        <test> <!-- 8 -->
             <repeat name="series">
                 <param name="inputs" value="input1.bam" ftype="bam" />
                 <param name="normalization" value="1.0" />
@@ -262,7 +304,7 @@
             <output file="input1_mean.tab" name="output_tab" />
             <output file="input1__single_plot_mean.pdf" name="output_pdf" />
         </test>
-        <test> <!-- 6 -->
+        <test> <!-- 9 -->
             <repeat name="series">
                 <param name="inputs" value="input1.bam" ftype="bam" />
                 <param name="normalization" value="1.0" />
@@ -274,7 +316,7 @@
             <output file="input1_median.tab" name="output_tab" />
             <output file="input1_single_plot_median.pdf" name="output_pdf" />
         </test>
-        <test> <!-- 7 -->
+        <test> <!-- 10 -->
             <repeat name="series">
                 <param name="inputs" value="input1.bam" ftype="bam" />
                 <param name="normalization" value="1.0" />
@@ -290,7 +332,7 @@
             <output file="input1_input2_norm_1_2_counts.tab" name="output_tab" />
             <output file="input1_input2_norm_1_2_single_plot_counts.pdf" name="output_pdf" />
         </test>
-        <test> <!-- 8 -->
+        <test> <!-- 11 -->
             <repeat name="series">
                 <param name="inputs" value="input1.bam" ftype="bam" />
                 <param name="normalization" value="1.0" />
@@ -311,7 +353,7 @@
             <output file="input1_input2_size.tab" name="extra_output_tab" />
             <output file="input1_input2_double_plot_counts_size_ylimneg5_5.pdf" name="output_pdf" />
         </test>
-        <test> <!-- 9 -->
+        <test> <!-- 12 -->
             <repeat name="series">
                 <param name="inputs" value="input_single_chr.bam" ftype="bam" />
                 <param name="normalization" value="1.0" />
@@ -343,7 +385,7 @@
             <output file="input_single_chr_x_6_single_plot_coverage.tab" name="output_tab" />
             <output file="input_single_chr_x_6_single_plot_coverage.pdf" name="output_pdf" />
         </test>
-        <test> <!-- 10 -->
+        <test> <!-- 13 -->
             <repeat name="series">
                 <param name="inputs" value="input1.bam" ftype="bam" />
                 <param name="normalization" value="1.0" />
@@ -360,7 +402,7 @@
             <output file="size.tab" name="output_tab" />
             <output file="global_nomerge.pdf" name="output_pdf" />
         </test>
-        <test> <!-- 11 -->
+        <test> <!-- 14 -->
             <repeat name="series">
