# HG changeset patch
# User mvdbeek
# Date 1567353822 14400
# Node ID e675e6d349bd3c5e379150a3ec3f9b7af7c9d8c9
# Parent  16eba798cbc691b70105d311189b3be8c2b8cb87
"planemo upload for repository https://github.com/bardin-lab/readtagger/tree/master/galaxy commit 8ed4215b007a3f552e1b1964907a505858822fb4"

diff -r 16eba798cbc6 -r e675e6d349bd add_matesequence.xml
--- a/add_matesequence.xml	Sat Aug 31 09:48:36 2019 -0400
+++ b/add_matesequence.xml	Sun Sep 01 12:03:42 2019 -0400
@@ -1,7 +1,7 @@
-<tool id="add_matesequence" name="Add matesequence" version="0.5.9">
+<tool id="add_matesequence" name="Add matesequence" version="0.5.10">
     <description>into tag field</description>
     <requirements>
-        <requirement type="package" version="0.5.9">readtagger</requirement>
+        <requirement type="package" version="0.5.10">readtagger</requirement>
     </requirements>
     <version_command>add_matesequence --version</version_command>
     <command detect_errors="aggressive"><![CDATA[
diff -r 16eba798cbc6 -r e675e6d349bd allow_dovetailing.xml
--- a/allow_dovetailing.xml	Sat Aug 31 09:48:36 2019 -0400
+++ b/allow_dovetailing.xml	Sun Sep 01 12:03:42 2019 -0400
@@ -1,7 +1,7 @@
-<tool id="allow_dovetailing" name="Allow dovetailing" version="0.5.9">
+<tool id="allow_dovetailing" name="Allow dovetailing" version="0.5.10">
     <description>modifies proper_pair flag in bam files</description>
     <requirements>
-        <requirement type="package" version="0.5.9">readtagger</requirement>
+        <requirement type="package" version="0.5.10">readtagger</requirement>
     </requirements>
     <command detect_errors="aggressive"><![CDATA[
         allow_dovetailing -i '$input' -o '$output'
diff -r 16eba798cbc6 -r e675e6d349bd bam_readtagger.xml
--- a/bam_readtagger.xml	Sat Aug 31 09:48:36 2019 -0400
+++ b/bam_readtagger.xml	Sun Sep 01 12:03:42 2019 -0400
@@ -1,10 +1,10 @@
-<tool id="bam_readtagger" name="Tag alignment files" version="0.5.9">
+<tool id="bam_readtagger" name="Tag alignment files" version="0.5.10">
     <description>from multiple bam files</description>
     <macros>
         <import>macros.xml</import>
     </macros>
     <requirements>
-        <requirement type="package" version="0.5.9">readtagger</requirement>
+        <requirement type="package" version="0.5.10">readtagger</requirement>
     </requirements>
     <command detect_errors="aggressive"><![CDATA[
         readtagger -t '$tag_file' -s
diff -r 16eba798cbc6 -r e675e6d349bd extract_variants.xml
--- a/extract_variants.xml	Sat Aug 31 09:48:36 2019 -0400
+++ b/extract_variants.xml	Sun Sep 01 12:03:42 2019 -0400
@@ -1,7 +1,7 @@
-<tool id="extract_variants" name="Extract variant fragments" version="0.5.9">
+<tool id="extract_variants" name="Extract variant fragments" version="0.5.10">
     <description>from long reads</description>
     <requirements>
-        <requirement type="package" version="0.5.9">readtagger</requirement>
+        <requirement type="package" version="0.5.10">readtagger</requirement>
     </requirements>
     <version_command>extract_variants --version</version_command>
     <command detect_errors="aggressive"><![CDATA[
