# HG changeset patch
# User artbio
# Date 1570178033 14400
# Node ID 8b56955927844683cd306331f5c20b57f811cad1
# Parent  14adf24603b64ee74d3df5dd8b1a5e60145a2b7a
"planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/small_rna_maps commit c3d728b98db4987821feae40952d9797c97eaf5a"

diff -r 14adf24603b6 -r 8b5695592784 delphine
--- a/delphine	Thu Apr 25 12:49:05 2019 -0400
+++ /dev/null	Thu Jan 01 00:00:00 1970 +0000
@@ -1,30 +0,0 @@
------BEGIN RSA PRIVATE KEY-----
-Proc-Type: 4,ENCRYPTED
-DEK-Info: AES-128-CBC,0F428118B5D165772A9B414AC1C31A31
-
-EjQgREw0ka00AK6us4JLeTo/M3/w74KeyrZLbuGvh5PC5LcrMjfCGC3tTbnD33MP
-lZNFdPBw3aGfhweRCThTtB9v+GxRYgYvv7IWoOycaCoAaR+KnYnalgQLgQUhSO5Q
-wCuoY4sI6liM5RmpScezlGjTcOr3FFDhtz+roeGI3Te/3KJX/B3nQHc8LeG3Xu8C
-yp76PGJQnZUAag+SUSMcxV/qYBnfqiTmtPZASyTtkNwgEHwjZcM+z/vAXit2rl8C
-LlU/IjD/82olYM2UTFVlW32DInlgX7oUjo7pKl1cFJpkCfbGKWg1MsdVPNb4uE0h
-KuDdOmHQFPluQUJEKPmhO9NfJypR+/7zJVZQSe20APBxZ3teGPR1Adk1A9VJQWyj
-imgvoJmnwFj+Xds5I0clin0nJle0WSZfj5nfV7UEgJGxXaszKV1bIbUVRRJY5FfL
-6meAo6AvgMRJD4fZp7CP8GtYJGLfD0vpBIMvj1Aqzu5OtxvGF5zls15K+NvVQIfg
-UyQxwJbVePqEdv5+vDum3faapYIjjNF/gbQ09U7iTmcTXTWyrJEB47Q7AKnBc/SV
-j7nR6/1HaKwpY5LmPp+CgoX7lm6L9B9hxFYZCiUsNSyl4nmjPDEvSST6yLNOYKgA
-2Ia12aKlakqm8p3rjJ2OVDyPO5kbKw0r7u3yqjdfnd/kL1mdM2//0ti9k1kEl928
-qeaYfKUXCXjVuG5a3m4KHIOXEKd/5hnkRaG+IZxR2ZBt/M4n+Uj1Rivw0FL503TL
-ms71iJ5YonaPoAgrj7mcKIWTHmcSARwUihuUaZGG9N0WX3S3A+z0HCoqWFHXyIEs
-UfsqVMiucTuHyeNwQLTYmvN5EB8r54c4NyACVt6nsnYz87CtLqmXpQDBMGUjXUYA
-dpIIXSml0WYoQiLw0jSrp18UlWEidaED2aukax6LNTHYrN0GQ+GCVoIYiVpAGQDX
-2LJ/VCVSYVStLZjOSRBWHskbLeXfUkQaoPQEL+5K/c7a0c4IJxSluirKufZ7xn3+
-LrUiyomy71kijrrpY1rIHwcAIHPxXI3avJMxq5tZYR5wEqQkH0eWsy8yew73ejyQ
-rY+k7nWVFaE/oW0cBo814HJ70BuFhaRJ2siEQvs5RpXevlnhyfZao1X/J7ZUg9l+
-+TUVcEGUwCyagIEQebzp38Y9rQfh3ek3j8TM5vxIuFxkdVNtH+pgF09vX/QyqLcE
-CwybkCYyOjEYveGCaHTHedih+YqCGbiBQvw+b14AnZBWivusnXHogpY9WJTis+eW
-6EXrdt05ExqypISt/B6EnZWEv3Tc80TPcvf64Z61PabY8f2lvbq2mPaKKxYEvuuy
-5R6qfX28zaRFp3MOQ753DAwNWwdwha1ZIglndLw3M9CAI2emn+4yLod7h6b/hl4Y
-TNAtcD4zUWH9KkN7diPjIc2W2njZ00bu1TcT/jShHiTdY7i9w7VrUWcvQISrpbCS
-TpYLYqY10D9SLO7lPU27jFGe5Mcbsw2JFkJjG+JwEIkLzoIDDSFL3RIkZ+Ql1nDT
-hk9pxr+k+V0dyp+Ul2TGFZC/vIB22a9sBRodNYzxKDtbRjNrDEqEe8QzQwfI/if5
------END RSA PRIVATE KEY-----
diff -r 14adf24603b6 -r 8b5695592784 delphine.pub
--- a/delphine.pub	Thu Apr 25 12:49:05 2019 -0400
+++ /dev/null	Thu Jan 01 00:00:00 1970 +0000
@@ -1,1 +0,0 @@
-ssh-rsa AAAAB3NzaC1yc2EAAAADAQABAAABAQCutrZRQSP+aGOboaDMnrazTziyuI9iAeK9CVtgOCKFzg5c+oBj7pkGPiYsWnJpYWn8vHyhAk/VSCmPHHlGR3aNMKg1x1NKNQXzodljdnXfAMs012rZnI4r8Gl/ww6rhVFfbxptVIKNdZxlLBDBxjvWJ6G6Y8MqGPCpFQsFWtKPRgYl9A8UNqtReindJKOc/TuIFFeHvuPMSU7m2ZqCMuKGCjbWPU9RwvPuYURxYiTXP7ooMZLRD1tbc+vQUGIMDX+gXpQ7ntonZVtDGxC5qQJeUKVtGgp1RKKJ4Zbje5UNd47E3TiJQPMgJJL8TqjjHcFQBqtQVyzBJdVlnHxCgnoB chris@GED-Server
diff -r 14adf24603b6 -r 8b5695592784 small_rna_maps.py
--- a/small_rna_maps.py	Thu Apr 25 12:49:05 2019 -0400
+++ b/small_rna_maps.py	Fri Oct 04 04:33:53 2019 -0400
@@ -243,9 +243,9 @@
                         map_dictionary[(chrom, pos+1, 'F')] = []
         for key in map_dictionary:
             coverage = self.bam_object.count_coverage(
-                                                reference=key[0],
+                                                contig=key[0],
                                                 start=key[1]-1,
-                                                end=key[1],
+                                                stop=key[1],
                                                 quality_threshold=quality)
             """ Add the 4 coverage values """
             coverage = [sum(x) for x in zip(*coverage)]
@@ -298,7 +298,7 @@
                     sizeness[size] += sizedic[chrom][polarity][size]
             Strandbias = strandness['F'] + strandness['R']
             if Strandbias:
-                Strandbias = strandness['F'] / float(Strandbias)
+                Strandbias = round(strandness['F'] / float(Strandbias), 2)
             else:
                 Strandbias = 2
             Mean = numpy.mean(sizeness.values())
@@ -313,10 +313,10 @@
                     try:
                         line = [self.sample_name, chrom, polarity, size,
                                 sizedic[chrom][polarity][size],
-                                Strandbias, sizeness[size]]
+                                Strandbias, round(sizeness[size], 3)]
                     except KeyError:
                         line = [self.sample_name, chrom, polarity, size, 0,
-                                Strandbias, sizeness[size]]
+                                Strandbias, round(sizeness[size], 3)]
                     line = [str(i) for i in line]
                     out.write('\t'.join(line) + '\n')
 
diff -r 14adf24603b6 -r 8b5695592784 small_rna_maps.xml
--- a/small_rna_maps.xml	Thu Apr 25 12:49:05 2019 -0400
+++ b/small_rna_maps.xml	Fri Oct 04 04:33:53 2019 -0400
@@ -1,13 +1,15 @@
-<tool id="small_rna_maps" name="small_rna_maps" version="2.14.0">
+<tool id="small_rna_maps" name="small_rna_maps" version="2.15.0">
   <description></description>
   <requirements>
         <requirement type="package" version="1.11.2=py27_0">numpy</requirement>
-        <requirement type="package" version="0.11.2.1=py27_0">pysam</requirement>
-        <requirement type="package" version="1.3.2=r3.3.2_0">r-optparse</requirement>
-        <requirement type="package" version="0.6_28=r3.3.2_0">r-latticeextra</requirement>
-        <requirement type="package" version="2.2.1=r3.3.2_0">r-gridextra</requirement>
-        <requirement type="package" version="1.4.2=r3.3.2_0">r-reshape2</requirement>
+        <requirement type="package" version="0.15.3=py27hda2845c_1">pysam</requirement>
+        <requirement type="package" version="1.6.4=r36h6115d3f_0">r-optparse</requirement>
+        <requirement type="package" version="0.6_28=r36h6115d3f_1002">r-latticeextra</requirement>
+        <requirement type="package" version="2.3=r36h6115d3f_1002">r-gridextra</requirement>
+        <requirement type="package" version="1.4.3=r36h29659fb_0">r-reshape2</requirement>
         <requirement type="package" version="0.6.6">sambamba</requirement>
+        <requirement type="package" version="1.9=h10a08f8_12">samtools</requirement>
+        <requirement type="package" version="64.2=he1b5a44_1">icu</requirement>
   </requirements>
   <stdio>
       <exit_code range="1:" level="fatal" description="Tool exception" />
@@ -79,7 +81,9 @@
     <param name="inputs" type="data" format="bam" label="Select a alignment files to parse" multiple="true"
            help="maps from these bam inputs will be collected in a single pdf output" />
     <param name="normalization" type="text" label="Enter a size/normalization factor."