                 <param name="inputs" value="input1.bam" ftype="bam" />
                 <param name="normalization" value="1.0" />
--- a/test-data/bed1.bed	Thu Nov 22 20:05:32 2018 -0500
+++ b/test-data/bed1.bed	Sun Nov 25 06:56:40 2018 -0500
@@ -1,118 +1,84 @@
-FBtr0070001	0	1	cluster	1	+
-FBtr0070001	6	18	cluster	14	+
-FBtr0070001	26	34	cluster	42	+
-FBtr0070001	71	72	cluster	0	+
-FBtr0070533	0	1	cluster	1	+
-FBtr0070533	11	38	cluster	23	+
-FBtr0070533	71	72	cluster	0	+
-FBtr0070603	0	42	cluster	68	+
-FBtr0070603	50	56	cluster	2	+
-FBtr0070603	71	72	cluster	0	+
-FBtr0070604	0	1	cluster	1	+
-FBtr0070604	17	22	cluster	2	+
-FBtr0070604	29	32	cluster	36	+
-FBtr0070604	56	57	cluster	1	+
-FBtr0070604	71	72	cluster	0	+
-FBtr0070911	0	1	cluster	0	+
-FBtr0070911	14	15	cluster	1	+
-FBtr0070911	37	38	cluster	1	+
-FBtr0070911	72	73	cluster	0	+
-FBtr0078490	0	1	cluster	0	+
-FBtr0078490	12	18	cluster	4	+
-FBtr0078490	24	28	cluster	3	+
-FBtr0078490	37	38	cluster	1	+
-FBtr0078490	71	72	cluster	0	+
-FBtr0078580	0	31	cluster	1102	+
-FBtr0078580	51	52	cluster	2	+
-FBtr0078580	71	72	cluster	0	+
-FBtr0078790	0	1	cluster	1	+
-FBtr0078790	16	17	cluster	2	+
-FBtr0078790	32	33	cluster	1	+
-FBtr0078790	41	52	cluster	9	+
-FBtr0078790	68	69	cluster	1	-
-FBtr0078790	72	73	cluster	0	+
-FBtr0079064	0	3	cluster	2	+
-FBtr0079064	32	33	cluster	1	+
-FBtr0079064	51	52	cluster	1	+
-FBtr0079064	71	72	cluster	0	+
-FBtr0079090	0	1	cluster	2	+
-FBtr0079090	25	26	cluster	1	+
-FBtr0079090	32	33	cluster	1	+
-FBtr0079090	52	53	cluster	1	+
-FBtr0079090	55	56	cluster	1	-
-FBtr0079090	71	72	cluster	0	+
-FBtr0079338	0	1	cluster	0	+
-FBtr0079338	11	17	cluster	5	+
-FBtr0079338	24	25	cluster	1	+
-FBtr0079338	41	46	cluster	10	+
-FBtr0079338	72	73	cluster	0	+
-FBtr0079528	0	18	cluster	97	+
-FBtr0079528	27	28	cluster	1	+
-FBtr0079528	34	37	cluster	3	+
-FBtr0079528	50	51	cluster	5	+
-FBtr0079528	70	71	cluster	0	+
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-FBtr0079596	52	54	cluster	4	+
-FBtr0079596	72	73	cluster	0	+
-FBtr0079677	0	5	cluster	2	+
-FBtr0079677	51	53	cluster	2	+
-FBtr0079677	71	72	cluster	0	+
-FBtr0079690	0	1	cluster	1	+
-FBtr0079690	21	27	cluster	2	+
-FBtr0079690	32	33	cluster	2	+
-FBtr0079690	71	72	cluster	0	+
-FBtr0079692	0	1	cluster	3	+
-FBtr0079692	17	18	cluster	1	+
-FBtr0079692	24	25	cluster	1	+
-FBtr0079692	31	32	cluster	1	+
-FBtr0079692	72	73	cluster	0	+
-FBtr0079693	0	1	cluster	5	+
-FBtr0079693	24	25	cluster	1	+
-FBtr0079693	71	72	cluster	0	+
-FBtr0079694	0	1	cluster	5	+
-FBtr0079694	17	18	cluster	1	+
-FBtr0079694	51	52	cluster	1	+
-FBtr0079694	71	72	cluster	0	+
-FBtr0079702	0	1	cluster	1	+
