changeset 1:40972a8dfab9 draft

planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/small_rna_maps commit ad60e6655aabe30246043d95f14646b2527c9255
author artbio
date Mon, 24 Jul 2017 12:31:04 -0400
parents 6d48150495e3
children 507383cce5a8
files small_rna_maps.py small_rna_maps.xml test-data/coverage.pdf test-data/doubled.tab test-data/doubled_mean.pdf test-data/mean.pdf test-data/median.pdf test-data/output.tab test-data/sizes.pdf
diffstat 9 files changed, 2 insertions(+), 6174 deletions(-) [+]
line wrap: on
line diff
--- a/small_rna_maps.py	Mon Jul 24 06:28:45 2017 -0400
+++ b/small_rna_maps.py	Mon Jul 24 12:31:04 2017 -0400
@@ -51,8 +51,6 @@
                 for pos in positions:
                     if not map_dictionary[(chrom, pos+1, 'F')]:
                         map_dictionary[(chrom, pos+1, 'F')] = []
-                    if not map_dictionary[(chrom, pos+1, 'R')]:
-                        map_dictionary[(chrom, pos+1, 'R')] = []
                 if read.is_reverse:
                     map_dictionary[(chrom, positions[-1]+1,
                                     'R')].append(read.query_alignment_length)
@@ -113,7 +111,6 @@
         for chrom in self.chromosomes:
             coverage_dictionary[(chrom, 1, 'F')] = 0
             coverage_dictionary[(chrom, self.chromosomes[chrom], 'F')] = 0
-
         for key in map_dictionary:
             coverage = self.bam_object.count_coverage(
                                                 reference=key[0],
@@ -132,7 +129,7 @@
         {chrom: {polarity: {size: nbre of reads}}}
         '''
         size_dictionary = defaultdict(lambda: defaultdict(
-                                      lambda: defaultdict( int )))
+                                      lambda: defaultdict(int)))
         #  to track empty chromosomes
         for chrom in self.chromosomes:
             if self.bam_object.count(chrom) == 0:
--- a/small_rna_maps.xml	Mon Jul 24 06:28:45 2017 -0400
+++ b/small_rna_maps.xml	Mon Jul 24 12:31:04 2017 -0400
@@ -1,4 +1,4 @@
-<tool id="small_rna_maps" name="small_rna_maps" version="0.9.0">
+<tool id="small_rna_maps" name="small_rna_maps" version="0.9.1">
   <description></description>
   <requirements>
         <requirement type="package" version="1.11.2=py27_0">numpy</requirement>
Binary file test-data/coverage.pdf has changed
--- a/test-data/doubled.tab	Mon Jul 24 06:28:45 2017 -0400
+++ b/test-data/doubled.tab	Mon Jul 24 12:31:04 2017 -0400
@@ -1,6339 +1,3205 @@
 Dataset	Chromosome	Chrom_length	Coordinate	Nbr_reads	Polarity	Max	Mean	Median	Coverage
 input1.bam_0	FBtr0070001	72	1	1	F	27	17.0	17.0	1
-input1.bam_0	FBtr0070001	72	1	0	R	27	0	0	1
 input1.bam_0	FBtr0070001	72	2	0	F	27	0	0	1
-input1.bam_0	FBtr0070001	72	2	0	R	27	0	0	1
 input1.bam_0	FBtr0070001	72	3	0	F	27	0	0	1
-input1.bam_0	FBtr0070001	72	3	0	R	27	0	0	1
 input1.bam_0	FBtr0070001	72	4	0	F	27	0	0	1
-input1.bam_0	FBtr0070001	72	4	0	R	27	0	0	1
 input1.bam_0	FBtr0070001	72	5	0	F	27	0	0	1
-input1.bam_0	FBtr0070001	72	5	0	R	27	0	0	1
 input1.bam_0	FBtr0070001	72	6	0	F	27	0	0	1
-input1.bam_0	FBtr0070001	72	6	0	R	27	0	0	1
 input1.bam_0	FBtr0070001	72	7	6	F	27	20.3	21.0	7
-input1.bam_0	FBtr0070001	72	7	0	R	27	0	0	7
 input1.bam_0	FBtr0070001	72	8	3	F	27	21.3	21.0	10
-input1.bam_0	FBtr0070001	72	8	0	R	27	0	0	10
 input1.bam_0	FBtr0070001	72	9	0	F	27	0	0	10
-input1.bam_0	FBtr0070001	72	9	0	R	27	0	0	10
 input1.bam_0	FBtr0070001	72	10	0	F	27	0	0	10
-input1.bam_0	FBtr0070001	72	10	0	R	27	0	0	10
 input1.bam_0	FBtr0070001	72	11	2	F	27	20.5	20.5	12
