# HG changeset patch
# User mvdbeek
# Date 1521105202 14400
# Node ID f6311a04a6c968d143015624b600e9ca1e97c8fa
# Parent  93f7962a3e19506bfb0dc33a76b59b2de1024fc7
planemo upload for repository https://github.com/bardin-lab/readtagger/tree/master/galaxy commit 6ac744bd9d610990d1d54a2c36ddfca671b15205-dirty

diff -r 93f7962a3e19 -r f6311a04a6c9 add_matesequence.xml
--- a/add_matesequence.xml	Sat Jan 06 07:21:25 2018 -0500
+++ b/add_matesequence.xml	Thu Mar 15 05:13:22 2018 -0400
@@ -1,7 +1,7 @@
-<tool id="add_matesequence" name="Add matesequence" version="0.4.6">
+<tool id="add_matesequence" name="Add matesequence" version="0.4.9">
     <description>into tag field</description>
     <requirements>
-        <requirement type="package" version="0.4.6">readtagger</requirement>
+        <requirement type="package" version="0.4.9">readtagger</requirement>
     </requirements>
     <version_command>add_matesequence --version</version_command>
     <command detect_errors="aggressive"><![CDATA[
diff -r 93f7962a3e19 -r f6311a04a6c9 allow_dovetailing.xml
--- a/allow_dovetailing.xml	Sat Jan 06 07:21:25 2018 -0500
+++ b/allow_dovetailing.xml	Thu Mar 15 05:13:22 2018 -0400
@@ -1,7 +1,7 @@
-<tool id="allow_dovetailing" name="Allow dovetailing" version="0.4.6">
+<tool id="allow_dovetailing" name="Allow dovetailing" version="0.4.9">
     <description>modifies proper_pair flag in bam files</description>
     <requirements>
-        <requirement type="package" version="0.4.6">readtagger</requirement>
+        <requirement type="package" version="0.4.9">readtagger</requirement>
     </requirements>
     <command detect_errors="aggressive"><![CDATA[
         allow_dovetailing -i '$input' -o '$output'
diff -r 93f7962a3e19 -r f6311a04a6c9 bam_readtagger.xml
--- a/bam_readtagger.xml	Sat Jan 06 07:21:25 2018 -0500
+++ b/bam_readtagger.xml	Thu Mar 15 05:13:22 2018 -0400
@@ -1,10 +1,10 @@
-<tool id="bam_readtagger" name="Tag alignment files" version="0.4.6">
+<tool id="bam_readtagger" name="Tag alignment files" version="0.4.9">
     <description>from multiple bam files</description>
     <macros>
         <import>macros.xml</import>
     </macros>
     <requirements>
-        <requirement type="package" version="0.4.6">readtagger</requirement>
+        <requirement type="package" version="0.4.9">readtagger</requirement>
     </requirements>
     <command detect_errors="aggressive"><![CDATA[
         readtagger -t '$tag_file' -s
diff -r 93f7962a3e19 -r f6311a04a6c9 deploy.sh
diff -r 93f7962a3e19 -r f6311a04a6c9 filter_insertions.xml
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/filter_insertions.xml	Thu Mar 15 05:13:22 2018 -0400
@@ -0,0 +1,56 @@
+<tool id="confirm_insertions" name="Confirm or discard insertions" version="0.4.9">
+    <description>based on softclips in control files</description>
+    <requirements>
+        <requirement type="package" version="0.4.9">readtagger</requirement>
+    </requirements>
+    <version_command>confirm_insertions --version</version_command>
+    <command detect_errors="aggressive"><![CDATA[
+        confirm_insertions
+        --putative_insertions_path '$putative_insertions'
+        --all_treatments_path '$all_insertions'
+        --all_controls_path '$all_controls'
+        --output_path '$output'
+        $output_discard
+    ]]></command>
+    <inputs>
+        <param name="putative_insertions" label="Path to filtered putative insertinos" argument="--putative_insertions_path" type="data" format="gff3"/>
+        <param name="all_insertions" label="Path to all unfiltered insertions" argument="--all_treatments_path" type="data" format="gff3"/>
+        <param name="all_controls" label="Path to all unfiltered insertions from control sample" argument="--all_controls_path" type="data" format="gff3"/>
+        <param name="output_discard" label="Output discarded records? Thye will be marked as failed." truevalue="--output_discarded_records" falsevalue="--no_output_discarded_records" checked="True" type="boolean"/>
+    </inputs>
+    <outputs>
+        <data name="output" format="gff3"/>
+    </outputs>
+    <tests>
+        <test>
+            <param name="putative_insertions" value="putative_insertions.gff" ftype="gff3"/>
+            <param name="all_insertions" value="all_treatment_insertions.gff" ftype="gff3"/>
+            <param name="all_controls" value="all_control_insertions.gff" ftype="gff3"/>
+            <output name="output" file="confirmed_insertions.gff" ftype="gff3"/>
+        </test>
+    </tests>
+    <help><![CDATA[
+.. code-block::
+
+
+    Usage: confirm_insertions [OPTIONS]
+
+      Confirm insertions by checking that control file does not contain the same
+      clipping pattern.