-FBtr0079702	18	19	cluster	2	+
-FBtr0079702	55	56	cluster	1	+
-FBtr0079702	71	72	cluster	0	+
-FBtr0079728	0	1	cluster	2	+
-FBtr0079728	7	8	cluster	1	+
-FBtr0079728	18	19	cluster	1	+
-FBtr0079728	32	33	cluster	3	+
-FBtr0079728	55	56	cluster	1	+
-FBtr0079728	71	72	cluster	0	+
-FBtr0079729	0	1	cluster	1	+
-FBtr0079729	12	13	cluster	1	+
-FBtr0079729	51	57	cluster	2	+
-FBtr0079729	71	72	cluster	0	+
-FBtr0079752	0	1	cluster	2	+
-FBtr0079752	6	12	cluster	2	+
-FBtr0079752	32	33	cluster	2	+
-FBtr0079752	51	52	cluster	2	+
-FBtr0079752	71	72	cluster	0	+
-FBtr0079820	0	1	cluster	0	+
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-FBtr0079820	73	74	cluster	0	+
-FBtr0080609	0	20	cluster	60	+
-FBtr0080609	41	42	cluster	1	+
-FBtr0080609	50	52	cluster	2	+
-FBtr0080609	71	72	cluster	0	+
-FBtr0080644	0	12	cluster	6	+
-FBtr0080644	71	72	cluster	0	+
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-FBtr0080646	71	72	cluster	0	+
-FBtr0080647	0	12	cluster	10	+
-FBtr0080647	71	72	cluster	0	+
-FBtr0080660	0	7	cluster	7	+
-FBtr0080660	71	72	cluster	0	+
-FBtr0080663	0	17	cluster	102	+
-FBtr0080663	25	26	cluster	1	+
-FBtr0080663	31	32	cluster	2	+
-FBtr0080663	49	51	cluster	10	+
-FBtr0080663	70	71	cluster	0	+
-FBtr0080664	0	21	cluster	108	+
-FBtr0080664	27	38	cluster	9	+
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-FBtr0080664	70	71	cluster	0	+
+FBtr0070001	0	1	cluster_1	1	+	1.0
+FBtr0070001	6	18	cluster_2	14	+	1.16666666667
+FBtr0070001	26	34	cluster_3	42	+	5.25
+FBtr0070533	0	1	cluster_4	1	+	1.0
+FBtr0070533	11	38	cluster_5	23	+	0.851851851852
+FBtr0070603	0	42	cluster_6	68	+	1.61904761905
+FBtr0070603	50	56	cluster_7	2	+	0.333333333333
+FBtr0070604	0	1	cluster_8	1	+	1.0
+FBtr0070604	17	22	cluster_9	2	+	0.4
+FBtr0070604	29	32	cluster_10	36	+	12.0
+FBtr0070604	56	57	cluster_11	1	+	1.0
+FBtr0070911	14	15	cluster_12	1	+	1.0
+FBtr0070911	37	38	cluster_13	1	+	1.0
+FBtr0078490	12	18	cluster_14	4	+	0.666666666667
+FBtr0078490	24	28	cluster_15	3	+	0.75
+FBtr0078490	37	38	cluster_16	1	+	1.0
+FBtr0078580	0	31	cluster_17	1102	+	35.5483870968
+FBtr0078580	51	52	cluster_18	2	+	2.0
+FBtr0078790	0	1	cluster_19	1	+	1.0
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+FBtr0078790	41	52	cluster_22	9	+	0.818181818182
+FBtr0078790	68	69	cluster_23	1	-	1.0
+FBtr0079064	0	3	cluster_24	2	+	0.666666666667
+FBtr0079064	32	33	cluster_25	1	+	1.0
+FBtr0079064	51	52	cluster_26	1	+	1.0
+FBtr0079090	0	1	cluster_27	2	+	2.0
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+FBtr0079090	32	33	cluster_29	1	+	1.0
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+FBtr0079090	55	56	cluster_31	1	-	1.0