-input1.bam_0	FBtr0070001	72	11	0	R	27	0	0	12
 input1.bam_0	FBtr0070001	72	12	0	F	27	0	0	12
-input1.bam_0	FBtr0070001	72	12	0	R	27	0	0	12
 input1.bam_0	FBtr0070001	72	13	0	F	27	0	0	12
-input1.bam_0	FBtr0070001	72	13	0	R	27	0	0	12
 input1.bam_0	FBtr0070001	72	14	0	F	27	0	0	12
-input1.bam_0	FBtr0070001	72	14	0	R	27	0	0	12
 input1.bam_0	FBtr0070001	72	15	0	F	27	0	0	12
-input1.bam_0	FBtr0070001	72	15	0	R	27	0	0	12
 input1.bam_0	FBtr0070001	72	16	1	F	27	19.0	19.0	13
-input1.bam_0	FBtr0070001	72	16	0	R	27	0	0	13
 input1.bam_0	FBtr0070001	72	17	1	F	27	23.0	23.0	14
-input1.bam_0	FBtr0070001	72	17	0	R	27	0	0	14
 input1.bam_0	FBtr0070001	72	18	1	F	27	16.0	16.0	14
-input1.bam_0	FBtr0070001	72	18	0	R	27	0	0	14
 input1.bam_0	FBtr0070001	72	19	0	F	27	0	0	14
-input1.bam_0	FBtr0070001	72	19	0	R	27	0	0	14
 input1.bam_0	FBtr0070001	72	20	0	F	27	0	0	14
-input1.bam_0	FBtr0070001	72	20	0	R	27	0	0	14
 input1.bam_0	FBtr0070001	72	21	0	F	27	0	0	14
-input1.bam_0	FBtr0070001	72	21	0	R	27	0	0	14
 input1.bam_0	FBtr0070001	72	22	0	F	27	0	0	14
-input1.bam_0	FBtr0070001	72	22	0	R	27	0	0	14
 input1.bam_0	FBtr0070001	72	23	0	F	27	0	0	13
-input1.bam_0	FBtr0070001	72	23	0	R	27	0	0	13
 input1.bam_0	FBtr0070001	72	24	0	F	27	0	0	13
-input1.bam_0	FBtr0070001	72	24	0	R	27	0	0	13
 input1.bam_0	FBtr0070001	72	25	0	F	27	0	0	13
-input1.bam_0	FBtr0070001	72	25	0	R	27	0	0	13
 input1.bam_0	FBtr0070001	72	26	0	F	27	0	0	13
-input1.bam_0	FBtr0070001	72	26	0	R	27	0	0	13
 input1.bam_0	FBtr0070001	72	27	2	F	27	23.5	23.5	14
-input1.bam_0	FBtr0070001	72	27	0	R	27	0	0	14
 input1.bam_0	FBtr0070001	72	28	0	F	27	0	0	11
-input1.bam_0	FBtr0070001	72	28	0	R	27	0	0	11
 input1.bam_0	FBtr0070001	72	29	0	F	27	0	0	8
-input1.bam_0	FBtr0070001	72	29	0	R	27	0	0	8
 input1.bam_0	FBtr0070001	72	30	1	F	27	23.0	23.0	9
-input1.bam_0	FBtr0070001	72	30	0	R	27	0	0	9
 input1.bam_0	FBtr0070001	72	31	11	F	27	23.0	23.0	18
-input1.bam_0	FBtr0070001	72	31	0	R	27	0	0	18
 input1.bam_0	FBtr0070001	72	32	27	F	27	22.0	22.0	44
-input1.bam_0	FBtr0070001	72	32	0	R	27	0	0	44
 input1.bam_0	FBtr0070001	72	33	0	F	27	0	0	44
-input1.bam_0	FBtr0070001	72	33	0	R	27	0	0	44
 input1.bam_0	FBtr0070001	72	34	1	F	27	20.0	20.0	44
-input1.bam_0	FBtr0070001	72	34	0	R	27	0	0	44
 input1.bam_0	FBtr0070001	72	35	0	F	27	0	0	43
-input1.bam_0	FBtr0070001	72	35	0	R	27	0	0	43
 input1.bam_0	FBtr0070001	72	36	0	F	27	0	0	43
-input1.bam_0	FBtr0070001	72	36	0	R	27	0	0	43
 input1.bam_0	FBtr0070001	72	37	0	F	27	0	0	43
-input1.bam_0	FBtr0070001	72	37	0	R	27	0	0	43
 input1.bam_0	FBtr0070001	72	38	0	F	27	0	0	43
-input1.bam_0	FBtr0070001	72	38	0	R	27	0	0	43
 input1.bam_0	FBtr0070001	72	39	0	F	27	0	0	43
-input1.bam_0	FBtr0070001	72	39	0	R	27	0	0	43
 input1.bam_0	FBtr0070001	72	40	0	F	27	0	0	42
-input1.bam_0	FBtr0070001	72	40	0	R	27	0	0	42
 input1.bam_0	FBtr0070001	72	41	0	F	27	0	0	42
-input1.bam_0	FBtr0070001	72	41	0	R	27	0	0	42
 input1.bam_0	FBtr0070001	72	42	0	F	27	0	0	42
-input1.bam_0	FBtr0070001	72	42	0	R	27	0	0	42
 input1.bam_0	FBtr0070001	72	43	0	F	27	0	0	42
-input1.bam_0	FBtr0070001	72	43	0	R	27	0	0	42
 input1.bam_0	FBtr0070001	72	44	0	F	27	0	0	42
-input1.bam_0	FBtr0070001	72	44	0	R	27	0	0	42
 input1.bam_0	FBtr0070001	72	45	0	F	27	0	0	42
-input1.bam_0	FBtr0070001	72	45	0	R	27	0	0	42
 input1.bam_0	FBtr0070001	72	46	0	F	27	0	0	42
-input1.bam_0	FBtr0070001	72	46	0	R	27	0	0	42
 input1.bam_0	FBtr0070001	72	47	0	F	27	0	0	42
-input1.bam_0	FBtr0070001	72	47	0	R	27	0	0	42
 input1.bam_0	FBtr0070001	72	48	0	F	27	0	0	42
-input1.bam_0	FBtr0070001	72	48	0	R	27	0	0	42
 input1.bam_0	FBtr0070001	72	49	0	F	27	0	0	42