+
+    Options:
+      -p, --putative_insertions_path PATH
+                                      Path to file containing putative somatic
+                                      insertions  [required]
+      -t, --all_treatments_path PATH  Path to file containing all treatment
+                                      insertions  [required]
+      -c, --all_controls_path PATH    Path to file containing all control
+                                      insertions  [required]
+      -o, --output_path TEXT          Write annotated output to this Path.
+      --output_discarded_records / --no_output_discarded_records
+                                      Discard an alternative flag if the current
+                                      read is in a proper pair.
+      --version                       Show the version and exit.
+      --help                          Show this message and exit.
+    ]]></help>
+</tool>
diff -r 93f7962a3e19 -r f6311a04a6c9 findcluster.xml
--- a/findcluster.xml	Sat Jan 06 07:21:25 2018 -0500
+++ b/findcluster.xml	Thu Mar 15 05:13:22 2018 -0400
@@ -1,10 +1,10 @@
-<tool id="findcluster" name="Find clusters of reads" version="0.4.6">
+<tool id="findcluster" name="Find clusters of reads" version="0.4.9">
     <description>in bam files</description>
     <macros>
         <import>macros.xml</import>
     </macros>
     <requirements>
-        <requirement type="package" version="0.4.6">readtagger</requirement>
+        <requirement type="package" version="0.4.9">readtagger</requirement>
     </requirements>
     <version_command>findcluster --version</version_command>
     <command detect_errors="aggressive"><![CDATA[
@@ -49,7 +49,7 @@
         <test>
             <param name="input" value="extended_and_annotated_roi.bam" ftype="bam"/>
             <output name="output_bam" file="three_cluster_out.bam" ftype="bam" lines_diff="2"/>
-            <output name="output_gff" file="three_cluster_out.gff" ftype="gff3" lines_diff="0"/>
+            <output name="output_gff" file="three_cluster_out.gff" ftype="gff3" lines_diff="0" sort="True"/>
         </test>
         <test>
             <param name="input" value="extended_and_annotated_roi.bam" ftype="bam"/>
diff -r 93f7962a3e19 -r f6311a04a6c9 plot_coverage.xml
--- a/plot_coverage.xml	Sat Jan 06 07:21:25 2018 -0500
+++ b/plot_coverage.xml	Thu Mar 15 05:13:22 2018 -0400
@@ -1,7 +1,7 @@
-<tool id="plot_coverage" name="Plot coverage" version="0.4.6">
+<tool id="plot_coverage" name="Plot coverage" version="0.4.9">
     <description>as area plot between BAM files</description>
     <requirements>
-        <requirement type="package" version="0.4.6">readtagger</requirement>
+        <requirement type="package" version="0.4.9">readtagger</requirement>
     </requirements>
     <command detect_errors="aggressive"><![CDATA[
         #import re
@@ -17,6 +17,7 @@
                 <valid initial="string.letters,string.digits">
                     <add value="-" />