-        help="Enter normalisation factors separated by space eg [0.75 1.23 1.1], no normalization if no values" value="1"/>
+           help="Enter normalisation factors separated by space eg [0.75 1.23 1.1], no normalization if no values,
+                 ignored if a single sample"
+           value="1"/>
     <param name="minsize" type="integer" label="Minimal size of reads for inclusion in analysis"
            value="19" help="default value: 19" />
     <param name="maxsize" type="integer" label="Maximal size of reads for inclusion in analysis"
diff -r 14adf24603b6 -r 8b5695592784 test-data/clustering.pdf
Binary file test-data/clustering.pdf has changed
diff -r 14adf24603b6 -r 8b5695592784 test-data/clustering_unstranded.pdf
Binary file test-data/clustering_unstranded.pdf has changed
diff -r 14adf24603b6 -r 8b5695592784 test-data/global_merge.pdf
Binary file test-data/global_merge.pdf has changed
diff -r 14adf24603b6 -r 8b5695592784 test-data/global_nomerge.pdf
Binary file test-data/global_nomerge.pdf has changed
diff -r 14adf24603b6 -r 8b5695592784 test-data/input1__single_plot_mean.pdf
Binary file test-data/input1__single_plot_mean.pdf has changed
diff -r 14adf24603b6 -r 8b5695592784 test-data/input1_input2_double_plot_counts_size_ylimneg5_5.pdf
Binary file test-data/input1_input2_double_plot_counts_size_ylimneg5_5.pdf has changed
diff -r 14adf24603b6 -r 8b5695592784 test-data/input1_input2_norm_1_2_single_plot_counts.pdf
Binary file test-data/input1_input2_norm_1_2_single_plot_counts.pdf has changed
diff -r 14adf24603b6 -r 8b5695592784 test-data/input1_input2_size.tab
--- a/test-data/input1_input2_size.tab	Thu Apr 25 12:49:05 2019 -0400
+++ b/test-data/input1_input2_size.tab	Fri Oct 04 04:33:53 2019 -0400
@@ -1,694 +1,694 @@
 # Dataset	Chromosome	Polarity	Size	Counts	Strandness	z-score
-input1.bam	FBtr0070001	F	19	1	1.0	-0.448696330732
-input1.bam	FBtr0070001	F	20	4	1.0	-0.104347983891
-input1.bam	FBtr0070001	F	21	4	1.0	-0.104347983891
-input1.bam	FBtr0070001	F	22	29	1.0	2.76522157312
-input1.bam	FBtr0070001	F	23	15	1.0	1.15826262119
-input1.bam	FBtr0070001	F	24	1	1.0	-0.448696330732
-input1.bam	FBtr0070001	F	25	0	1.0	-0.563479113013
-input1.bam	FBtr0070001	F	26	0	1.0	-0.563479113013
-input1.bam	FBtr0070001	F	27	0	1.0	-0.563479113013
-input1.bam	FBtr0070001	F	28	0	1.0	-0.563479113013
-input1.bam	FBtr0070001	F	29	0	1.0	-0.563479113013
-input1.bam	FBtr0070533	F	19	3	1.0	1.27519650491
-input1.bam	FBtr0070533	F	20	2	1.0	0.536924844171
-input1.bam	FBtr0070533	F	21	2	1.0	0.536924844171
-input1.bam	FBtr0070533	F	22	4	1.0	2.01346816564
-input1.bam	FBtr0070533	F	23	2	1.0	0.536924844171
-input1.bam	FBtr0070533	F	24	0	1.0	-0.9396184773
-input1.bam	FBtr0070533	F	25	1	1.0	-0.201346816564
-input1.bam	FBtr0070533	F	26	0	1.0	-0.9396184773
-input1.bam	FBtr0070533	F	27	0	1.0	-0.9396184773
-input1.bam	FBtr0070533	F	28	0	1.0	-0.9396184773
-input1.bam	FBtr0070533	F	29	0	1.0	-0.9396184773
-input1.bam	FBtr0070603	F	19	1	1.0	-0.874157276122
-input1.bam	FBtr0070603	F	20	6	1.0	0.906533471533
-input1.bam	FBtr0070603	F	21	3	1.0	-0.16188097706
-input1.bam	FBtr0070603	F	22	3	1.0	-0.16188097706
-input1.bam	FBtr0070603	F	23	10	1.0	2.33108606966
-input1.bam	FBtr0070603	F	24	2	1.0	-0.518019126591
-input1.bam	FBtr0070603	F	25	5	1.0	0.550395322002
-input1.bam	FBtr0070603	F	26	5	1.0	0.550395322002
-input1.bam	FBtr0070603	F	27	3	1.0	-0.16188097706
-input1.bam	FBtr0070603	F	28	0	1.0	-1.23029542565
-input1.bam	FBtr0070603	F	29	0	1.0	-1.23029542565
-input1.bam	FBtr0070604	F	19	2	1.0	-0.185793425342
-input1.bam	FBtr0070604	F	20	0	1.0	-0.477754522308
-input1.bam	FBtr0070604	F	21	1	1.0	-0.331773973825
-input1.bam	FBtr0070604	F	22	23	1.0	2.8797980928
-input1.bam	FBtr0070604	F	23	10	1.0	0.982050962522
-input1.bam	FBtr0070604	F	24	0	1.0	-0.477754522308
-input1.bam	FBtr0070604	F	25	0	1.0	-0.477754522308
-input1.bam	FBtr0070604	F	26	0	1.0	-0.477754522308
-input1.bam	FBtr0070604	F	27	0	1.0	-0.477754522308
-input1.bam	FBtr0070604	F	28	0	1.0	-0.477754522308
-input1.bam	FBtr0070604	F	29	0	1.0	-0.477754522308
-input1.bam	FBtr0070911	F	19	0	1.0	-0.316227766017
-input1.bam	FBtr0070911	F	20	0	1.0	-0.316227766017
-input1.bam	FBtr0070911	F	21	1	1.0	3.16227766017
-input1.bam	FBtr0070911	F	22	0	1.0	-0.316227766017
-input1.bam	FBtr0070911	F	23	0	1.0	-0.316227766017
-input1.bam	FBtr0070911	F	24	0	1.0	-0.316227766017
-input1.bam	FBtr0070911	F	25	0	1.0	-0.316227766017
-input1.bam	FBtr0070911	F	26	0	1.0	-0.316227766017
-input1.bam	FBtr0070911	F	27	0	1.0	-0.316227766017
-input1.bam	FBtr0070911	F	28	0	1.0	-0.316227766017
-input1.bam	FBtr0070911	F	29	0	1.0	-0.316227766017
-input1.bam	FBtr0078490	F	19	0	1.0	-0.316227766017
-input1.bam	FBtr0078490	F	20	0	1.0	-0.316227766017
-input1.bam	FBtr0078490	F	21	0	1.0	-0.316227766017
-input1.bam	FBtr0078490	F	22	0	1.0	-0.316227766017
-input1.bam	FBtr0078490	F	23	1	1.0	3.16227766017