-input1.bam_0	FBtr0070001	72	49	0	R	27	0	0	42
 input1.bam_0	FBtr0070001	72	50	0	F	27	0	0	41
-input1.bam_0	FBtr0070001	72	50	0	R	27	0	0	41
 input1.bam_0	FBtr0070001	72	51	0	F	27	0	0	40
-input1.bam_0	FBtr0070001	72	51	0	R	27	0	0	40
 input1.bam_0	FBtr0070001	72	52	0	F	27	0	0	40
-input1.bam_0	FBtr0070001	72	52	0	R	27	0	0	40
 input1.bam_0	FBtr0070001	72	53	0	F	27	0	0	39
-input1.bam_0	FBtr0070001	72	53	0	R	27	0	0	39
 input1.bam_0	FBtr0070001	72	72	0	F	27	0	0	0
 input1.bam_0	FBtr0070533	72	1	1	F	5	15.0	15.0	1
-input1.bam_0	FBtr0070533	72	1	0	R	5	0	0	1
 input1.bam_0	FBtr0070533	72	2	0	F	5	0	0	1
-input1.bam_0	FBtr0070533	72	2	0	R	5	0	0	1
 input1.bam_0	FBtr0070533	72	3	0	F	5	0	0	1
-input1.bam_0	FBtr0070533	72	3	0	R	5	0	0	1
 input1.bam_0	FBtr0070533	72	4	0	F	5	0	0	1
-input1.bam_0	FBtr0070533	72	4	0	R	5	0	0	1
 input1.bam_0	FBtr0070533	72	5	0	F	5	0	0	1
-input1.bam_0	FBtr0070533	72	5	0	R	5	0	0	1
 input1.bam_0	FBtr0070533	72	6	0	F	5	0	0	1
-input1.bam_0	FBtr0070533	72	6	0	R	5	0	0	1
 input1.bam_0	FBtr0070533	72	7	0	F	5	0	0	1
-input1.bam_0	FBtr0070533	72	7	0	R	5	0	0	1
 input1.bam_0	FBtr0070533	72	8	0	F	5	0	0	1
-input1.bam_0	FBtr0070533	72	8	0	R	5	0	0	1
 input1.bam_0	FBtr0070533	72	9	0	F	5	0	0	1
-input1.bam_0	FBtr0070533	72	9	0	R	5	0	0	1
 input1.bam_0	FBtr0070533	72	10	0	F	5	0	0	1
-input1.bam_0	FBtr0070533	72	10	0	R	5	0	0	1
 input1.bam_0	FBtr0070533	72	11	0	F	5	0	0	1
-input1.bam_0	FBtr0070533	72	11	0	R	5	0	0	1
 input1.bam_0	FBtr0070533	72	12	2	F	5	18.0	18.0	3
-input1.bam_0	FBtr0070533	72	12	0	R	5	0	0	3
 input1.bam_0	FBtr0070533	72	13	0	F	5	0	0	3
-input1.bam_0	FBtr0070533	72	13	0	R	5	0	0	3
 input1.bam_0	FBtr0070533	72	14	0	F	5	0	0	3
-input1.bam_0	FBtr0070533	72	14	0	R	5	0	0	3
 input1.bam_0	FBtr0070533	72	15	1	F	5	15.0	15.0	4
-input1.bam_0	FBtr0070533	72	15	0	R	5	0	0	4
 input1.bam_0	FBtr0070533	72	16	0	F	5	0	0	3
-input1.bam_0	FBtr0070533	72	16	0	R	5	0	0	3
 input1.bam_0	FBtr0070533	72	17	0	F	5	0	0	3
-input1.bam_0	FBtr0070533	72	17	0	R	5	0	0	3
 input1.bam_0	FBtr0070533	72	18	0	F	5	0	0	3
-input1.bam_0	FBtr0070533	72	18	0	R	5	0	0	3
 input1.bam_0	FBtr0070533	72	19	5	F	5	21.8	22.0	8
-input1.bam_0	FBtr0070533	72	19	0	R	5	0	0	8
 input1.bam_0	FBtr0070533	72	20	1	F	5	23.0	23.0	9
-input1.bam_0	FBtr0070533	72	20	0	R	5	0	0	9
 input1.bam_0	FBtr0070533	72	21	1	F	5	18.0	18.0	10
-input1.bam_0	FBtr0070533	72	21	0	R	5	0	0	10
 input1.bam_0	FBtr0070533	72	22	1	F	5	20.0	20.0	11
-input1.bam_0	FBtr0070533	72	22	0	R	5	0	0	11
 input1.bam_0	FBtr0070533	72	23	0	F	5	0	0	11
-input1.bam_0	FBtr0070533	72	23	0	R	5	0	0	11
 input1.bam_0	FBtr0070533	72	24	0	F	5	0	0	11
-input1.bam_0	FBtr0070533	72	24	0	R	5	0	0	11
 input1.bam_0	FBtr0070533	72	25	1	F	5	17.0	17.0	12
-input1.bam_0	FBtr0070533	72	25	0	R	5	0	0	12
 input1.bam_0	FBtr0070533	72	26	1	F	5	16.0	16.0	13
-input1.bam_0	FBtr0070533	72	26	0	R	5	0	0	13
 input1.bam_0	FBtr0070533	72	27	0	F	5	0	0	13
-input1.bam_0	FBtr0070533	72	27	0	R	5	0	0	13
 input1.bam_0	FBtr0070533	72	28	1	F	5	25.0	25.0	14
-input1.bam_0	FBtr0070533	72	28	0	R	5	0	0	14
 input1.bam_0	FBtr0070533	72	29	0	F	5	0	0	14
-input1.bam_0	FBtr0070533	72	29	0	R	5	0	0	14
 input1.bam_0	FBtr0070533	72	30	0	F	5	0	0	11
-input1.bam_0	FBtr0070533	72	30	0	R	5	0	0	11
 input1.bam_0	FBtr0070533	72	31	0	F	5	0	0	11
-input1.bam_0	FBtr0070533	72	31	0	R	5	0	0	11
 input1.bam_0	FBtr0070533	72	32	4	F	5	20.5	21.0	15
-input1.bam_0	FBtr0070533	72	32	0	R	5	0	0	15
 input1.bam_0	FBtr0070533	72	33	0	F	5	0	0	15
-input1.bam_0	FBtr0070533	72	33	0	R	5	0	0	15
 input1.bam_0	FBtr0070533	72	34	0	F	5	0	0	15
-input1.bam_0	FBtr0070533	72	34	0	R	5	0	0	15