diff -r 16eba798cbc6 -r e675e6d349bd filter_insertions.xml
--- a/filter_insertions.xml	Sat Aug 31 09:48:36 2019 -0400
+++ b/filter_insertions.xml	Sun Sep 01 12:03:42 2019 -0400
@@ -1,7 +1,7 @@
-<tool id="confirm_insertions" name="Confirm or discard insertions" version="0.5.9">
+<tool id="confirm_insertions" name="Confirm or discard insertions" version="0.5.10">
     <description>based on softclips in control files</description>
     <requirements>
-        <requirement type="package" version="0.5.9">readtagger</requirement>
+        <requirement type="package" version="0.5.10">readtagger</requirement>
     </requirements>
     <version_command>confirm_insertions --version</version_command>
     <command detect_errors="aggressive"><![CDATA[
diff -r 16eba798cbc6 -r e675e6d349bd findcluster.xml
--- a/findcluster.xml	Sat Aug 31 09:48:36 2019 -0400
+++ b/findcluster.xml	Sun Sep 01 12:03:42 2019 -0400
@@ -1,10 +1,10 @@
-<tool id="findcluster" name="Find clusters of reads" version="0.5.9">
+<tool id="findcluster" name="Find clusters of reads" version="0.5.10">
     <description>in bam files</description>
     <macros>
         <import>macros.xml</import>
     </macros>
     <requirements>
-        <requirement type="package" version="0.5.9">readtagger</requirement>
+        <requirement type="package" version="0.5.10">readtagger</requirement>
     </requirements>
     <version_command>findcluster --version</version_command>
     <command detect_errors="aggressive"><![CDATA[
diff -r 16eba798cbc6 -r e675e6d349bd plot_coverage.xml
--- a/plot_coverage.xml	Sat Aug 31 09:48:36 2019 -0400
+++ b/plot_coverage.xml	Sun Sep 01 12:03:42 2019 -0400
@@ -1,7 +1,7 @@
-<tool id="plot_coverage" name="Plot coverage" version="0.5.9">
+<tool id="plot_coverage" name="Plot coverage" version="0.5.10">
     <description>as area plot between BAM files</description>
     <requirements>
-        <requirement type="package" version="0.5.9">readtagger</requirement>
+        <requirement type="package" version="0.5.10">readtagger</requirement>
     </requirements>
     <command detect_errors="aggressive"><![CDATA[
         #import re
diff -r 16eba798cbc6 -r e675e6d349bd test-data/confirmed_insertions.gff
--- a/test-data/confirmed_insertions.gff	Sat Aug 31 09:48:36 2019 -0400
+++ b/test-data/confirmed_insertions.gff	Sun Sep 01 12:03:42 2019 -0400
@@ -1,4 +1,4 @@
 2R	findcluster	jockey2	16727068	16727111	6	+	.	ID=R37_27;softclip_clusters=softclip_test1
 TEST	findcluster	jockey2	16727068	16727111	6	+	.	ID=R37_27;softclip_clusters=softclip_test1
 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;softclip_clusters=softclip_2,softclip_3;total_left_count=3;total_right_count=4;valid_TSD=True;FAIL=clip_seq_in_control
+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;softclip_clusters=softclip_2,softclip_3;total_left_count=3;total_right_count=4;valid_TSD=True;FAIL=clip_seq_matches_softclip_0
diff -r 16eba798cbc6 -r e675e6d349bd test-data/three_cluster_out.gff
--- a/test-data/three_cluster_out.gff	Sat Aug 31 09:48:36 2019 -0400
+++ b/test-data/three_cluster_out.gff	Sun Sep 01 12:03:42 2019 -0400
@@ -1,8 +1,8 @@
 ##gff-version 3