-input1.bam	FBtr0078490	F	24	0	1.0	-0.316227766017
-input1.bam	FBtr0078490	F	25	0	1.0	-0.316227766017
-input1.bam	FBtr0078490	F	26	0	1.0	-0.316227766017
-input1.bam	FBtr0078490	F	27	0	1.0	-0.316227766017
-input1.bam	FBtr0078490	F	28	0	1.0	-0.316227766017
-input1.bam	FBtr0078490	F	29	0	1.0	-0.316227766017
-input1.bam	FBtr0078580	F	19	8	1.0	-0.450200695898
-input1.bam	FBtr0078580	F	20	9	1.0	-0.436595729813
-input1.bam	FBtr0078580	F	21	5	1.0	-0.491015594153
-input1.bam	FBtr0078580	F	22	13	1.0	-0.382175865474
-input1.bam	FBtr0078580	F	23	5	1.0	-0.491015594153
-input1.bam	FBtr0078580	F	24	180	1.0	1.88985347069
-input1.bam	FBtr0078580	F	25	212	1.0	2.32521238541
-input1.bam	FBtr0078580	F	26	1	1.0	-0.545435458492
-input1.bam	FBtr0078580	F	27	2	1.0	-0.531830492407
-input1.bam	FBtr0078580	F	28	17	1.0	-0.327756001135
-input1.bam	FBtr0078580	F	29	0	1.0	-0.559040424577
-input1.bam	FBtr0078790	F	19	2	1.0	1.54713186939
-input1.bam	FBtr0078790	F	20	2	1.0	1.54713186939
-input1.bam	FBtr0078790	F	21	0	1.0	-0.721994872381
-input1.bam	FBtr0078790	F	22	2	1.0	1.54713186939
-input1.bam	FBtr0078790	F	23	1	1.0	0.412568498504
-input1.bam	FBtr0078790	F	24	0	1.0	-0.721994872381
-input1.bam	FBtr0078790	F	25	0	1.0	-0.721994872381
-input1.bam	FBtr0078790	F	26	0	1.0	-0.721994872381
-input1.bam	FBtr0078790	F	27	0	1.0	-0.721994872381
-input1.bam	FBtr0078790	F	28	0	1.0	-0.721994872381
-input1.bam	FBtr0078790	F	29	0	1.0	-0.721994872381
-input1.bam	FBtr0079064	F	19	0	1.0	-0.316227766017
-input1.bam	FBtr0079064	F	20	0	1.0	-0.316227766017
-input1.bam	FBtr0079064	F	21	1	1.0	3.16227766017
-input1.bam	FBtr0079064	F	22	0	1.0	-0.316227766017
-input1.bam	FBtr0079064	F	23	0	1.0	-0.316227766017
-input1.bam	FBtr0079064	F	24	0	1.0	-0.316227766017
-input1.bam	FBtr0079064	F	25	0	1.0	-0.316227766017
-input1.bam	FBtr0079064	F	26	0	1.0	-0.316227766017
-input1.bam	FBtr0079064	F	27	0	1.0	-0.316227766017
-input1.bam	FBtr0079064	F	28	0	1.0	-0.316227766017
-input1.bam	FBtr0079064	F	29	0	1.0	-0.316227766017
-input1.bam	FBtr0079090	F	19	0	0.666666666667	-0.612372435696
-input1.bam	FBtr0079090	F	20	0	0.666666666667	-0.612372435696
-input1.bam	FBtr0079090	F	21	0	0.666666666667	1.63299316186
-input1.bam	FBtr0079090	F	22	0	0.666666666667	-0.612372435696
-input1.bam	FBtr0079090	F	23	0	0.666666666667	-0.612372435696
-input1.bam	FBtr0079090	F	24	1	0.666666666667	1.63299316186
-input1.bam	FBtr0079090	F	25	0	0.666666666667	-0.612372435696
-input1.bam	FBtr0079090	F	26	0	0.666666666667	-0.612372435696
-input1.bam	FBtr0079090	F	27	0	0.666666666667	-0.612372435696
-input1.bam	FBtr0079090	F	28	1	0.666666666667	1.63299316186
-input1.bam	FBtr0079090	F	29	0	0.666666666667	-0.612372435696
-input1.bam	FBtr0079090	R	19	0	0.666666666667	-0.612372435696
-input1.bam	FBtr0079090	R	20	0	0.666666666667	-0.612372435696
-input1.bam	FBtr0079090	R	21	1	0.666666666667	1.63299316186
-input1.bam	FBtr0079090	R	22	0	0.666666666667	-0.612372435696
-input1.bam	FBtr0079090	R	23	0	0.666666666667	-0.612372435696
-input1.bam	FBtr0079090	R	24	0	0.666666666667	1.63299316186
-input1.bam	FBtr0079090	R	25	0	0.666666666667	-0.612372435696
-input1.bam	FBtr0079090	R	26	0	0.666666666667	-0.612372435696
-input1.bam	FBtr0079090	R	27	0	0.666666666667	-0.612372435696
-input1.bam	FBtr0079090	R	28	0	0.666666666667	1.63299316186
-input1.bam	FBtr0079090	R	29	0	0.666666666667	-0.612372435696
-input1.bam	FBtr0079338	F	19	1	1.0	0.0496291666985
-input1.bam	FBtr0079338	F	20	0	1.0	-0.496291666985
-input1.bam	FBtr0079338	F	21	3	1.0	1.14147083407
-input1.bam	FBtr0079338	F	22	6	1.0	2.77923333512
-input1.bam	FBtr0079338	F	23	0	1.0	-0.496291666985
-input1.bam	FBtr0079338	F	24	0	1.0	-0.496291666985
-input1.bam	FBtr0079338	F	25	0	1.0	-0.496291666985
-input1.bam	FBtr0079338	F	26	0	1.0	-0.496291666985
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+input2.bam	FBtr0079690	F	29	0	1.0	-0.442
+input2.bam	FBtr0079692	F	19	0	1.0	-0.471
+input2.bam	FBtr0079692	F	20	0	1.0	-0.471
+input2.bam	FBtr0079692	F	21	1	1.0	2.121
+input2.bam	FBtr0079692	F	22	1	1.0	2.121
+input2.bam	FBtr0079692	F	23	0	1.0	-0.471
+input2.bam	FBtr0079692	F	24	0	1.0	-0.471
+input2.bam	FBtr0079692	F	25	0	1.0	-0.471
+input2.bam	FBtr0079692	F	26	0	1.0	-0.471
+input2.bam	FBtr0079692	F	27	0	1.0	-0.471
+input2.bam	FBtr0079692	F	28	0	1.0	-0.471
+input2.bam	FBtr0079692	F	29	0	1.0	-0.471
+input2.bam	FBtr0079693	F	19	0	1.0	-0.316
+input2.bam	FBtr0079693	F	20	2	1.0	3.162
+input2.bam	FBtr0079693	F	21	0	1.0	-0.316
+input2.bam	FBtr0079693	F	22	0	1.0	-0.316
+input2.bam	FBtr0079693	F	23	0	1.0	-0.316
+input2.bam	FBtr0079693	F	24	0	1.0	-0.316
+input2.bam	FBtr0079693	F	25	0	1.0	-0.316
+input2.bam	FBtr0079693	F	26	0	1.0	-0.316
+input2.bam	FBtr0079693	F	27	0	1.0	-0.316
+input2.bam	FBtr0079693	F	28	0	1.0	-0.316
+input2.bam	FBtr0079693	F	29	0	1.0	-0.316
+input2.bam	FBtr0079694	F	19	1	1.0	3.162
+input2.bam	FBtr0079694	F	20	0	1.0	-0.316