                     <add value="," />
+                    <add value=":" />
                 </valid>
             </sanitizer>
         </param>
diff -r 93f7962a3e19 -r f6311a04a6c9 test-data/a_pasteurianus_tagged_with_dm6.bam
Binary file test-data/a_pasteurianus_tagged_with_dm6.bam has changed
diff -r 93f7962a3e19 -r f6311a04a6c9 test-data/a_pasteurianus_tagged_with_dm6_discarded.bam
Binary file test-data/a_pasteurianus_tagged_with_dm6_discarded.bam has changed
diff -r 93f7962a3e19 -r f6311a04a6c9 test-data/a_pasteurianus_tagged_with_dm6_verified.bam
Binary file test-data/a_pasteurianus_tagged_with_dm6_verified.bam has changed
diff -r 93f7962a3e19 -r f6311a04a6c9 test-data/all_control_insertions.gff
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/all_control_insertions.gff	Thu Mar 15 05:13:22 2018 -0400
@@ -0,0 +1,2 @@
+X	find_softclip	5p_clip	16727068	16727067	3	+	.	ID=R38_2472;consensus=ACTTAATA;max_mapq=25
+X	find_softclip	3p_clip	16727112	16727111	4	+	.	ID=R38_2473;consensus=TTTAATAAAATTAAAGGACAACTAAACGGAAGGAAAATATCGTGAGCAG;max_mapq=28
diff -r 93f7962a3e19 -r f6311a04a6c9 test-data/all_treatment_insertions.gff
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/all_treatment_insertions.gff	Thu Mar 15 05:13:22 2018 -0400
@@ -0,0 +1,12 @@
+X	feature	predicted_insertion	10766937	10766942	.	+	.	Parent=R37_49;contig_support=2;fraction_full_length=0.03132530120481928;sbjct=RR48388_transposable_element_rover_Gypsy;sbjct_end=7308;sbjct_start=7074;type=predicted_insertion
+X	findcluster	transposable_element_rover	10766937	10766942	24	+	.	ID=R37_49;genotype=heterozygous;genotype_likelihoods=6.86863481923e-26,0.999999994797,5.2033283093e-09;insert_reference_name=transposable_element_rover;left_inserts=0,GGGGTGCATATATAGCGCACATATGTACATATTTGTACATATATAGTAACATAATATGCTTCTCATATTACGTTTACATACTTACACTAATTGTACATACAATCTTGCACATGCA,1,CAACAATGTATTATCCTACCGACTGCGCCACTTACGTATTTTACTATTCGAGTCGAACAAATGATCCGTCGTTTGACTAAGATCAACGCCTTTAAAGAAGTTTCAGAATCAACACGAGGTATTTTTTTAGTTTGGA;left_mate_count=4;max_mapq=60;nref=12;right_inserts=0,GGCGTTGATCTTAGTCAAACGACGGATCATTTGTTCGACTCGAATAGTAAAATACGTAAGTATATACATATGCATATGCAGTCCGAATCAAAATCGAAAACAAGAACTGCACTTTTCGCTGCGATTGGGGCACCTTCAGC,1,GTTTACATACTTACACTAATTGTACATACAATCTTGCACATGCATAAACACATCAAACCAGCTTACATTTTTACTTACACTTAAGCGCATGATTTGTTGTGCATCCATACCGTTATTTTTCCGTTCTTTTTTTGTACACATATACTGATTAGACATTCCCGTTTAT,2,CACATATACTGATTAGACATTCCCGTTTATCGCGACTCACTTCGAGCCGATCAAAAACTCTGTACAGTCAGTCTTAAGCCGACAACGAAGAAATAAAGATCCAAACTAAAAAAATACCTCGTGTTGATTCTGAAACTTCTTTAAAGGCGTTGATCTTAGTCAAACGACGGATCATTTGTT;right_mate_count=14;total_left_count=6;total_right_count=18;valid_TSD=True
+X	find_softclip	5p_clip	10766937	10766936	6	+	.	ID=R37_2667;consensus=GGCGTTGATCTTAGTCAAACGACGGATCATTTGTTCGACTCGAATAGTAAAATACGTAAG;max_mapq=60
+X	find_softclip	3p_clip	10766943	10766942	3	+	.	ID=R37_2668;consensus=GTAACATAATATGCTTCTCATATTACGTTTACATACTTACACTAATTGTACATACAATCTTGCACATGCA;max_mapq=60