+FBtr0079338	11	17	cluster_32	5	+	0.833333333333
+FBtr0079338	24	25	cluster_33	1	+	1.0
+FBtr0079338	41	46	cluster_34	10	+	2.0
+FBtr0079528	0	18	cluster_35	97	+	5.38888888889
+FBtr0079528	27	28	cluster_36	1	+	1.0
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+FBtr0079596	0	19	cluster_39	148	+	7.78947368421
+FBtr0079596	52	54	cluster_40	4	+	2.0
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+FBtr0079692	0	1	cluster_46	3	+	3.0
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+FBtr0079692	24	25	cluster_48	1	+	1.0
+FBtr0079692	31	32	cluster_49	1	+	1.0
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+FBtr0079729	0	1	cluster_63	1	+	1.0
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+FBtr0079752	6	12	cluster_67	2	+	0.333333333333
+FBtr0079752	32	33	cluster_68	2	+	2.0
+FBtr0079752	51	52	cluster_69	2	+	2.0
+FBtr0079820	44	56	cluster_70	13	+	1.08333333333
+FBtr0080609	0	20	cluster_71	60	+	3.0
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+FBtr0080644	0	12	cluster_74	6	+	0.5
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+FBtr0080647	0	12	cluster_76	10	+	0.833333333333
+FBtr0080660	0	7	cluster_77	7	+	1.0
+FBtr0080663	0	17	cluster_78	102	+	6.0
+FBtr0080663	25	26	cluster_79	1	+	1.0
+FBtr0080663	31	32	cluster_80	2	+	2.0
+FBtr0080663	49	51	cluster_81	10	+	5.0
+FBtr0080664	0	21	cluster_82	108	+	5.14285714286
+FBtr0080664	27	38	cluster_83	9	+	0.818181818182
+FBtr0080664	49	56	cluster_84	11	+	1.57142857143
--- a/test-data/bed2.bed	Thu Nov 22 20:05:32 2018 -0500
+++ b/test-data/bed2.bed	Sun Nov 25 06:56:40 2018 -0500
@@ -1,116 +1,83 @@
-FBtr0070001	0	1	cluster	1	.
-FBtr0070001	6	18	cluster	14	.
-FBtr0070001	26	34	cluster	42	.
-FBtr0070001	71	72	cluster	0	.
-FBtr0070533	0	1	cluster	1	.
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-FBtr0070533	71	72	cluster	0	.
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-FBtr0070604	0	1	cluster	1	.
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-FBtr0078490	0	1	cluster	0	.
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-FBtr0078490	71	72	cluster	0	.
-FBtr0078580	0	31	cluster	1102	.
-FBtr0078580	51	52	cluster	2	.
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-FBtr0078790	0	1	cluster	1	.
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+FBtr0070001	0	1	cluster_1	1	.	1.0
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+FBtr0070603	0	42	cluster_6	68	.	1.61904761905
+FBtr0070603	50	56	cluster_7	2	.	0.333333333333
+FBtr0070604	0	1	cluster_8	1	.	1.0
+FBtr0070604	17	22	cluster_9	2	.	0.4
+FBtr0070604	29	32	cluster_10	36	.	12.0
+FBtr0070604	56	57	cluster_11	1	.	1.0