+input2.bam	FBtr0079694	F	21	0	1.0	-0.316
+input2.bam	FBtr0079694	F	22	0	1.0	-0.316
+input2.bam	FBtr0079694	F	23	0	1.0	-0.316
+input2.bam	FBtr0079694	F	24	0	1.0	-0.316
+input2.bam	FBtr0079694	F	25	0	1.0	-0.316
+input2.bam	FBtr0079694	F	26	0	1.0	-0.316
+input2.bam	FBtr0079694	F	27	0	1.0	-0.316
+input2.bam	FBtr0079694	F	28	0	1.0	-0.316
+input2.bam	FBtr0079694	F	29	0	1.0	-0.316
+input2.bam	FBtr0079702	F	19	0	2	0.0
+input2.bam	FBtr0079702	F	20	0	2	0.0
+input2.bam	FBtr0079702	F	21	0	2	0.0
+input2.bam	FBtr0079702	F	22	0	2	0.0
+input2.bam	FBtr0079702	F	23	0	2	0.0
+input2.bam	FBtr0079702	F	24	0	2	0.0
+input2.bam	FBtr0079702	F	25	0	2	0.0
+input2.bam	FBtr0079702	F	26	0	2	0.0
+input2.bam	FBtr0079702	F	27	0	2	0.0
+input2.bam	FBtr0079702	F	28	0	2	0.0
+input2.bam	FBtr0079702	F	29	0	2	0.0
+input2.bam	FBtr0079728	F	19	0	2	0.0
+input2.bam	FBtr0079728	F	20	0	2	0.0
+input2.bam	FBtr0079728	F	21	0	2	0.0
+input2.bam	FBtr0079728	F	22	0	2	0.0
+input2.bam	FBtr0079728	F	23	0	2	0.0
+input2.bam	FBtr0079728	F	24	0	2	0.0
+input2.bam	FBtr0079728	F	25	0	2	0.0
+input2.bam	FBtr0079728	F	26	0	2	0.0
+input2.bam	FBtr0079728	F	27	0	2	0.0
+input2.bam	FBtr0079728	F	28	0	2	0.0
+input2.bam	FBtr0079728	F	29	0	2	0.0
+input2.bam	FBtr0079729	F	19	0	2	0.0
+input2.bam	FBtr0079729	F	20	0	2	0.0
+input2.bam	FBtr0079729	F	21	0	2	0.0
+input2.bam	FBtr0079729	F	22	0	2	0.0
+input2.bam	FBtr0079729	F	23	0	2	0.0
+input2.bam	FBtr0079729	F	24	0	2	0.0
+input2.bam	FBtr0079729	F	25	0	2	0.0
+input2.bam	FBtr0079729	F	26	0	2	0.0
+input2.bam	FBtr0079729	F	27	0	2	0.0
+input2.bam	FBtr0079729	F	28	0	2	0.0
+input2.bam	FBtr0079729	F	29	0	2	0.0
+input2.bam	FBtr0079752	F	19	0	1.0	-0.316
+input2.bam	FBtr0079752	F	20	0	1.0	-0.316
+input2.bam	FBtr0079752	F	21	0	1.0	-0.316
+input2.bam	FBtr0079752	F	22	0	1.0	-0.316
+input2.bam	FBtr0079752	F	23	0	1.0	-0.316
+input2.bam	FBtr0079752	F	24	1	1.0	3.162
+input2.bam	FBtr0079752	F	25	0	1.0	-0.316
+input2.bam	FBtr0079752	F	26	0	1.0	-0.316
+input2.bam	FBtr0079752	F	27	0	1.0	-0.316
+input2.bam	FBtr0079752	F	28	0	1.0	-0.316
+input2.bam	FBtr0079752	F	29	0	1.0	-0.316
+input2.bam	FBtr0079820	F	19	25	1.0	2.126
+input2.bam	FBtr0079820	F	20	24	1.0	2.019
+input2.bam	FBtr0079820	F	21	7	1.0	0.195
+input2.bam	FBtr0079820	F	22	1	1.0	-0.449
+input2.bam	FBtr0079820	F	23	0	1.0	-0.556
+input2.bam	FBtr0079820	F	24	0	1.0	-0.556
+input2.bam	FBtr0079820	F	25	0	1.0	-0.556
+input2.bam	FBtr0079820	F	26	0	1.0	-0.556
+input2.bam	FBtr0079820	F	27	0	1.0	-0.556
+input2.bam	FBtr0079820	F	28	0	1.0	-0.556
+input2.bam	FBtr0079820	F	29	0	1.0	-0.556
+input2.bam	FBtr0080609	F	19	2	1.0	2.357
+input2.bam	FBtr0080609	F	20	0	1.0	-0.693
+input2.bam	FBtr0080609	F	21	0	1.0	-0.693
+input2.bam	FBtr0080609	F	22	1	1.0	0.832
+input2.bam	FBtr0080609	F	23	1	1.0	0.832
+input2.bam	FBtr0080609	F	24	0	1.0	-0.693
+input2.bam	FBtr0080609	F	25	1	1.0	0.832
+input2.bam	FBtr0080609	F	26	0	1.0	-0.693
+input2.bam	FBtr0080609	F	27	0	1.0	-0.693
+input2.bam	FBtr0080609	F	28	0	1.0	-0.693
+input2.bam	FBtr0080609	F	29	0	1.0	-0.693
+input2.bam	FBtr0080644	F	19	0	2	0.0
+input2.bam	FBtr0080644	F	20	0	2	0.0
+input2.bam	FBtr0080644	F	21	0	2	0.0
+input2.bam	FBtr0080644	F	22	0	2	0.0
+input2.bam	FBtr0080644	F	23	0	2	0.0
+input2.bam	FBtr0080644	F	24	0	2	0.0
+input2.bam	FBtr0080644	F	25	0	2	0.0
+input2.bam	FBtr0080644	F	26	0	2	0.0
+input2.bam	FBtr0080644	F	27	0	2	0.0
+input2.bam	FBtr0080644	F	28	0	2	0.0
+input2.bam	FBtr0080644	F	29	0	2	0.0
+input2.bam	FBtr0080646	F	19	0	1.0	-0.316
+input2.bam	FBtr0080646	F	20	0	1.0	-0.316
+input2.bam	FBtr0080646	F	21	1	1.0	3.162
+input2.bam	FBtr0080646	F	22	0	1.0	-0.316
+input2.bam	FBtr0080646	F	23	0	1.0	-0.316
+input2.bam	FBtr0080646	F	24	0	1.0	-0.316
+input2.bam	FBtr0080646	F	25	0	1.0	-0.316
+input2.bam	FBtr0080646	F	26	0	1.0	-0.316
+input2.bam	FBtr0080646	F	27	0	1.0	-0.316
+input2.bam	FBtr0080646	F	28	0	1.0	-0.316
+input2.bam	FBtr0080646	F	29	0	1.0	-0.316
+input2.bam	FBtr0080647	F	19	0	2	0.0
+input2.bam	FBtr0080647	F	20	0	2	0.0
+input2.bam	FBtr0080647	F	21	0	2	0.0
+input2.bam	FBtr0080647	F	22	0	2	0.0
+input2.bam	FBtr0080647	F	23	0	2	0.0
+input2.bam	FBtr0080647	F	24	0	2	0.0
+input2.bam	FBtr0080647	F	25	0	2	0.0
+input2.bam	FBtr0080647	F	26	0	2	0.0
+input2.bam	FBtr0080647	F	27	0	2	0.0
+input2.bam	FBtr0080647	F	28	0	2	0.0
+input2.bam	FBtr0080647	F	29	0	2	0.0
+input2.bam	FBtr0080660	F	19	0	2	0.0
+input2.bam	FBtr0080660	F	20	0	2	0.0
+input2.bam	FBtr0080660	F	21	0	2	0.0
+input2.bam	FBtr0080660	F	22	0	2	0.0
+input2.bam	FBtr0080660	F	23	0	2	0.0
+input2.bam	FBtr0080660	F	24	0	2	0.0
+input2.bam	FBtr0080660	F	25	0	2	0.0
+input2.bam	FBtr0080660	F	26	0	2	0.0
+input2.bam	FBtr0080660	F	27	0	2	0.0
+input2.bam	FBtr0080660	F	28	0	2	0.0
+input2.bam	FBtr0080660	F	29	0	2	0.0
+input2.bam	FBtr0080663	F	19	9	1.0	2.093
+input2.bam	FBtr0080663	F	20	7	1.0	1.463
+input2.bam	FBtr0080663	F	21	4	1.0	0.516
+input2.bam	FBtr0080663	F	22	5	1.0	0.832