+X	feature	left_insert	16726713	16727261	.	+	.	Parent=R37_26;fraction_full_length=0.003280519299225239;read_support=1;sbjct=FBti0059747_gtwin_Gypsy;sbjct_end=2536;sbjct_start=2489;type=left_insert
+X	findcluster	gtwin	16726713	16727261	1	+	.	ID=R37_26;genotype=reference;genotype_likelihoods=1.0,1.93425522512e-14,6.88207144991e-72;insert_reference_name=gtwin;left_inserts=;left_mate_count=0;max_mapq=60;nref=47;right_inserts=;right_mate_count=1;total_left_count=0;total_right_count=1;valid_TSD=False
+X	feature	left_insert	16727068	16727111	.	+	.	Parent=R37_27;fraction_full_length=0.6875;read_support=1;sbjct=FBti0062261_jockey2_Jockey;sbjct_end=63;sbjct_start=19;type=left_insert
+X	feature	right_insert	16727068	16727111	.	+	.	Parent=R37_27;fraction_full_length=0.0017704870646047116;read_support=1;sbjct=FBti0062666_HMS-Beagle_Gypsy;sbjct_end=10537;sbjct_start=10488;type=right_insert
+X	findcluster	jockey2	16727068	16727111	6	+	.	ID=R37_27;genotype=heterozygous;genotype_likelihoods=8.55882087985e-05,0.999914411654,1.37666001367e-10;insert_reference_name=jockey2;left_inserts=;left_mate_count=0;max_mapq=25;nref=9;right_inserts=0,GATATGGACTTAATTGGAAATTAATTAATGCAATAATCCAATTAAGAATTTAATATTTAAAAAGGTGGACTGAATACTTAATACAAGAAGGATAATAGTACGCTAGTCAATTAAATAAAATAATTTCTTTAATAAAATTAAAGGAC;right_mate_count=2;total_left_count=3;total_right_count=4;valid_TSD=True
+X	find_softclip	3p_clip	16727068	16727111	6	+	.	Parent=R37_27;consensus=TTTAATAAAATTAAAGGAC;max_mapq=34
+X	find_softclip	5p_clip	16727068	16727111	5	+	.	Parent=R37_27;consensus=GAATTTAATATTTAAAAAGGTGGACTGAATACTTAATA;max_mapq=34
+X	find_softclip	3p_clip	16727110	16727109	1	+	.	ID=R37_2929;consensus=CCTTTAATAAAATTAAAGGACAACTAAACGGAAGGAAAATATCGTGAGCAGAAAATAATATTAAGTCTTTAAAAG;max_mapq=34
diff -r 93f7962a3e19 -r f6311a04a6c9 test-data/confirmed_insertions.gff
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/confirmed_insertions.gff	Thu Mar 15 05:13:22 2018 -0400
@@ -0,0 +1,2 @@
+X	findcluster	transposable_element_rover	10766937	10766942	24	+	.	ID=R37_49;genotype=heterozygous;genotype_likelihoods=6.86863481923e-26,0.999999994797,5.2033283093e-09;insert_reference_name=transposable_element_rover;left_inserts=0,GGGGTGCATATATAGCGCACATATGTACATATTTGTACATATATAGTAACATAATATGCTTCTCATATTACGTTTACATACTTACACTAATTGTACATACAATCTTGCACATGCA,1,CAACAATGTATTATCCTACCGACTGCGCCACTTACGTATTTTACTATTCGAGTCGAACAAATGATCCGTCGTTTGACTAAGATCAACGCCTTTAAAGAAGTTTCAGAATCAACACGAGGTATTTTTTTAGTTTGGA;left_mate_count=4;max_mapq=60;nref=12;right_inserts=0,GGCGTTGATCTTAGTCAAACGACGGATCATTTGTTCGACTCGAATAGTAAAATACGTAAGTATATACATATGCATATGCAGTCCGAATCAAAATCGAAAACAAGAACTGCACTTTTCGCTGCGATTGGGGCACCTTCAGC,1,GTTTACATACTTACACTAATTGTACATACAATCTTGCACATGCATAAACACATCAAACCAGCTTACATTTTTACTTACACTTAAGCGCATGATTTGTTGTGCATCCATACCGTTATTTTTCCGTTCTTTTTTTGTACACATATACTGATTAGACATTCCCGTTTAT,2,CACATATACTGATTAGACATTCCCGTTTATCGCGACTCACTTCGAGCCGATCAAAAACTCTGTACAGTCAGTCTTAAGCCGACAACGAAGAAATAAAGATCCAAACTAAAAAAATACCTCGTGTTGATTCTGAAACTTCTTTAAAGGCGTTGATCTTAGTCAAACGACGGATCATTTGTT;right_mate_count=14;total_left_count=6;total_right_count=18;valid_TSD=True