 input1.bam_0	FBtr0070533	72	35	1	F	5	19.0	19.0	16
-input1.bam_0	FBtr0070533	72	35	0	R	5	0	0	16
 input1.bam_0	FBtr0070533	72	36	0	F	5	0	0	16
-input1.bam_0	FBtr0070533	72	36	0	R	5	0	0	16
 input1.bam_0	FBtr0070533	72	37	2	F	5	19.0	19.0	18
-input1.bam_0	FBtr0070533	72	37	0	R	5	0	0	18
 input1.bam_0	FBtr0070533	72	38	2	F	5	18.0	18.0	20
-input1.bam_0	FBtr0070533	72	38	0	R	5	0	0	20
 input1.bam_0	FBtr0070533	72	39	0	F	5	0	0	19
-input1.bam_0	FBtr0070533	72	39	0	R	5	0	0	19
 input1.bam_0	FBtr0070533	72	40	0	F	5	0	0	17
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 input1.bam_0	FBtr0070533	72	41	0	F	5	0	0	15
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 input1.bam_0	FBtr0070533	72	42	0	F	5	0	0	11
-input1.bam_0	FBtr0070533	72	42	0	R	5	0	0	11
 input1.bam_0	FBtr0070533	72	43	0	F	5	0	0	10
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 input1.bam_0	FBtr0070533	72	44	0	F	5	0	0	10
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 input1.bam_0	FBtr0070533	72	45	0	F	5	0	0	10
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 input1.bam_0	FBtr0070533	72	46	0	F	5	0	0	10
-input1.bam_0	FBtr0070533	72	46	0	R	5	0	0	10
 input1.bam_0	FBtr0070533	72	47	0	F	5	0	0	10
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 input1.bam_0	FBtr0070533	72	48	0	F	5	0	0	10
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 input1.bam_0	FBtr0070533	72	49	0	F	5	0	0	10
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 input1.bam_0	FBtr0070533	72	50	0	F	5	0	0	9
-input1.bam_0	FBtr0070533	72	50	0	R	5	0	0	9
 input1.bam_0	FBtr0070533	72	51	0	F	5	0	0	9
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 input1.bam_0	FBtr0070533	72	52	0	F	5	0	0	8
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 input1.bam_0	FBtr0070533	72	53	0	F	5	0	0	7
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 input1.bam_0	FBtr0070533	72	54	0	F	5	0	0	4
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 input1.bam_0	FBtr0070533	72	55	0	F	5	0	0	4
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 input1.bam_0	FBtr0070533	72	72	0	F	5	0	0	0
 input1.bam_0	FBtr0070603	72	1	2	F	9	16.5	16.5	2
-input1.bam_0	FBtr0070603	72	1	0	R	9	0	0	2
 input1.bam_0	FBtr0070603	72	2	0	F	9	0	0	2
-input1.bam_0	FBtr0070603	72	2	0	R	9	0	0	2
 input1.bam_0	FBtr0070603	72	3	1	F	9	21.0	21.0	3
-input1.bam_0	FBtr0070603	72	3	0	R	9	0	0	3
 input1.bam_0	FBtr0070603	72	4	1	F	9	20.0	20.0	4
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 input1.bam_0	FBtr0070603	72	5	0	F	9	0	0	4
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 input1.bam_1	FBtr0080663	71	36	0	F	56	0	0	3
-input1.bam_1	FBtr0080663	71	36	0	R	56	0	0	3
 input1.bam_1	FBtr0080663	71	37	0	F	56	0	0	3
-input1.bam_1	FBtr0080663	71	37	0	R	56	0	0	3
 input1.bam_1	FBtr0080663	71	38	0	F	56	0	0	3
-input1.bam_1	FBtr0080663	71	38	0	R	56	0	0	3
 input1.bam_1	FBtr0080663	71	39	0	F	56	0	0	3
-input1.bam_1	FBtr0080663	71	39	0	R	56	0	0	3
 input1.bam_1	FBtr0080663	71	40	0	F	56	0	0	3
-input1.bam_1	FBtr0080663	71	40	0	R	56	0	0	3
 input1.bam_1	FBtr0080663	71	41	0	F	56	0	0	3
-input1.bam_1	FBtr0080663	71	41	0	R	56	0	0	3
 input1.bam_1	FBtr0080663	71	42	0	F	56	0	0	3
-input1.bam_1	FBtr0080663	71	42	0	R	56	0	0	3
 input1.bam_1	FBtr0080663	71	43	0	F	56	0	0	3
-input1.bam_1	FBtr0080663	71	43	0	R	56	0	0	3
 input1.bam_1	FBtr0080663	71	44	0	F	56	0	0	2
-input1.bam_1	FBtr0080663	71	44	0	R	56	0	0	2
 input1.bam_1	FBtr0080663	71	45	0	F	56	0	0	2
-input1.bam_1	FBtr0080663	71	45	0	R	56	0	0	2
 input1.bam_1	FBtr0080663	71	46	0	F	56	0	0	2
-input1.bam_1	FBtr0080663	71	46	0	R	56	0	0	2