+input2.bam	FBtr0080663	F	23	0	1.0	-0.746
+input2.bam	FBtr0080663	F	24	1	1.0	-0.43
+input2.bam	FBtr0080663	F	25	0	1.0	-0.746
+input2.bam	FBtr0080663	F	26	0	1.0	-0.746
+input2.bam	FBtr0080663	F	27	0	1.0	-0.746
+input2.bam	FBtr0080663	F	28	0	1.0	-0.746
+input2.bam	FBtr0080663	F	29	0	1.0	-0.746
+input2.bam	FBtr0080664	F	19	24	0.97	2.194
+input2.bam	FBtr0080664	F	20	21	0.97	1.821
+input2.bam	FBtr0080664	F	21	8	0.97	0.204
+input2.bam	FBtr0080664	F	22	4	0.97	-0.17
+input2.bam	FBtr0080664	F	23	4	0.97	-0.17
+input2.bam	FBtr0080664	F	24	0	0.97	-0.792
+input2.bam	FBtr0080664	F	25	3	0.97	-0.419
+input2.bam	FBtr0080664	F	26	4	0.97	-0.294
+input2.bam	FBtr0080664	F	27	0	0.97	-0.792
+input2.bam	FBtr0080664	F	28	0	0.97	-0.792
+input2.bam	FBtr0080664	F	29	0	0.97	-0.792
+input2.bam	FBtr0080664	R	19	0	0.97	2.194
+input2.bam	FBtr0080664	R	20	0	0.97	1.821
+input2.bam	FBtr0080664	R	21	0	0.97	0.204
+input2.bam	FBtr0080664	R	22	1	0.97	-0.17
+input2.bam	FBtr0080664	R	23	1	0.97	-0.17
+input2.bam	FBtr0080664	R	24	0	0.97	-0.792
+input2.bam	FBtr0080664	R	25	0	0.97	-0.419
+input2.bam	FBtr0080664	R	26	0	0.97	-0.294
+input2.bam	FBtr0080664	R	27	0	0.97	-0.792
+input2.bam	FBtr0080664	R	28	0	0.97	-0.792
+input2.bam	FBtr0080664	R	29	0	0.97	-0.792
diff -r 14adf24603b6 -r 8b5695592784 test-data/input1_input2new_norm_1_2_single_plot_counts.pdf
Binary file test-data/input1_input2new_norm_1_2_single_plot_counts.pdf has changed
diff -r 14adf24603b6 -r 8b5695592784 test-data/input1_min20_max30_single_plot_size.pdf
Binary file test-data/input1_min20_max30_single_plot_size.pdf has changed
diff -r 14adf24603b6 -r 8b5695592784 test-data/input1_min20_max30_size.tab
--- a/test-data/input1_min20_max30_size.tab	Thu Apr 25 12:49:05 2019 -0400
+++ b/test-data/input1_min20_max30_size.tab	Fri Oct 04 04:33:53 2019 -0400
@@ -1,342 +1,342 @@
 # Dataset	Chromosome	Polarity	Size	Counts	Strandness	z-score
-input1.bam	FBtr0070001	F	19	1	1.0	-0.448696330732
-input1.bam	FBtr0070001	F	20	4	1.0	-0.104347983891
-input1.bam	FBtr0070001	F	21	4	1.0	-0.104347983891
-input1.bam	FBtr0070001	F	22	29	1.0	2.76522157312
-input1.bam	FBtr0070001	F	23	15	1.0	1.15826262119
-input1.bam	FBtr0070001	F	24	1	1.0	-0.448696330732
-input1.bam	FBtr0070001	F	25	0	1.0	-0.563479113013
-input1.bam	FBtr0070001	F	26	0	1.0	-0.563479113013
-input1.bam	FBtr0070001	F	27	0	1.0	-0.563479113013
-input1.bam	FBtr0070001	F	28	0	1.0	-0.563479113013
-input1.bam	FBtr0070001	F	29	0	1.0	-0.563479113013
-input1.bam	FBtr0070533	F	19	3	1.0	1.27519650491
-input1.bam	FBtr0070533	F	20	2	1.0	0.536924844171
-input1.bam	FBtr0070533	F	21	2	1.0	0.536924844171
-input1.bam	FBtr0070533	F	22	4	1.0	2.01346816564
-input1.bam	FBtr0070533	F	23	2	1.0	0.536924844171
-input1.bam	FBtr0070533	F	24	0	1.0	-0.9396184773
-input1.bam	FBtr0070533	F	25	1	1.0	-0.201346816564
-input1.bam	FBtr0070533	F	26	0	1.0	-0.9396184773
-input1.bam	FBtr0070533	F	27	0	1.0	-0.9396184773
-input1.bam	FBtr0070533	F	28	0	1.0	-0.9396184773
-input1.bam	FBtr0070533	F	29	0	1.0	-0.9396184773
-input1.bam	FBtr0070603	F	19	1	1.0	-0.874157276122
-input1.bam	FBtr0070603	F	20	6	1.0	0.906533471533
-input1.bam	FBtr0070603	F	21	3	1.0	-0.16188097706
-input1.bam	FBtr0070603	F	22	3	1.0	-0.16188097706
-input1.bam	FBtr0070603	F	23	10	1.0	2.33108606966
-input1.bam	FBtr0070603	F	24	2	1.0	-0.518019126591
-input1.bam	FBtr0070603	F	25	5	1.0	0.550395322002
-input1.bam	FBtr0070603	F	26	5	1.0	0.550395322002
-input1.bam	FBtr0070603	F	27	3	1.0	-0.16188097706
-input1.bam	FBtr0070603	F	28	0	1.0	-1.23029542565
-input1.bam	FBtr0070603	F	29	0	1.0	-1.23029542565
-input1.bam	FBtr0070604	F	19	2	1.0	-0.185793425342
-input1.bam	FBtr0070604	F	20	0	1.0	-0.477754522308
-input1.bam	FBtr0070604	F	21	1	1.0	-0.331773973825
-input1.bam	FBtr0070604	F	22	23	1.0	2.8797980928
-input1.bam	FBtr0070604	F	23	10	1.0	0.982050962522
-input1.bam	FBtr0070604	F	24	0	1.0	-0.477754522308
-input1.bam	FBtr0070604	F	25	0	1.0	-0.477754522308
-input1.bam	FBtr0070604	F	26	0	1.0	-0.477754522308
-input1.bam	FBtr0070604	F	27	0	1.0	-0.477754522308
-input1.bam	FBtr0070604	F	28	0	1.0	-0.477754522308
-input1.bam	FBtr0070604	F	29	0	1.0	-0.477754522308
-input1.bam	FBtr0070911	F	19	0	1.0	-0.316227766017
-input1.bam	FBtr0070911	F	20	0	1.0	-0.316227766017
-input1.bam	FBtr0070911	F	21	1	1.0	3.16227766017
-input1.bam	FBtr0070911	F	22	0	1.0	-0.316227766017
-input1.bam	FBtr0070911	F	23	0	1.0	-0.316227766017
-input1.bam	FBtr0070911	F	24	0	1.0	-0.316227766017
-input1.bam	FBtr0070911	F	25	0	1.0	-0.316227766017
-input1.bam	FBtr0070911	F	26	0	1.0	-0.316227766017
-input1.bam	FBtr0070911	F	27	0	1.0	-0.316227766017
-input1.bam	FBtr0070911	F	28	0	1.0	-0.316227766017
-input1.bam	FBtr0070911	F	29	0	1.0	-0.316227766017
-input1.bam	FBtr0078490	F	19	0	1.0	-0.316227766017
-input1.bam	FBtr0078490	F	20	0	1.0	-0.316227766017
-input1.bam	FBtr0078490	F	21	0	1.0	-0.316227766017