+X	findcluster	jockey2	16727068	16727111	6	+	.	ID=R37_27;genotype=heterozygous;genotype_likelihoods=8.55882087985e-05,0.999914411654,1.37666001367e-10;insert_reference_name=jockey2;left_inserts=;left_mate_count=0;max_mapq=25;nref=9;right_inserts=0,GATATGGACTTAATTGGAAATTAATTAATGCAATAATCCAATTAAGAATTTAATATTTAAAAAGGTGGACTGAATACTTAATACAAGAAGGATAATAGTACGCTAGTCAATTAAATAAAATAATTTCTTTAATAAAATTAAAGGAC;right_mate_count=2;total_left_count=3;total_right_count=4;valid_TSD=True;FAIL=clip_seq_in_control
diff -r 93f7962a3e19 -r f6311a04a6c9 test-data/dm6_mate_annotated.bam
Binary file test-data/dm6_mate_annotated.bam has changed
diff -r 93f7962a3e19 -r f6311a04a6c9 test-data/dm6_tagged_with_a_pasteurianus.bam
Binary file test-data/dm6_tagged_with_a_pasteurianus.bam has changed
diff -r 93f7962a3e19 -r f6311a04a6c9 test-data/dm6_tagged_with_a_pasteurianus_discarded.bam
Binary file test-data/dm6_tagged_with_a_pasteurianus_discarded.bam has changed
diff -r 93f7962a3e19 -r f6311a04a6c9 test-data/dm6_tagged_with_a_pasteurianus_verified.bam
Binary file test-data/dm6_tagged_with_a_pasteurianus_verified.bam has changed
diff -r 93f7962a3e19 -r f6311a04a6c9 test-data/proper_pair_discard_out.bam
Binary file test-data/proper_pair_discard_out.bam has changed
diff -r 93f7962a3e19 -r f6311a04a6c9 test-data/proper_pair_discard_verified_empty.bam
Binary file test-data/proper_pair_discard_verified_empty.bam has changed
diff -r 93f7962a3e19 -r f6311a04a6c9 test-data/proper_pair_out_suboptimal_tags.bam
Binary file test-data/proper_pair_out_suboptimal_tags.bam has changed
diff -r 93f7962a3e19 -r f6311a04a6c9 test-data/putative_insertions.gff
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/putative_insertions.gff	Thu Mar 15 05:13:22 2018 -0400
@@ -0,0 +1,2 @@
+X	findcluster	transposable_element_rover	10766937	10766942	24	+	.	ID=R37_49;genotype=heterozygous;genotype_likelihoods=6.86863481923e-26,0.999999994797,5.2033283093e-09;insert_reference_name=transposable_element_rover;left_inserts=0,GGGGTGCATATATAGCGCACATATGTACATATTTGTACATATATAGTAACATAATATGCTTCTCATATTACGTTTACATACTTACACTAATTGTACATACAATCTTGCACATGCA,1,CAACAATGTATTATCCTACCGACTGCGCCACTTACGTATTTTACTATTCGAGTCGAACAAATGATCCGTCGTTTGACTAAGATCAACGCCTTTAAAGAAGTTTCAGAATCAACACGAGGTATTTTTTTAGTTTGGA;left_mate_count=4;max_mapq=60;nref=12;right_inserts=0,GGCGTTGATCTTAGTCAAACGACGGATCATTTGTTCGACTCGAATAGTAAAATACGTAAGTATATACATATGCATATGCAGTCCGAATCAAAATCGAAAACAAGAACTGCACTTTTCGCTGCGATTGGGGCACCTTCAGC,1,GTTTACATACTTACACTAATTGTACATACAATCTTGCACATGCATAAACACATCAAACCAGCTTACATTTTTACTTACACTTAAGCGCATGATTTGTTGTGCATCCATACCGTTATTTTTCCGTTCTTTTTTTGTACACATATACTGATTAGACATTCCCGTTTAT,2,CACATATACTGATTAGACATTCCCGTTTATCGCGACTCACTTCGAGCCGATCAAAAACTCTGTACAGTCAGTCTTAAGCCGACAACGAAGAAATAAAGATCCAAACTAAAAAAATACCTCGTGTTGATTCTGAAACTTCTTTAAAGGCGTTGATCTTAGTCAAACGACGGATCATTTGTT;right_mate_count=14;total_left_count=6;total_right_count=18;valid_TSD=True