 input1.bam_1	FBtr0080663	71	47	0	F	56	0	0	1
-input1.bam_1	FBtr0080663	71	47	0	R	56	0	0	1
 input1.bam_1	FBtr0080663	71	50	1	F	56	17.0	17.0	1
-input1.bam_1	FBtr0080663	71	50	0	R	56	0	0	1
 input1.bam_1	FBtr0080663	71	51	9	F	56	15.6	15.0	10
-input1.bam_1	FBtr0080663	71	51	0	R	56	0	0	10
 input1.bam_1	FBtr0080663	71	52	0	F	56	0	0	10
-input1.bam_1	FBtr0080663	71	52	0	R	56	0	0	10
 input1.bam_1	FBtr0080663	71	53	0	F	56	0	0	10
-input1.bam_1	FBtr0080663	71	53	0	R	56	0	0	10
 input1.bam_1	FBtr0080663	71	54	0	F	56	0	0	10
-input1.bam_1	FBtr0080663	71	54	0	R	56	0	0	10
 input1.bam_1	FBtr0080663	71	55	0	F	56	0	0	10
-input1.bam_1	FBtr0080663	71	55	0	R	56	0	0	10
 input1.bam_1	FBtr0080663	71	56	0	F	56	0	0	10
-input1.bam_1	FBtr0080663	71	56	0	R	56	0	0	10
 input1.bam_1	FBtr0080663	71	57	0	F	56	0	0	10
-input1.bam_1	FBtr0080663	71	57	0	R	56	0	0	10
 input1.bam_1	FBtr0080663	71	58	0	F	56	0	0	10
-input1.bam_1	FBtr0080663	71	58	0	R	56	0	0	10
 input1.bam_1	FBtr0080663	71	59	0	F	56	0	0	10
-input1.bam_1	FBtr0080663	71	59	0	R	56	0	0	10
 input1.bam_1	FBtr0080663	71	60	0	F	56	0	0	10
-input1.bam_1	FBtr0080663	71	60	0	R	56	0	0	10
 input1.bam_1	FBtr0080663	71	61	0	F	56	0	0	10
-input1.bam_1	FBtr0080663	71	61	0	R	56	0	0	10
 input1.bam_1	FBtr0080663	71	62	0	F	56	0	0	10
-input1.bam_1	FBtr0080663	71	62	0	R	56	0	0	10
 input1.bam_1	FBtr0080663	71	63	0	F	56	0	0	10
-input1.bam_1	FBtr0080663	71	63	0	R	56	0	0	10
 input1.bam_1	FBtr0080663	71	64	0	F	56	0	0	10
-input1.bam_1	FBtr0080663	71	64	0	R	56	0	0	10
 input1.bam_1	FBtr0080663	71	65	0	F	56	0	0	10
-input1.bam_1	FBtr0080663	71	65	0	R	56	0	0	10
 input1.bam_1	FBtr0080663	71	66	0	F	56	0	0	2
-input1.bam_1	FBtr0080663	71	66	0	R	56	0	0	2
 input1.bam_1	FBtr0080663	71	67	0	F	56	0	0	1
-input1.bam_1	FBtr0080663	71	67	0	R	56	0	0	1
 input1.bam_1	FBtr0080663	71	68	0	F	56	0	0	1
-input1.bam_1	FBtr0080663	71	68	0	R	56	0	0	1
 input1.bam_1	FBtr0080663	71	69	0	F	56	0	0	1
-input1.bam_1	FBtr0080663	71	69	0	R	56	0	0	1
 input1.bam_1	FBtr0080663	71	70	0	F	56	0	0	1
-input1.bam_1	FBtr0080663	71	70	0	R	56	0	0	1
 input1.bam_1	FBtr0080663	71	71	0	F	56	0	0	0
 input1.bam_1	FBtr0080664	71	1	16	F	56	19.5	17.0	16
-input1.bam_1	FBtr0080664	71	1	0	R	56	0	0	16
 input1.bam_1	FBtr0080664	71	2	0	F	56	0	0	16
-input1.bam_1	FBtr0080664	71	2	0	R	56	0	0	16
 input1.bam_1	FBtr0080664	71	3	56	F	56	23.8	24.0	72
-input1.bam_1	FBtr0080664	71	3	0	R	56	0	0	72
 input1.bam_1	FBtr0080664	71	4	4	F	56	23.5	23.5	76
-input1.bam_1	FBtr0080664	71	4	0	R	56	0	0	76
 input1.bam_1	FBtr0080664	71	5	0	F	56	0	0	76
-input1.bam_1	FBtr0080664	71	5	0	R	56	0	0	76
 input1.bam_1	FBtr0080664	71	6	1	F	56	23.0	23.0	77
-input1.bam_1	FBtr0080664	71	6	0	R	56	0	0	77
 input1.bam_1	FBtr0080664	71	7	1	F	56	21.0	21.0	78
-input1.bam_1	FBtr0080664	71	7	0	R	56	0	0	78
 input1.bam_1	FBtr0080664	71	8	4	F	56	20.5	20.0	82
-input1.bam_1	FBtr0080664	71	8	0	R	56	0	0	82
 input1.bam_1	FBtr0080664	71	9	1	F	56	20.0	20.0	83
-input1.bam_1	FBtr0080664	71	9	0	R	56	0	0	83
 input1.bam_1	FBtr0080664	71	10	0	F	56	0	0	83
-input1.bam_1	FBtr0080664	71	10	0	R	56	0	0	83
 input1.bam_1	FBtr0080664	71	11	3	F	56	16.7	17.0	86
-input1.bam_1	FBtr0080664	71	11	0	R	56	0	0	86
 input1.bam_1	FBtr0080664	71	12	3	F	56	18.0	17.0	89
-input1.bam_1	FBtr0080664	71	12	0	R	56	0	0	89
 input1.bam_1	FBtr0080664	71	13	2	F	56	20.0	20.0	91
-input1.bam_1	FBtr0080664	71	13	0	R	56	0	0	91
 input1.bam_1	FBtr0080664	71	14	3	F	56	18.3	18.0	94
-input1.bam_1	FBtr0080664	71	14	0	R	56	0	0	94
 input1.bam_1	FBtr0080664	71	15	0	F	56	0	0	94
-input1.bam_1	FBtr0080664	71	15	0	R	56	0	0	94
 input1.bam_1	FBtr0080664	71	16	2	F	56	15.0	15.0	95