-input1.bam	FBtr0078490	F	22	0	1.0	-0.316227766017
-input1.bam	FBtr0078490	F	23	1	1.0	3.16227766017
-input1.bam	FBtr0078490	F	24	0	1.0	-0.316227766017
-input1.bam	FBtr0078490	F	25	0	1.0	-0.316227766017
-input1.bam	FBtr0078490	F	26	0	1.0	-0.316227766017
-input1.bam	FBtr0078490	F	27	0	1.0	-0.316227766017
-input1.bam	FBtr0078490	F	28	0	1.0	-0.316227766017
-input1.bam	FBtr0078490	F	29	0	1.0	-0.316227766017
-input1.bam	FBtr0078580	F	19	8	1.0	-0.450200695898
-input1.bam	FBtr0078580	F	20	9	1.0	-0.436595729813
-input1.bam	FBtr0078580	F	21	5	1.0	-0.491015594153
-input1.bam	FBtr0078580	F	22	13	1.0	-0.382175865474
-input1.bam	FBtr0078580	F	23	5	1.0	-0.491015594153
-input1.bam	FBtr0078580	F	24	180	1.0	1.88985347069
-input1.bam	FBtr0078580	F	25	212	1.0	2.32521238541
-input1.bam	FBtr0078580	F	26	1	1.0	-0.545435458492
-input1.bam	FBtr0078580	F	27	2	1.0	-0.531830492407
-input1.bam	FBtr0078580	F	28	17	1.0	-0.327756001135
-input1.bam	FBtr0078580	F	29	0	1.0	-0.559040424577
-input1.bam	FBtr0078790	F	19	2	1.0	1.54713186939
-input1.bam	FBtr0078790	F	20	2	1.0	1.54713186939
-input1.bam	FBtr0078790	F	21	0	1.0	-0.721994872381
-input1.bam	FBtr0078790	F	22	2	1.0	1.54713186939
-input1.bam	FBtr0078790	F	23	1	1.0	0.412568498504
-input1.bam	FBtr0078790	F	24	0	1.0	-0.721994872381
-input1.bam	FBtr0078790	F	25	0	1.0	-0.721994872381
-input1.bam	FBtr0078790	F	26	0	1.0	-0.721994872381
-input1.bam	FBtr0078790	F	27	0	1.0	-0.721994872381
-input1.bam	FBtr0078790	F	28	0	1.0	-0.721994872381
-input1.bam	FBtr0078790	F	29	0	1.0	-0.721994872381
-input1.bam	FBtr0079064	F	19	0	1.0	-0.316227766017
-input1.bam	FBtr0079064	F	20	0	1.0	-0.316227766017
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+input1.bam	FBtr0080646	F	20	0	1.0	-0.471
+input1.bam	FBtr0080646	F	21	1	1.0	2.121
+input1.bam	FBtr0080646	F	22	1	1.0	2.121
+input1.bam	FBtr0080646	F	23	0	1.0	-0.471
+input1.bam	FBtr0080646	F	24	0	1.0	-0.471
+input1.bam	FBtr0080646	F	25	0	1.0	-0.471
+input1.bam	FBtr0080646	F	26	0	1.0	-0.471
+input1.bam	FBtr0080646	F	27	0	1.0	-0.471
+input1.bam	FBtr0080646	F	28	0	1.0	-0.471
+input1.bam	FBtr0080646	F	29	0	1.0	-0.471
+input1.bam	FBtr0080647	F	19	0	1.0	-0.471
+input1.bam	FBtr0080647	F	20	1	1.0	2.121
+input1.bam	FBtr0080647	F	21	0	1.0	-0.471
+input1.bam	FBtr0080647	F	22	1	1.0	2.121
+input1.bam	FBtr0080647	F	23	0	1.0	-0.471
+input1.bam	FBtr0080647	F	24	0	1.0	-0.471
+input1.bam	FBtr0080647	F	25	0	1.0	-0.471
+input1.bam	FBtr0080647	F	26	0	1.0	-0.471
+input1.bam	FBtr0080647	F	27	0	1.0	-0.471
+input1.bam	FBtr0080647	F	28	0	1.0	-0.471
+input1.bam	FBtr0080647	F	29	0	1.0	-0.471
+input1.bam	FBtr0080660	F	19	0	1.0	-0.442
+input1.bam	FBtr0080660	F	20	0	1.0	-0.442
+input1.bam	FBtr0080660	F	21	2	1.0	1.18
+input1.bam	FBtr0080660	F	22	0	1.0	-0.442
+input1.bam	FBtr0080660	F	23	0	1.0	-0.442
+input1.bam	FBtr0080660	F	24	4	1.0	2.801
+input1.bam	FBtr0080660	F	25	0	1.0	-0.442
+input1.bam	FBtr0080660	F	26	0	1.0	-0.442
+input1.bam	FBtr0080660	F	27	0	1.0	-0.442
+input1.bam	FBtr0080660	F	28	0	1.0	-0.442
+input1.bam	FBtr0080660	F	29	0	1.0	-0.442
+input1.bam	FBtr0080663	F	19	3	1.0	-0.388
+input1.bam	FBtr0080663	F	20	10	1.0	0.378
+input1.bam	FBtr0080663	F	21	0	1.0	-0.717
+input1.bam	FBtr0080663	F	22	1	1.0	-0.607
+input1.bam	FBtr0080663	F	23	7	1.0	0.05
+input1.bam	FBtr0080663	F	24	33	1.0	2.898
+input1.bam	FBtr0080663	F	25	10	1.0	0.378
+input1.bam	FBtr0080663	F	26	6	1.0	-0.06
+input1.bam	FBtr0080663	F	27	0	1.0	-0.717
+input1.bam	FBtr0080663	F	28	2	1.0	-0.498
+input1.bam	FBtr0080663	F	29	0	1.0	-0.717
+input1.bam	FBtr0080664	F	19	3	1.0	-0.466
+input1.bam	FBtr0080664	F	20	12	1.0	0.515
+input1.bam	FBtr0080664	F	21	5	1.0	-0.248
+input1.bam	FBtr0080664	F	22	0	1.0	-0.793
+input1.bam	FBtr0080664	F	23	11	1.0	0.406
+input1.bam	FBtr0080664	F	24	33	1.0	2.804
+input1.bam	FBtr0080664	F	25	10	1.0	0.297
+input1.bam	FBtr0080664	F	26	4	1.0	-0.357
+input1.bam	FBtr0080664	F	27	0	1.0	-0.793
+input1.bam	FBtr0080664	F	28	2	1.0	-0.575
+input1.bam	FBtr0080664	F	29	0	1.0	-0.793
diff -r 14adf24603b6 -r 8b5695592784 test-data/input1_single_plot_median.pdf
Binary file test-data/input1_single_plot_median.pdf has changed
diff -r 14adf24603b6 -r 8b5695592784 test-data/input1_yminneg5_5_single_plot_counts.pdf
Binary file test-data/input1_yminneg5_5_single_plot_counts.pdf has changed
diff -r 14adf24603b6 -r 8b5695592784 test-data/input_single_chr_x_6_single_plot_coverage.pdf
Binary file test-data/input_single_chr_x_6_single_plot_coverage.pdf has changed
diff -r 14adf24603b6 -r 8b5695592784 test-data/size.tab
--- a/test-data/size.tab	Thu Apr 25 12:49:05 2019 -0400
+++ b/test-data/size.tab	Fri Oct 04 04:33:53 2019 -0400
@@ -1,694 +1,694 @@
 # Dataset	Chromosome	Polarity	Size	Counts	Strandness	z-score
-input1.bam	FBtr0070001	F	19	1	1.0	-0.448696330732
-input1.bam	FBtr0070001	F	20	4	1.0	-0.104347983891
-input1.bam	FBtr0070001	F	21	4	1.0	-0.104347983891
-input1.bam	FBtr0070001	F	22	29	1.0	2.76522157312