+X	findcluster	jockey2	16727068	16727111	6	+	.	ID=R37_27;genotype=heterozygous;genotype_likelihoods=8.55882087985e-05,0.999914411654,1.37666001367e-10;insert_reference_name=jockey2;left_inserts=;left_mate_count=0;max_mapq=25;nref=9;right_inserts=0,GATATGGACTTAATTGGAAATTAATTAATGCAATAATCCAATTAAGAATTTAATATTTAAAAAGGTGGACTGAATACTTAATACAAGAAGGATAATAGTACGCTAGTCAATTAAATAAAATAATTTCTTTAATAAAATTAAAGGAC;right_mate_count=2;total_left_count=3;total_right_count=4;valid_TSD=True
diff -r 93f7962a3e19 -r f6311a04a6c9 test-data/three_cluster_out.bam
Binary file test-data/three_cluster_out.bam has changed
diff -r 93f7962a3e19 -r f6311a04a6c9 test-data/three_cluster_out.gff
--- a/test-data/three_cluster_out.gff	Sat Jan 06 07:21:25 2018 -0500
+++ b/test-data/three_cluster_out.gff	Thu Mar 15 05:13:22 2018 -0400
@@ -1,3 +1,8 @@
 ##gff-version 3
-3R	findcluster	TE	13373515	13373524	22	+	.	ID=extended_and_annotated_roi.bam_0;genotype=homozygous;genotype_likelihoods=1.8828617809e-31,9.53673406912e-07,0.999999046327;left_insert=0,CTCGGAATGTATCTAACTAACAAACTCATATCAAATATAAGCAAGTGCGCCAATTCGTATGCATATGGACATATGGACATATACATATAGTAACATAATATGCTTCTCATATTACGTTTACATACTTACACTAATTGTACATACAATCTTGCACATGCATAAACACATCAAACCAGCTTACATTTTTACTTACACTTAAGCGCATGATTTGTTGTGCATCCATACCGTTATTTTTCC;left_mate_support=8;left_support=11;non_support=0;right_insert=0,GACAACGAAGAAATAAAGATCCAAACTAAAAAAATACCTCGTGTTGATTCTGAAACTTCTTTAAAGGCGTTGATCTTAGTCAAACGACGGATCATTTGTTCGACTCGAATAGTAAAATACGTAAGTATATAGATAGTCTATATTAATTTTAAAAGCTCAAAGGGGCGCAAGTCTCTCTCATCAGTTGTGTCTTTAGTTTTTTTGATTTGGTTTGGTG;right_mate_support=6;right_support=11;valid_TSD=False
-3R	findcluster	TE	13374595	13374676	3	+	.	ID=extended_and_annotated_roi.bam_1;genotype=homozygous;genotype_likelihoods=0.00038864889331,0.199922270221,0.799689080885;left_insert=0,GTTCACCCGCGTCCGAGTTCCTGCTCCACTACTCCCTGGCTGCTGACTCACTGTTGTTATAGGGGTGGCTTCCCCTCTGTTCTTCCTGGGGGAATGCTGCATCTTCCCCAGCTCCAAAATGGCGG;left_mate_support=2;left_support=2;non_support=0;right_insert=;right_mate_support=1;right_support=1;valid_TSD=False
+3R	findcluster	TE	13373206	13373206	2	+	.	ID=extended_and_annotated_roi.bam_0;genotype=homozygous;genotype_likelihoods=0.010684606252473286,0.32977179791584216,0.6595435958316843;insert_reference_name=None;left_inserts=;left_mate_count=2;max_mapq=60;nref=0;right_inserts=;right_mate_count=0;total_left_count=2;total_right_count=0;valid_TSD=False
+3R	find_softclip	3p_clip	13373515	13373524	7	+	.	Parent=extended_and_annotated_roi.bam_1;consensus=ACATATAGTAACATAATATGCTTCTCATATTACGTTTACATACTTACACTAATTGTAC;max_mapq=60
+3R	find_softclip	5p_clip	13373515	13373524	6	+	.	Parent=extended_and_annotated_roi.bam_1;consensus=CTTAGTCAAACGACGGATCATTTGTTCGACTCGAATAGTAAAATACGTAAGT;max_mapq=60