+FBtr0070911	14	15	cluster_12	1	.	1.0
+FBtr0070911	37	38	cluster_13	1	.	1.0
+FBtr0078490	12	18	cluster_14	4	.	0.666666666667
+FBtr0078490	24	28	cluster_15	3	.	0.75
+FBtr0078490	37	38	cluster_16	1	.	1.0
+FBtr0078580	0	31	cluster_17	1102	.	35.5483870968
+FBtr0078580	51	52	cluster_18	2	.	2.0
+FBtr0078790	0	1	cluster_19	1	.	1.0
+FBtr0078790	16	17	cluster_20	2	.	2.0
+FBtr0078790	32	33	cluster_21	1	.	1.0
+FBtr0078790	41	52	cluster_22	9	.	0.818181818182
+FBtr0078790	68	73	cluster_23	1	.	0.2
+FBtr0079064	0	3	cluster_24	2	.	0.666666666667
+FBtr0079064	32	33	cluster_25	1	.	1.0
+FBtr0079064	51	52	cluster_26	1	.	1.0
+FBtr0079090	0	1	cluster_27	2	.	2.0
+FBtr0079090	25	26	cluster_28	1	.	1.0
+FBtr0079090	32	33	cluster_29	1	.	1.0
+FBtr0079090	52	56	cluster_30	2	.	0.5
+FBtr0079338	11	17	cluster_31	5	.	0.833333333333
+FBtr0079338	24	25	cluster_32	1	.	1.0
+FBtr0079338	41	46	cluster_33	10	.	2.0
+FBtr0079528	0	18	cluster_34	97	.	5.38888888889
+FBtr0079528	27	28	cluster_35	1	.	1.0
+FBtr0079528	34	37	cluster_36	3	.	1.0
+FBtr0079528	50	51	cluster_37	5	.	5.0
+FBtr0079596	0	19	cluster_38	148	.	7.78947368421
+FBtr0079596	52	54	cluster_39	4	.	2.0
+FBtr0079677	0	5	cluster_40	2	.	0.4
+FBtr0079677	51	53	cluster_41	2	.	1.0
+FBtr0079690	0	1	cluster_42	1	.	1.0
+FBtr0079690	21	27	cluster_43	2	.	0.333333333333
+FBtr0079690	32	33	cluster_44	2	.	2.0
+FBtr0079692	0	1	cluster_45	3	.	3.0
+FBtr0079692	17	18	cluster_46	1	.	1.0
+FBtr0079692	24	25	cluster_47	1	.	1.0
+FBtr0079692	31	32	cluster_48	1	.	1.0
+FBtr0079693	0	1	cluster_49	5	.	5.0
+FBtr0079693	24	25	cluster_50	1	.	1.0
+FBtr0079694	0	1	cluster_51	5	.	5.0
+FBtr0079694	17	18	cluster_52	1	.	1.0
+FBtr0079694	51	52	cluster_53	1	.	1.0
+FBtr0079702	0	1	cluster_54	1	.	1.0
+FBtr0079702	18	19	cluster_55	2	.	2.0
+FBtr0079702	55	56	cluster_56	1	.	1.0
+FBtr0079728	0	1	cluster_57	2	.	2.0
+FBtr0079728	7	8	cluster_58	1	.	1.0
+FBtr0079728	18	19	cluster_59	1	.	1.0
+FBtr0079728	32	33	cluster_60	3	.	3.0
+FBtr0079728	55	56	cluster_61	1	.	1.0
+FBtr0079729	0	1	cluster_62	1	.	1.0
+FBtr0079729	12	13	cluster_63	1	.	1.0
+FBtr0079729	51	57	cluster_64	2	.	0.333333333333
+FBtr0079752	0	1	cluster_65	2	.	2.0
+FBtr0079752	6	12	cluster_66	2	.	0.333333333333
+FBtr0079752	32	33	cluster_67	2	.	2.0
+FBtr0079752	51	52	cluster_68	2	.	2.0
+FBtr0079820	44	56	cluster_69	13	.	1.08333333333
+FBtr0080609	0	20	cluster_70	60	.	3.0
+FBtr0080609	41	42	cluster_71	1	.	1.0
+FBtr0080609	50	52	cluster_72	2	.	1.0
+FBtr0080644	0	12	cluster_73	6	.	0.5
+FBtr0080646	0	7	cluster_74	3	.	0.428571428571
+FBtr0080647	0	12	cluster_75	10	.	0.833333333333
+FBtr0080660	0	7	cluster_76	7	.	1.0
+FBtr0080663	0	17	cluster_77	102	.	6.0