-input1.bam	FBtr0070001	F	23	15	1.0	1.15826262119
-input1.bam	FBtr0070001	F	24	1	1.0	-0.448696330732
-input1.bam	FBtr0070001	F	25	0	1.0	-0.563479113013
-input1.bam	FBtr0070001	F	26	0	1.0	-0.563479113013
-input1.bam	FBtr0070001	F	27	0	1.0	-0.563479113013
-input1.bam	FBtr0070001	F	28	0	1.0	-0.563479113013
-input1.bam	FBtr0070001	F	29	0	1.0	-0.563479113013
-input1.bam	FBtr0070533	F	19	3	1.0	1.27519650491
-input1.bam	FBtr0070533	F	20	2	1.0	0.536924844171
-input1.bam	FBtr0070533	F	21	2	1.0	0.536924844171
-input1.bam	FBtr0070533	F	22	4	1.0	2.01346816564
-input1.bam	FBtr0070533	F	23	2	1.0	0.536924844171
-input1.bam	FBtr0070533	F	24	0	1.0	-0.9396184773
-input1.bam	FBtr0070533	F	25	1	1.0	-0.201346816564
-input1.bam	FBtr0070533	F	26	0	1.0	-0.9396184773
-input1.bam	FBtr0070533	F	27	0	1.0	-0.9396184773
-input1.bam	FBtr0070533	F	28	0	1.0	-0.9396184773
-input1.bam	FBtr0070533	F	29	0	1.0	-0.9396184773
-input1.bam	FBtr0070603	F	19	1	1.0	-0.874157276122
-input1.bam	FBtr0070603	F	20	6	1.0	0.906533471533
-input1.bam	FBtr0070603	F	21	3	1.0	-0.16188097706
-input1.bam	FBtr0070603	F	22	3	1.0	-0.16188097706
-input1.bam	FBtr0070603	F	23	10	1.0	2.33108606966
-input1.bam	FBtr0070603	F	24	2	1.0	-0.518019126591
-input1.bam	FBtr0070603	F	25	5	1.0	0.550395322002
-input1.bam	FBtr0070603	F	26	5	1.0	0.550395322002
-input1.bam	FBtr0070603	F	27	3	1.0	-0.16188097706
-input1.bam	FBtr0070603	F	28	0	1.0	-1.23029542565
-input1.bam	FBtr0070603	F	29	0	1.0	-1.23029542565
-input1.bam	FBtr0070604	F	19	2	1.0	-0.185793425342
-input1.bam	FBtr0070604	F	20	0	1.0	-0.477754522308
-input1.bam	FBtr0070604	F	21	1	1.0	-0.331773973825
-input1.bam	FBtr0070604	F	22	23	1.0	2.8797980928
-input1.bam	FBtr0070604	F	23	10	1.0	0.982050962522
-input1.bam	FBtr0070604	F	24	0	1.0	-0.477754522308
-input1.bam	FBtr0070604	F	25	0	1.0	-0.477754522308
-input1.bam	FBtr0070604	F	26	0	1.0	-0.477754522308
-input1.bam	FBtr0070604	F	27	0	1.0	-0.477754522308
-input1.bam	FBtr0070604	F	28	0	1.0	-0.477754522308
-input1.bam	FBtr0070604	F	29	0	1.0	-0.477754522308
-input1.bam	FBtr0070911	F	19	0	1.0	-0.316227766017
-input1.bam	FBtr0070911	F	20	0	1.0	-0.316227766017
-input1.bam	FBtr0070911	F	21	1	1.0	3.16227766017
-input1.bam	FBtr0070911	F	22	0	1.0	-0.316227766017
-input1.bam	FBtr0070911	F	23	0	1.0	-0.316227766017
-input1.bam	FBtr0070911	F	24	0	1.0	-0.316227766017
-input1.bam	FBtr0070911	F	25	0	1.0	-0.316227766017
-input1.bam	FBtr0070911	F	26	0	1.0	-0.316227766017
-input1.bam	FBtr0070911	F	27	0	1.0	-0.316227766017
-input1.bam	FBtr0070911	F	28	0	1.0	-0.316227766017
-input1.bam	FBtr0070911	F	29	0	1.0	-0.316227766017
-input1.bam	FBtr0078490	F	19	0	1.0	-0.316227766017
-input1.bam	FBtr0078490	F	20	0	1.0	-0.316227766017
-input1.bam	FBtr0078490	F	21	0	1.0	-0.316227766017
-input1.bam	FBtr0078490	F	22	0	1.0	-0.316227766017
-input1.bam	FBtr0078490	F	23	1	1.0	3.16227766017
-input1.bam	FBtr0078490	F	24	0	1.0	-0.316227766017
-input1.bam	FBtr0078490	F	25	0	1.0	-0.316227766017
-input1.bam	FBtr0078490	F	26	0	1.0	-0.316227766017
-input1.bam	FBtr0078490	F	27	0	1.0	-0.316227766017
-input1.bam	FBtr0078490	F	28	0	1.0	-0.316227766017
-input1.bam	FBtr0078490	F	29	0	1.0	-0.316227766017
-input1.bam	FBtr0078580	F	19	8	1.0	-0.450200695898
-input1.bam	FBtr0078580	F	20	9	1.0	-0.436595729813
-input1.bam	FBtr0078580	F	21	5	1.0	-0.491015594153
-input1.bam	FBtr0078580	F	22	13	1.0	-0.382175865474
-input1.bam	FBtr0078580	F	23	5	1.0	-0.491015594153
-input1.bam	FBtr0078580	F	24	180	1.0	1.88985347069
-input1.bam	FBtr0078580	F	25	212	1.0	2.32521238541
-input1.bam	FBtr0078580	F	26	1	1.0	-0.545435458492
-input1.bam	FBtr0078580	F	27	2	1.0	-0.531830492407
-input1.bam	FBtr0078580	F	28	17	1.0	-0.327756001135
-input1.bam	FBtr0078580	F	29	0	1.0	-0.559040424577
-input1.bam	FBtr0078790	F	19	2	1.0	1.54713186939
-input1.bam	FBtr0078790	F	20	2	1.0	1.54713186939
-input1.bam	FBtr0078790	F	21	0	1.0	-0.721994872381
-input1.bam	FBtr0078790	F	22	2	1.0	1.54713186939
-input1.bam	FBtr0078790	F	23	1	1.0	0.412568498504
-input1.bam	FBtr0078790	F	24	0	1.0	-0.721994872381
-input1.bam	FBtr0078790	F	25	0	1.0	-0.721994872381
-input1.bam	FBtr0078790	F	26	0	1.0	-0.721994872381
-input1.bam	FBtr0078790	F	27	0	1.0	-0.721994872381
-input1.bam	FBtr0078790	F	28	0	1.0	-0.721994872381
-input1.bam	FBtr0078790	F	29	0	1.0	-0.721994872381
-input1.bam	FBtr0079064	F	19	0	1.0	-0.316227766017
-input1.bam	FBtr0079064	F	20	0	1.0	-0.316227766017
-input1.bam	FBtr0079064	F	21	1	1.0	3.16227766017
-input1.bam	FBtr0079064	F	22	0	1.0	-0.316227766017
-input1.bam	FBtr0079064	F	23	0	1.0	-0.316227766017
-input1.bam	FBtr0079064	F	24	0	1.0	-0.316227766017
-input1.bam	FBtr0079064	F	25	0	1.0	-0.316227766017
-input1.bam	FBtr0079064	F	26	0	1.0	-0.316227766017
-input1.bam	FBtr0079064	F	27	0	1.0	-0.316227766017
-input1.bam	FBtr0079064	F	28	0	1.0	-0.316227766017
-input1.bam	FBtr0079064	F	29	0	1.0	-0.316227766017