+3R	findcluster	TE	13373515	13373524	20	+	.	ID=extended_and_annotated_roi.bam_1;genotype=homozygous;genotype_likelihoods=6.2761999508986e-30,1.9073449948406318e-06,0.9999980926550052;insert_reference_name=None;left_inserts=0,GGAAAAATAACGGTATGGATGCACAACAAATCATGCGCTTAAGTGTAAGTAAAAATGTAAGCTGGTTTGATGTGTTTATGCATGTGCAAGATTGTATGTACAATTAGTGTAAGTATGTAAACGTAATATGAGAAGCATATTATGTTACTATATGTATATGTCCATATGTCCATATGCATACGAATTGGCGCACTTGCTTATATTTGATATGAGTTTGTTAGTTAGATACATTCCGAG;left_mate_count=6;max_mapq=60;nref=0;right_inserts=0,GACAACGAAGAAATAAAGATCCAAACTAAAAAAATACCTCGTGTTGATTCTGAAACTTCTTTAAAGGCGTTGATCTTAGTCAAACGACGGATCATTTGTTCGACTCGAATAGTAAAATACGTAAGTATATAGATAGTCTATATTAATTTTAAAAGCTCAAAGGGGCGCAAGTCTCTCTCATCAGTTGTGTCTTTAGTTTTTTTGATTTGGTTTGGTG;right_mate_count=6;total_left_count=9;total_right_count=11;valid_TSD=False
+3R	findcluster	TE	13374539	13374676	1	+	.	ID=extended_and_annotated_roi.bam_2;genotype=homozygous;genotype_likelihoods=0.21259842519685054,0.3937007874015747;insert_reference_name=None;left_inserts=;left_mate_count=0;max_mapq=60;nref=0;right_inserts=;right_mate_count=1;total_left_count=0;total_right_count=1;valid_TSD=False
+3R	findcluster	TE	13374595	13374709	2	+	.	ID=extended_and_annotated_roi.bam_3;genotype=homozygous;genotype_likelihoods=0.010684606252473286,0.32977179791584216,0.6595435958316843;insert_reference_name=None;left_inserts=0,GTTCACCCGCGTCCGAGTTCCTGCTCCACTACTCCCTGGCTGCTGACTCACTGTTGTTATAGGGGTGGCTTCCCCTCTGTTCTTCCTGGGGGAATGCTGCATCTTCCCCAGCTCCAAAATGGCGG;left_mate_count=2;max_mapq=60;nref=0;right_inserts=;right_mate_count=0;total_left_count=2;total_right_count=0;valid_TSD=False
+3R	find_softclip	5p_clip	13374677	13374676	1	+	.	ID=extended_and_annotated_roi.bam_4;consensus=TGGCAAAACATATGCAAAGTGCA;max_mapq=60
diff -r 93f7962a3e19 -r f6311a04a6c9 test-data/three_cluster_plot.pdf
Binary file test-data/three_cluster_plot.pdf has changed
diff -r 93f7962a3e19 -r f6311a04a6c9 update_mapq.xml
--- a/update_mapq.xml	Sat Jan 06 07:21:25 2018 -0500
+++ b/update_mapq.xml	Thu Mar 15 05:13:22 2018 -0400
@@ -1,7 +1,7 @@
-<tool id="update_mapq" name="Update MAPQ score" version="0.4.6">
+<tool id="update_mapq" name="Update MAPQ score" version="0.4.9">
     <description>of supplementary alignments</description>
     <requirements>
-        <requirement type="package" version="0.4.6">readtagger</requirement>
+        <requirement type="package" version="0.4.9">readtagger</requirement>
     </requirements>
     <version_command>update_mapq --version</version_command>
     <command detect_errors="aggressive"><![CDATA[
diff -r 93f7962a3e19 -r f6311a04a6c9 write_supplementary_fastq.xml
--- a/write_supplementary_fastq.xml	Sat Jan 06 07:21:25 2018 -0500
+++ b/write_supplementary_fastq.xml	Thu Mar 15 05:13:22 2018 -0400
@@ -1,7 +1,7 @@
-<tool id="write_supplementary_fastq" name="Extract supplementary alignments" version="0.4.6">
+<tool id="write_supplementary_fastq" name="Extract supplementary alignments" version="0.4.9">
     <description>from SAM/BAM alignment files as FASTQ</description>
     <requirements>
-        <requirement type="package" version="0.4.6">readtagger</requirement>
+        <requirement type="package" version="0.4.9">readtagger</requirement>
     </requirements>
     <version_command>write_supplementary_fastq --version</version_command>
     <command detect_errors="aggressive"><![CDATA[