-input1.bam_1	FBtr0080664	71	16	0	R	56	0	0	95
 input1.bam_1	FBtr0080664	71	17	10	F	56	15.8	15.5	100
-input1.bam_1	FBtr0080664	71	17	0	R	56	0	0	100
 input1.bam_1	FBtr0080664	71	18	1	F	56	15.0	15.0	98
-input1.bam_1	FBtr0080664	71	18	0	R	56	0	0	98
 input1.bam_1	FBtr0080664	71	19	0	F	56	0	0	97
-input1.bam_1	FBtr0080664	71	19	0	R	56	0	0	97
 input1.bam_1	FBtr0080664	71	20	0	F	56	0	0	97
-input1.bam_1	FBtr0080664	71	20	0	R	56	0	0	97
 input1.bam_1	FBtr0080664	71	21	1	F	56	15.0	15.0	97
-input1.bam_1	FBtr0080664	71	21	0	R	56	0	0	97
 input1.bam_1	FBtr0080664	71	22	0	F	56	0	0	97
-input1.bam_1	FBtr0080664	71	22	0	R	56	0	0	97
 input1.bam_1	FBtr0080664	71	23	0	F	56	0	0	93
-input1.bam_1	FBtr0080664	71	23	0	R	56	0	0	93
 input1.bam_1	FBtr0080664	71	24	0	F	56	0	0	88
-input1.bam_1	FBtr0080664	71	24	0	R	56	0	0	88
 input1.bam_1	FBtr0080664	71	25	0	F	56	0	0	88
-input1.bam_1	FBtr0080664	71	25	0	R	56	0	0	88
 input1.bam_1	FBtr0080664	71	26	0	F	56	0	0	82
-input1.bam_1	FBtr0080664	71	26	0	R	56	0	0	82
 input1.bam_1	FBtr0080664	71	27	0	F	56	0	0	47
-input1.bam_1	FBtr0080664	71	27	0	R	56	0	0	47
 input1.bam_1	FBtr0080664	71	28	2	F	56	16.0	16.0	33
-input1.bam_1	FBtr0080664	71	28	0	R	56	0	0	33
 input1.bam_1	FBtr0080664	71	29	0	F	56	0	0	23
-input1.bam_1	FBtr0080664	71	29	0	R	56	0	0	23
 input1.bam_1	FBtr0080664	71	30	0	F	56	0	0	23
-input1.bam_1	FBtr0080664	71	30	0	R	56	0	0	23
 input1.bam_1	FBtr0080664	71	31	0	F	56	0	0	20
-input1.bam_1	FBtr0080664	71	31	0	R	56	0	0	20
 input1.bam_1	FBtr0080664	71	32	1	F	56	15.0	15.0	13
-input1.bam_1	FBtr0080664	71	32	0	R	56	0	0	13
 input1.bam_1	FBtr0080664	71	33	1	F	56	20.0	20.0	6
-input1.bam_1	FBtr0080664	71	33	0	R	56	0	0	6
 input1.bam_1	FBtr0080664	71	34	1	F	56	16.0	16.0	7
-input1.bam_1	FBtr0080664	71	34	0	R	56	0	0	7
 input1.bam_1	FBtr0080664	71	35	1	F	56	15.0	15.0	8
-input1.bam_1	FBtr0080664	71	35	0	R	56	0	0	8
 input1.bam_1	FBtr0080664	71	36	1	F	56	21.0	21.0	7
-input1.bam_1	FBtr0080664	71	36	0	R	56	0	0	7
 input1.bam_1	FBtr0080664	71	37	1	F	56	18.0	18.0	8
-input1.bam_1	FBtr0080664	71	37	0	R	56	0	0	8
 input1.bam_1	FBtr0080664	71	38	1	F	56	15.0	15.0	9
-input1.bam_1	FBtr0080664	71	38	0	R	56	0	0	9
 input1.bam_1	FBtr0080664	71	39	0	F	56	0	0	9
-input1.bam_1	FBtr0080664	71	39	0	R	56	0	0	9
 input1.bam_1	FBtr0080664	71	40	0	F	56	0	0	9
-input1.bam_1	FBtr0080664	71	40	0	R	56	0	0	9
 input1.bam_1	FBtr0080664	71	41	0	F	56	0	0	9
-input1.bam_1	FBtr0080664	71	41	0	R	56	0	0	9
 input1.bam_1	FBtr0080664	71	42	0	F	56	0	0	9
-input1.bam_1	FBtr0080664	71	42	0	R	56	0	0	9
 input1.bam_1	FBtr0080664	71	43	0	F	56	0	0	9
-input1.bam_1	FBtr0080664	71	43	0	R	56	0	0	9
 input1.bam_1	FBtr0080664	71	44	0	F	56	0	0	7
-input1.bam_1	FBtr0080664	71	44	0	R	56	0	0	7
 input1.bam_1	FBtr0080664	71	45	0	F	56	0	0	7
-input1.bam_1	FBtr0080664	71	45	0	R	56	0	0	7
 input1.bam_1	FBtr0080664	71	46	0	F	56	0	0	7
-input1.bam_1	FBtr0080664	71	46	0	R	56	0	0	7
 input1.bam_1	FBtr0080664	71	47	0	F	56	0	0	6
-input1.bam_1	FBtr0080664	71	47	0	R	56	0	0	6
 input1.bam_1	FBtr0080664	71	48	0	F	56	0	0	6
-input1.bam_1	FBtr0080664	71	48	0	R	56	0	0	6
 input1.bam_1	FBtr0080664	71	49	0	F	56	0	0	6
-input1.bam_1	FBtr0080664	71	49	0	R	56	0	0	6
 input1.bam_1	FBtr0080664	71	50	2	F	56	16.0	16.0	6
-input1.bam_1	FBtr0080664	71	50	0	R	56	0	0	6
 input1.bam_1	FBtr0080664	71	51	7	F	56	15.0	15.0	13
-input1.bam_1	FBtr0080664	71	51	0	R	56	0	0	13
 input1.bam_1	FBtr0080664	71	52	1	F	56	15.0	15.0	14
-input1.bam_1	FBtr0080664	71	52	0	R	56	0	0	14
 input1.bam_1	FBtr0080664	71	53	0	F	56	0	0	12
-input1.bam_1	FBtr0080664	71	53	0	R	56	0	0	12
 input1.bam_1	FBtr0080664	71	54	0	F	56	0	0	12