+FBtr0080663	25	26	cluster_78	1	.	1.0
+FBtr0080663	31	32	cluster_79	2	.	2.0
+FBtr0080663	49	51	cluster_80	10	.	5.0
+FBtr0080664	0	21	cluster_81	108	.	5.14285714286
+FBtr0080664	27	38	cluster_82	9	.	0.818181818182
+FBtr0080664	49	56	cluster_83	11	.	1.57142857143
--- a/test-data/bed3.bed	Thu Nov 22 20:05:32 2018 -0500
+++ b/test-data/bed3.bed	Sun Nov 25 06:56:40 2018 -0500
@@ -1,35 +1,35 @@
-FBtr0070001	6	18	cluster	14	+
-FBtr0070001	26	34	cluster	42	+
-FBtr0070533	11	38	cluster	23	+
-FBtr0070603	0	42	cluster	68	+
-FBtr0070603	50	56	cluster	2	+
-FBtr0070604	17	22	cluster	2	+
-FBtr0070604	29	32	cluster	36	+
-FBtr0078490	12	18	cluster	4	+
-FBtr0078490	24	28	cluster	3	+
-FBtr0078580	0	31	cluster	1102	+
-FBtr0078790	41	52	cluster	9	+
-FBtr0079064	0	3	cluster	2	+
-FBtr0079338	11	17	cluster	5	+
-FBtr0079338	41	46	cluster	10	+
-FBtr0079528	0	18	cluster	97	+
-FBtr0079528	34	37	cluster	3	+
-FBtr0079596	0	19	cluster	148	+
-FBtr0079596	52	54	cluster	4	+
-FBtr0079677	0	5	cluster	2	+
-FBtr0079677	51	53	cluster	2	+
-FBtr0079690	21	27	cluster	2	+
-FBtr0079729	51	57	cluster	2	+
-FBtr0079752	6	12	cluster	2	+
-FBtr0079820	44	56	cluster	13	+
-FBtr0080609	0	20	cluster	60	+
-FBtr0080609	50	52	cluster	2	+
-FBtr0080644	0	12	cluster	6	+
-FBtr0080646	0	7	cluster	3	+
-FBtr0080647	0	12	cluster	10	+
-FBtr0080660	0	7	cluster	7	+
-FBtr0080663	0	17	cluster	102	+
-FBtr0080663	49	51	cluster	10	+
-FBtr0080664	0	21	cluster	108	+
-FBtr0080664	27	38	cluster	9	+
-FBtr0080664	49	56	cluster	11	+
+FBtr0070001	6	18	cluster_1	14	+	1.16666666667
+FBtr0070001	26	34	cluster_2	42	+	5.25
+FBtr0070533	11	38	cluster_3	23	+	0.851851851852
+FBtr0070603	0	42	cluster_4	68	+	1.61904761905
+FBtr0070603	50	56	cluster_5	2	+	0.333333333333
+FBtr0070604	17	22	cluster_6	2	+	0.4
+FBtr0070604	29	32	cluster_7	36	+	12.0
+FBtr0078490	12	18	cluster_8	4	+	0.666666666667
+FBtr0078490	24	28	cluster_9	3	+	0.75
+FBtr0078580	0	31	cluster_10	1102	+	35.5483870968
+FBtr0078790	41	52	cluster_11	9	+	0.818181818182
+FBtr0079064	0	3	cluster_12	2	+	0.666666666667
+FBtr0079338	11	17	cluster_13	5	+	0.833333333333
+FBtr0079338	41	46	cluster_14	10	+	2.0
+FBtr0079528	0	18	cluster_15	97	+	5.38888888889
+FBtr0079528	34	37	cluster_16	3	+	1.0
+FBtr0079596	0	19	cluster_17	148	+	7.78947368421
+FBtr0079596	52	54	cluster_18	4	+	2.0
+FBtr0079677	0	5	cluster_19	2	+	0.4
+FBtr0079677	51	53	cluster_20	2	+	1.0
+FBtr0079690	21	27	cluster_21	2	+	0.333333333333
+FBtr0079729	51	57	cluster_22	2	+	0.333333333333
+FBtr0079752	6	12	cluster_23	2	+	0.333333333333
+FBtr0079820	44	56	cluster_24	13	+	1.08333333333
+FBtr0080609	0	20	cluster_25	60	+	3.0