-input1.bam	FBtr0079090	F	19	0	0.666666666667	-0.612372435696
-input1.bam	FBtr0079090	F	20	0	0.666666666667	-0.612372435696
-input1.bam	FBtr0079090	F	21	0	0.666666666667	1.63299316186
-input1.bam	FBtr0079090	F	22	0	0.666666666667	-0.612372435696
-input1.bam	FBtr0079090	F	23	0	0.666666666667	-0.612372435696
-input1.bam	FBtr0079090	F	24	1	0.666666666667	1.63299316186
-input1.bam	FBtr0079090	F	25	0	0.666666666667	-0.612372435696
-input1.bam	FBtr0079090	F	26	0	0.666666666667	-0.612372435696
-input1.bam	FBtr0079090	F	27	0	0.666666666667	-0.612372435696
-input1.bam	FBtr0079090	F	28	1	0.666666666667	1.63299316186
-input1.bam	FBtr0079090	F	29	0	0.666666666667	-0.612372435696
-input1.bam	FBtr0079090	R	19	0	0.666666666667	-0.612372435696
-input1.bam	FBtr0079090	R	20	0	0.666666666667	-0.612372435696
-input1.bam	FBtr0079090	R	21	1	0.666666666667	1.63299316186
-input1.bam	FBtr0079090	R	22	0	0.666666666667	-0.612372435696
-input1.bam	FBtr0079090	R	23	0	0.666666666667	-0.612372435696
-input1.bam	FBtr0079090	R	24	0	0.666666666667	1.63299316186
-input1.bam	FBtr0079090	R	25	0	0.666666666667	-0.612372435696
-input1.bam	FBtr0079090	R	26	0	0.666666666667	-0.612372435696
-input1.bam	FBtr0079090	R	27	0	0.666666666667	-0.612372435696
-input1.bam	FBtr0079090	R	28	0	0.666666666667	1.63299316186
-input1.bam	FBtr0079090	R	29	0	0.666666666667	-0.612372435696
-input1.bam	FBtr0079338	F	19	1	1.0	0.0496291666985
-input1.bam	FBtr0079338	F	20	0	1.0	-0.496291666985
-input1.bam	FBtr0079338	F	21	3	1.0	1.14147083407
-input1.bam	FBtr0079338	F	22	6	1.0	2.77923333512
-input1.bam	FBtr0079338	F	23	0	1.0	-0.496291666985
-input1.bam	FBtr0079338	F	24	0	1.0	-0.496291666985
-input1.bam	FBtr0079338	F	25	0	1.0	-0.496291666985
-input1.bam	FBtr0079338	F	26	0	1.0	-0.496291666985
-input1.bam	FBtr0079338	F	27	0	1.0	-0.496291666985
-input1.bam	FBtr0079338	F	28	0	1.0	-0.496291666985
-input1.bam	FBtr0079338	F	29	0	1.0	-0.496291666985
-input1.bam	FBtr0079528	F	19	4	1.0	-0.320526584152
-input1.bam	FBtr0079528	F	20	12	1.0	0.509071633653
-input1.bam	FBtr0079528	F	21	3	1.0	-0.424226361378
-input1.bam	FBtr0079528	F	22	2	1.0	-0.527926138604
-input1.bam	FBtr0079528	F	23	3	1.0	-0.424226361378
-input1.bam	FBtr0079528	F	24	36	1.0	2.99786628707
-input1.bam	FBtr0079528	F	25	8	1.0	0.0942725247506
-input1.bam	FBtr0079528	F	26	5	1.0	-0.216826806926
-input1.bam	FBtr0079528	F	27	2	1.0	-0.527926138604
-input1.bam	FBtr0079528	F	28	2	1.0	-0.527926138604
-input1.bam	FBtr0079528	F	29	1	1.0	-0.631625915829
-input1.bam	FBtr0079596	F	19	10	1.0	0.911805452636
-input1.bam	FBtr0079596	F	20	13	1.0	1.44911938008
-input1.bam	FBtr0079596	F	21	3	1.0	-0.341927044739
-input1.bam	FBtr0079596	F	22	16	1.0	1.98643330753
-input1.bam	FBtr0079596	F	23	8	1.0	0.553596167672
-input1.bam	FBtr0079596	F	24	0	1.0	-0.879240972185
-input1.bam	FBtr0079596	F	25	0	1.0	-0.879240972185
-input1.bam	FBtr0079596	F	26	3	1.0	-0.341927044739
-input1.bam	FBtr0079596	F	27	1	1.0	-0.700136329703
-input1.bam	FBtr0079596	F	28	0	1.0	-0.879240972185
-input1.bam	FBtr0079596	F	29	0	1.0	-0.879240972185
-input1.bam	FBtr0079677	F	19	2	1.0	2.80139716694
-input1.bam	FBtr0079677	F	20	0	1.0	-0.442325868465
-input1.bam	FBtr0079677	F	21	0	1.0	-0.442325868465
-input1.bam	FBtr0079677	F	22	0	1.0	-0.442325868465
-input1.bam	FBtr0079677	F	23	1	1.0	1.17953564924
-input1.bam	FBtr0079677	F	24	0	1.0	-0.442325868465
-input1.bam	FBtr0079677	F	25	0	1.0	-0.442325868465
-input1.bam	FBtr0079677	F	26	0	1.0	-0.442325868465
-input1.bam	FBtr0079677	F	27	0	1.0	-0.442325868465
-input1.bam	FBtr0079677	F	28	0	1.0	-0.442325868465
-input1.bam	FBtr0079677	F	29	0	1.0	-0.442325868465
-input1.bam	FBtr0079690	F	19	0	1.0	-0.316227766017
-input1.bam	FBtr0079690	F	20	0	1.0	-0.316227766017
-input1.bam	FBtr0079690	F	21	0	1.0	-0.316227766017
-input1.bam	FBtr0079690	F	22	0	1.0	-0.316227766017
-input1.bam	FBtr0079690	F	23	0	1.0	-0.316227766017
-input1.bam	FBtr0079690	F	24	0	1.0	-0.316227766017
-input1.bam	FBtr0079690	F	25	1	1.0	3.16227766017
-input1.bam	FBtr0079690	F	26	0	1.0	-0.316227766017
-input1.bam	FBtr0079690	F	27	0	1.0	-0.316227766017
-input1.bam	FBtr0079690	F	28	0	1.0	-0.316227766017
-input1.bam	FBtr0079690	F	29	0	1.0	-0.316227766017
-input1.bam	FBtr0079692	F	19	1	1.0	1.63299316186
-input1.bam	FBtr0079692	F	20	1	1.0	1.63299316186
-input1.bam	FBtr0079692	F	21	0	1.0	-0.612372435696
-input1.bam	FBtr0079692	F	22	0	1.0	-0.612372435696
-input1.bam	FBtr0079692	F	23	1	1.0	1.63299316186
-input1.bam	FBtr0079692	F	24	0	1.0	-0.612372435696
-input1.bam	FBtr0079692	F	25	0	1.0	-0.612372435696
-input1.bam	FBtr0079692	F	26	0	1.0	-0.612372435696
-input1.bam	FBtr0079692	F	27	0	1.0	-0.612372435696
-input1.bam	FBtr0079692	F	28	0	1.0	-0.612372435696
-input1.bam	FBtr0079692	F	29	0	1.0	-0.612372435696
-input1.bam	FBtr0079693	F	19	0	1.0	-0.471404520791
-input1.bam	FBtr0079693	F	20	0	1.0	-0.471404520791
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