-input1.bam_1	FBtr0080664	71	54	0	R	56	0	0	12
 input1.bam_1	FBtr0080664	71	55	0	F	56	0	0	11
-input1.bam_1	FBtr0080664	71	55	0	R	56	0	0	11
 input1.bam_1	FBtr0080664	71	56	1	F	56	16.0	16.0	12
-input1.bam_1	FBtr0080664	71	56	0	R	56	0	0	12
 input1.bam_1	FBtr0080664	71	57	0	F	56	0	0	11
-input1.bam_1	FBtr0080664	71	57	0	R	56	0	0	11
 input1.bam_1	FBtr0080664	71	58	0	F	56	0	0	11
-input1.bam_1	FBtr0080664	71	58	0	R	56	0	0	11
 input1.bam_1	FBtr0080664	71	59	0	F	56	0	0	11
-input1.bam_1	FBtr0080664	71	59	0	R	56	0	0	11
 input1.bam_1	FBtr0080664	71	60	0	F	56	0	0	11
-input1.bam_1	FBtr0080664	71	60	0	R	56	0	0	11
 input1.bam_1	FBtr0080664	71	61	0	F	56	0	0	11
-input1.bam_1	FBtr0080664	71	61	0	R	56	0	0	11
 input1.bam_1	FBtr0080664	71	62	0	F	56	0	0	11
-input1.bam_1	FBtr0080664	71	62	0	R	56	0	0	11
 input1.bam_1	FBtr0080664	71	63	0	F	56	0	0	11
-input1.bam_1	FBtr0080664	71	63	0	R	56	0	0	11
 input1.bam_1	FBtr0080664	71	64	0	F	56	0	0	11
-input1.bam_1	FBtr0080664	71	64	0	R	56	0	0	11
 input1.bam_1	FBtr0080664	71	65	0	F	56	0	0	11
-input1.bam_1	FBtr0080664	71	65	0	R	56	0	0	11
 input1.bam_1	FBtr0080664	71	66	0	F	56	0	0	2
-input1.bam_1	FBtr0080664	71	66	0	R	56	0	0	2
 input1.bam_1	FBtr0080664	71	67	0	F	56	0	0	1
-input1.bam_1	FBtr0080664	71	67	0	R	56	0	0	1
 input1.bam_1	FBtr0080664	71	68	0	F	56	0	0	1
-input1.bam_1	FBtr0080664	71	68	0	R	56	0	0	1
 input1.bam_1	FBtr0080664	71	69	0	F	56	0	0	1
-input1.bam_1	FBtr0080664	71	69	0	R	56	0	0	1
 input1.bam_1	FBtr0080664	71	70	0	F	56	0	0	1
-input1.bam_1	FBtr0080664	71	70	0	R	56	0	0	1
 input1.bam_1	FBtr0080664	71	71	0	F	56	0	0	1
-input1.bam_1	FBtr0080664	71	71	0	R	56	0	0	1
Binary file test-data/doubled_mean.pdf has changed
Binary file test-data/mean.pdf has changed
Binary file test-data/median.pdf has changed
--- a/test-data/output.tab	Mon Jul 24 06:28:45 2017 -0400
+++ b/test-data/output.tab	Mon Jul 24 12:31:04 2017 -0400
@@ -1,6144 +1,3109 @@
 Dataset	Chromosome	Chrom_length	Coordinate	Nbr_reads	Polarity	Max	Mean	Median	Coverage
 input1.bam	FBtr0070001	72	1	1	F	27	17.0	17.0	1
-input1.bam	FBtr0070001	72	1	0	R	27	0	0	1
 input1.bam	FBtr0070001	72	2	0	F	27	0	0	1
-input1.bam	FBtr0070001	72	2	0	R	27	0	0	1
 input1.bam	FBtr0070001	72	3	0	F	27	0	0	1
-input1.bam	FBtr0070001	72	3	0	R	27	0	0	1
 input1.bam	FBtr0070001	72	4	0	F	27	0	0	1
-input1.bam	FBtr0070001	72	4	0	R	27	0	0	1
 input1.bam	FBtr0070001	72	5	0	F	27	0	0	1
-input1.bam	FBtr0070001	72	5	0	R	27	0	0	1
 input1.bam	FBtr0070001	72	6	0	F	27	0	0	1
-input1.bam	FBtr0070001	72	6	0	R	27	0	0	1
 input1.bam	FBtr0070001	72	7	6	F	27	20.3	21.0	7
-input1.bam	FBtr0070001	72	7	0	R	27	0	0	7
 input1.bam	FBtr0070001	72	8	3	F	27	21.3	21.0	10
-input1.bam	FBtr0070001	72	8	0	R	27	0	0	10
 input1.bam	FBtr0070001	72	9	0	F	27	0	0	10
-input1.bam	FBtr0070001	72	9	0	R	27	0	0	10
 input1.bam	FBtr0070001	72	10	0	F	27	0	0	10
-input1.bam	FBtr0070001	72	10	0	R	27	0	0	10
 input1.bam	FBtr0070001	72	11	2	F	27	20.5	20.5	12
-input1.bam	FBtr0070001	72	11	0	R	27	0	0	12
 input1.bam	FBtr0070001	72	12	0	F	27	0	0	12
-input1.bam	FBtr0070001	72	12	0	R	27	0	0	12
 input1.bam	FBtr0070001	72	13	0	F	27	0	0	12
-input1.bam	FBtr0070001	72	13	0	R	27	0	0	12
 input1.bam	FBtr0070001	72	14	0	F	27	0	0	12
-input1.bam	FBtr0070001	72	14	0	R	27	0	0	12
 input1.bam	FBtr0070001	72	15	0	F	27	0	0	12
-input1.bam	FBtr0070001	72	15	0	R	27	0	0	12
 input1.bam	FBtr0070001	72	16	1	F	27	19.0	19.0	13
-input1.bam	FBtr0070001	72	16	0	R	27	0	0	13
 input1.bam	FBtr0070001	72	17	1	F	27	23.0	23.0	14
-input1.bam	FBtr0070001	72	17	0	R	27	0	0	14
 input1.bam	FBtr0070001	72	18	1	F	27	16.0	16.0	14
