# HG changeset patch
# User artbio
# Date 1556210945 14400
# Node ID 14adf24603b64ee74d3df5dd8b1a5e60145a2b7a
# Parent  fe1a9cfaf5c3542dce8248868174864c5baf4dc3
planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/small_rna_maps commit ebb322e2ed6989d2a7520e8c5ffc7a7477907aef

diff -r fe1a9cfaf5c3 -r 14adf24603b6 delphine
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/delphine	Thu Apr 25 12:49:05 2019 -0400
@@ -0,0 +1,30 @@
+-----BEGIN RSA PRIVATE KEY-----
+Proc-Type: 4,ENCRYPTED
+DEK-Info: AES-128-CBC,0F428118B5D165772A9B414AC1C31A31
+
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+-----END RSA PRIVATE KEY-----
diff -r fe1a9cfaf5c3 -r 14adf24603b6 delphine.pub
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/delphine.pub	Thu Apr 25 12:49:05 2019 -0400
@@ -0,0 +1,1 @@
+ssh-rsa AAAAB3NzaC1yc2EAAAADAQABAAABAQCutrZRQSP+aGOboaDMnrazTziyuI9iAeK9CVtgOCKFzg5c+oBj7pkGPiYsWnJpYWn8vHyhAk/VSCmPHHlGR3aNMKg1x1NKNQXzodljdnXfAMs012rZnI4r8Gl/ww6rhVFfbxptVIKNdZxlLBDBxjvWJ6G6Y8MqGPCpFQsFWtKPRgYl9A8UNqtReindJKOc/TuIFFeHvuPMSU7m2ZqCMuKGCjbWPU9RwvPuYURxYiTXP7ooMZLRD1tbc+vQUGIMDX+gXpQ7ntonZVtDGxC5qQJeUKVtGgp1RKKJ4Zbje5UNd47E3TiJQPMgJJL8TqjjHcFQBqtQVyzBJdVlnHxCgnoB chris@GED-Server
diff -r fe1a9cfaf5c3 -r 14adf24603b6 small_rna_maps.py
--- a/small_rna_maps.py	Wed Apr 24 11:18:24 2019 -0400
+++ b/small_rna_maps.py	Thu Apr 25 12:49:05 2019 -0400
@@ -89,12 +89,8 @@
             else:
                 for read in bam_object.fetch(chrom):
                     positions = read.positions  # a list of covered positions
-                    if read.is_reverse:
-                        map_dictionary[(chrom, positions[-1]+1, 'F')].append(
-                                        read.query_alignment_length)
-                    else:
-                        map_dictionary[(chrom, positions[0]+1, 'F')].append(
-                                        read.query_alignment_length)
+                    map_dictionary[(chrom, positions[0]+1, 'F')].append(
+                                    read.query_alignment_length)
         return map_dictionary
 
     def grouper(self, iterable, clust_distance):
diff -r fe1a9cfaf5c3 -r 14adf24603b6 small_rna_maps.xml
--- a/small_rna_maps.xml	Wed Apr 24 11:18:24 2019 -0400
+++ b/small_rna_maps.xml	Thu Apr 25 12:49:05 2019 -0400
@@ -1,4 +1,4 @@
-<tool id="small_rna_maps" name="small_rna_maps" version="2.13.2">
+<tool id="small_rna_maps" name="small_rna_maps" version="2.14.0">
   <description></description>
   <requirements>
         <requirement type="package" version="1.11.2=py27_0">numpy</requirement>
diff -r fe1a9cfaf5c3 -r 14adf24603b6 test-data/bed2.bed
--- a/test-data/bed2.bed	Wed Apr 24 11:18:24 2019 -0400
+++ b/test-data/bed2.bed	Thu Apr 25 12:49:05 2019 -0400
@@ -17,7 +17,7 @@
 FBtr0079064	0	23	cluster_17	1	.	0.0434782608696
 FBtr0079090	0	28	cluster_18	1	.	0.0357142857143
 FBtr0079090	25	49	cluster_19	1	.	0.0416666666667
-FBtr0079090	55	76	cluster_20	1	.	0.047619047619
+FBtr0079090	35	56	cluster_20	1	.	0.047619047619
 FBtr0079338	12	31	cluster_21	1	.	0.0526315789474
 FBtr0079338	41	63	cluster_22	9	.	0.409090909091
 FBtr0079528	0	38	cluster_23	77	.	2.02631578947
diff -r fe1a9cfaf5c3 -r 14adf24603b6 test-data/clustering_unstranded.pdf
Binary file test-data/clustering_unstranded.pdf has changed
diff -r fe1a9cfaf5c3 -r 14adf24603b6 test-data/clustering_unstranded.tab
--- a/test-data/clustering_unstranded.tab	Wed Apr 24 11:18:24 2019 -0400
+++ b/test-data/clustering_unstranded.tab	Thu Apr 25 12:49:05 2019 -0400
@@ -32,7 +32,7 @@
 input1.bam	FBtr0079064	72	72	F	0	72-72	1	0.0
 input1.bam	FBtr0079090	72	1	F	1	1-28	28	0.0357142857143
 input1.bam	FBtr0079090	72	26	F	1	26-49	24	0.0416666666667
-input1.bam	FBtr0079090	72	56	F	1	56-76	21	0.047619047619
+input1.bam	FBtr0079090	72	36	F	1	36-56	21	0.047619047619
 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	13	F	1	13-31	19	0.0526315789474