+FBtr0080609	50	52	cluster_26	2	+	1.0
+FBtr0080644	0	12	cluster_27	6	+	0.5
+FBtr0080646	0	7	cluster_28	3	+	0.428571428571
+FBtr0080647	0	12	cluster_29	10	+	0.833333333333
+FBtr0080660	0	7	cluster_30	7	+	1.0
+FBtr0080663	0	17	cluster_31	102	+	6.0
+FBtr0080663	49	51	cluster_32	10	+	5.0
+FBtr0080664	0	21	cluster_33	108	+	5.14285714286
+FBtr0080664	27	38	cluster_34	9	+	0.818181818182
+FBtr0080664	49	56	cluster_35	11	+	1.57142857143
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/bed4.bed	Sun Nov 25 06:56:40 2018 -0500
@@ -0,0 +1,15 @@
+FBtr0070001	6	18	cluster_1	14	+	1.16666666667
+FBtr0070001	26	34	cluster_2	42	+	5.25
+FBtr0070603	0	42	cluster_3	68	+	1.61904761905
+FBtr0070604	29	32	cluster_4	36	+	12.0
+FBtr0078580	0	31	cluster_5	1102	+	35.5483870968
+FBtr0079338	41	46	cluster_6	10	+	2.0
+FBtr0079528	0	18	cluster_7	97	+	5.38888888889
+FBtr0079596	0	19	cluster_8	148	+	7.78947368421
+FBtr0079596	52	54	cluster_9	4	+	2.0
+FBtr0079820	44	56	cluster_10	13	+	1.08333333333
+FBtr0080609	0	20	cluster_11	60	+	3.0
+FBtr0080663	0	17	cluster_12	102	+	6.0
+FBtr0080663	49	51	cluster_13	10	+	5.0
+FBtr0080664	0	21	cluster_14	108	+	5.14285714286
+FBtr0080664	49	56	cluster_15	11	+	1.57142857143
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/bed5.bed	Sun Nov 25 06:56:40 2018 -0500
@@ -0,0 +1,30 @@
+FBtr0070001	6	18	cluster_1	14	.	1.16666666667
+FBtr0070001	26	34	cluster_2	42	.	5.25
+FBtr0070533	11	38	cluster_3	23	.	0.851851851852
+FBtr0070603	0	42	cluster_4	68	.	1.61904761905
+FBtr0070604	29	32	cluster_5	36	.	12.0
+FBtr0078490	12	18	cluster_6	4	.	0.666666666667
+FBtr0078490	24	28	cluster_7	3	.	0.75
+FBtr0078580	0	31	cluster_8	1102	.	35.5483870968
+FBtr0078790	41	52	cluster_9	9	.	0.818181818182
+FBtr0079064	0	3	cluster_10	2	.	0.666666666667
+FBtr0079090	52	56	cluster_11	2	.	0.5
+FBtr0079338	11	17	cluster_12	5	.	0.833333333333
+FBtr0079338	41	46	cluster_13	10	.	2.0
+FBtr0079528	0	18	cluster_14	97	.	5.38888888889
+FBtr0079528	34	37	cluster_15	3	.	1.0
+FBtr0079596	0	19	cluster_16	148	.	7.78947368421
+FBtr0079596	52	54	cluster_17	4	.	2.0
+FBtr0079677	51	53	cluster_18	2	.	1.0
+FBtr0079820	44	56	cluster_19	13	.	1.08333333333
+FBtr0080609	0	20	cluster_20	60	.	3.0
+FBtr0080609	50	52	cluster_21	2	.	1.0
+FBtr0080644	0	12	cluster_22	6	.	0.5
+FBtr0080646	0	7	cluster_23	3	.	0.428571428571
+FBtr0080647	0	12	cluster_24	10	.	0.833333333333
+FBtr0080660	0	7	cluster_25	7	.	1.0
+FBtr0080663	0	17	cluster_26	102	.	6.0
+FBtr0080663	49	51	cluster_27	10	.	5.0
+FBtr0080664	0	21	cluster_28	108	.	5.14285714286
+FBtr0080664	27	38	cluster_29	9	.	0.818181818182
+FBtr0080664	49	56	cluster_30	11	.	1.57142857143