-input1.bam	FBtr0070001	72	18	0	R	27	0	0	14
 input1.bam	FBtr0070001	72	19	0	F	27	0	0	14
-input1.bam	FBtr0070001	72	19	0	R	27	0	0	14
 input1.bam	FBtr0070001	72	20	0	F	27	0	0	14
-input1.bam	FBtr0070001	72	20	0	R	27	0	0	14
 input1.bam	FBtr0070001	72	21	0	F	27	0	0	14
-input1.bam	FBtr0070001	72	21	0	R	27	0	0	14
 input1.bam	FBtr0070001	72	22	0	F	27	0	0	14
-input1.bam	FBtr0070001	72	22	0	R	27	0	0	14
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 input2.bam	FBtr0080664	71	39	1	F	135	17.0	17.0	263
-input2.bam	FBtr0080664	71	39	0	R	135	0	0	263
 input2.bam	FBtr0080664	71	40	0	F	135	0	0	263
-input2.bam	FBtr0080664	71	40	0	R	135	0	0	263
 input2.bam	FBtr0080664	71	41	0	F	135	0	0	262
-input2.bam	FBtr0080664	71	41	0	R	135	0	0	262
 input2.bam	FBtr0080664	71	42	1	F	135	20.0	20.0	262
-input2.bam	FBtr0080664	71	42	0	R	135	0	0	262
 input2.bam	FBtr0080664	71	43	0	F	135	0	0	260
-input2.bam	FBtr0080664	71	43	0	R	135	0	0	260
 input2.bam	FBtr0080664	71	44	0	F	135	0	0	263
-input2.bam	FBtr0080664	71	44	0	R	135	0	0	263
 input2.bam	FBtr0080664	71	45	0	F	135	0	0	263
-input2.bam	FBtr0080664	71	45	0	R	135	0	0	263
 input2.bam	FBtr0080664	71	46	0	F	135	0	0	263
-input2.bam	FBtr0080664	71	46	0	R	135	0	0	263
 input2.bam	FBtr0080664	71	47	1	F	135	15.0	15.0	264
-input2.bam	FBtr0080664	71	47	0	R	135	0	0	264
 input2.bam	FBtr0080664	71	48	0	F	135	0	0	264
-input2.bam	FBtr0080664	71	48	0	R	135	0	0	264
 input2.bam	FBtr0080664	71	49	0	F	135	0	0	254
-input2.bam	FBtr0080664	71	49	0	R	135	0	0	254
 input2.bam	FBtr0080664	71	50	2	F	135	15.5	15.5	72
-input2.bam	FBtr0080664	71	50	0	R	135	0	0	72
 input2.bam	FBtr0080664	71	51	0	F	135	0	0	63
-input2.bam	FBtr0080664	71	51	0	R	135	0	0	63
 input2.bam	FBtr0080664	71	52	1	F	135	16.0	16.0	61
-input2.bam	FBtr0080664	71	52	0	R	135	0	0	61
 input2.bam	FBtr0080664	71	53	1	F	135	19.0	19.0	31
-input2.bam	FBtr0080664	71	53	0	R	135	0	0	31
 input2.bam	FBtr0080664	71	54	0	F	135	0	0	30
-input2.bam	FBtr0080664	71	54	0	R	135	0	0	30
 input2.bam	FBtr0080664	71	55	0	F	135	0	0	21
-input2.bam	FBtr0080664	71	55	0	R	135	0	0	21
 input2.bam	FBtr0080664	71	56	1	F	135	16.0	16.0	16
-input2.bam	FBtr0080664	71	56	0	R	135	0	0	16
 input2.bam	FBtr0080664	71	57	2	F	135	15.0	15.0	18
-input2.bam	FBtr0080664	71	57	0	R	135	0	0	18
 input2.bam	FBtr0080664	71	58	0	F	135	0	0	18
-input2.bam	FBtr0080664	71	58	0	R	135	0	0	18
 input2.bam	FBtr0080664	71	59	0	F	135	0	0	18
-input2.bam	FBtr0080664	71	59	0	R	135	0	0	18
 input2.bam	FBtr0080664	71	60	0	F	135	0	0	17
-input2.bam	FBtr0080664	71	60	0	R	135	0	0	17
 input2.bam	FBtr0080664	71	61	0	F	135	0	0	16
-input2.bam	FBtr0080664	71	61	0	R	135	0	0	16
 input2.bam	FBtr0080664	71	62	0	F	135	0	0	12
 input2.bam	FBtr0080664	71	62	1	R	135	23.0	23.0	12
 input2.bam	FBtr0080664	71	63	0	F	135	0	0	8
-input2.bam	FBtr0080664	71	63	0	R	135	0	0	8
 input2.bam	FBtr0080664	71	64	0	F	135	0	0	8
-input2.bam	FBtr0080664	71	64	0	R	135	0	0	8
 input2.bam	FBtr0080664	71	65	0	F	135	0	0	7
-input2.bam	FBtr0080664	71	65	0	R	135	0	0	7
 input2.bam	FBtr0080664	71	66	0	F	135	0	0	6
-input2.bam	FBtr0080664	71	66	0	R	135	0	0	6
 input2.bam	FBtr0080664	71	67	0	F	135	0	0	6
-input2.bam	FBtr0080664	71	67	0	R	135	0	0	6
 input2.bam	FBtr0080664	71	68	0	F	135	0	0	5
-input2.bam	FBtr0080664	71	68	0	R	135	0	0	5
 input2.bam	FBtr0080664	71	69	0	F	135	0	0	5
-input2.bam	FBtr0080664	71	69	0	R	135	0	0	5
 input2.bam	FBtr0080664	71	70	0	F	135	0	0	5
-input2.bam	FBtr0080664	71	70	0	R	135	0	0	5
 input2.bam	FBtr0080664	71	71	0	F	135	0	0	5
 input2.bam	FBtr0080664	71	71	1	R	135	22.0	22.0	5
Binary file test-data/sizes.pdf has changed