-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;softclip_clusters=;total_left_count=2;total_right_count=0;valid_TSD=False
-3R	find_softclip	3p_clip	13373515	13373514	7	+	.	ID=SOFTCLIP_8392192716115976782;consensus=ACATATAGTAACATAATATGCTTCTCATATTACGTTTACATACTTACACTAATTGTAC;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=GGAAAAATAACGGTATGGATGCACAACAAATCATGCGCTTAAGTGTAAGTAAAAATGTAAGCTGGTTTGATGTGTTTATGCATGTGCAAGATTGTATGTACAATTAGTGTAAGTATGTAAACGTAATATGAGAAGCATATTATGTTACTATATGTATATGTCCATATGTCCATATGCATACGAATTGGCGCACTTGCTTATATTTGATATGAGTTTGTTAGTTAGATACATTCCGAG;left_mate_count=6;max_mapq=60;nref=0;right_inserts=GACAACGAAGAAATAAAGATCCAAACTAAAAAAATACCTCGTGTTGATTCTGAAACTTCTTTAAAGGCGTTGATCTTAGTCAAACGACGGATCATTTGTTCGACTCGAATAGTAAAATACGTAAGTATATAGATAGTCTATATTAATTTTAAAAGCTCAAAGGGGCGCAAGTCTCTCTCATCAGTTGTGTCTTTAGTTTTTTTGATTTGGTTTGGTG;right_mate_count=6;softclip_clusters=SOFTCLIP_8392192716115976782,SOFTCLIP_3495167510329773485;total_left_count=9;total_right_count=11;valid_TSD=False
-3R	find_softclip	5p_clip	13373525	13373524	6	+	.	ID=SOFTCLIP_3495167510329773485;consensus=CTTAGTCAAACGACGGATCATTTGTTCGACTCGAATAGTAAAATACGTAAGT;max_mapq=60
+3R	findcluster	TE	13373206	13373206	2	+	.	ID=extended_and_annotated_roi.bam_0;genotype=homozygous;genotype_likelihoods=0.010684606252473288,0.32977179791584227,0.6595435958316845;insert_reference_name=None;left_inserts=;left_mate_count=2;max_mapq=60;nref=0;right_inserts=;right_mate_count=0;softclip_clusters=;total_left_count=2;total_right_count=0;valid_TSD=False
+3R	find_softclip	3p_clip	13373515	13373514	7	+	.	ID=SOFTCLIP_extended_and_annotated_roi.bam_3398f19a848a55cfd7c2bd0a378f055a;consensus=ACATATAGTAACATAATATGCTTCTCATATTACGTTTACATACTTACACTAATTGTAC;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=GGAAAAATAACGGTATGGATGCACAACAAATCATGCGCTTAAGTGTAAGTAAAAATGTAAGCTGGTTTGATGTGTTTATGCATGTGCAAGATTGTATGTACAATTAGTGTAAGTATGTAAACGTAATATGAGAAGCATATTATGTTACTATATGTATATGTCCATATGTCCATATGCATACGAATTGGCGCACTTGCTTATATTTGATATGAGTTTGTTAGTTAGATACATTCCGAG;left_mate_count=6;max_mapq=60;nref=0;right_inserts=GACAACGAAGAAATAAAGATCCAAACTAAAAAAATACCTCGTGTTGATTCTGAAACTTCTTTAAAGGCGTTGATCTTAGTCAAACGACGGATCATTTGTTCGACTCGAATAGTAAAATACGTAAGTATATAGATAGTCTATATTAATTTTAAAAGCTCAAAGGGGCGCAAGTCTCTCTCATCAGTTGTGTCTTTAGTTTTTTTGATTTGGTTTGGTG;right_mate_count=6;softclip_clusters=SOFTCLIP_extended_and_annotated_roi.bam_3398f19a848a55cfd7c2bd0a378f055a,SOFTCLIP_extended_and_annotated_roi.bam_32b958679d37cf982d968bf395ce0801;total_left_count=9;total_right_count=11;valid_TSD=False
+3R	find_softclip	5p_clip	13373525	13373524	6	+	.	ID=SOFTCLIP_extended_and_annotated_roi.bam_32b958679d37cf982d968bf395ce0801;consensus=CTTAGTCAAACGACGGATCATTTGTTCGACTCGAATAGTAAAATACGTAAGT;max_mapq=60
 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;softclip_clusters=;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=GTTCACCCGCGTCCGAGTTCCTGCTCCACTACTCCCTGGCTGCTGACTCACTGTTGTTATAGGGGTGGCTTCCCCTCTGTTCTTCCTGGGGGAATGCTGCATCTTCCCCAGCTCCAAAATGGCGG;left_mate_count=2;max_mapq=60;nref=0;right_inserts=;right_mate_count=0;softclip_clusters=;total_left_count=2;total_right_count=0;valid_TSD=False
-3R	find_softclip	5p_clip	13374677	13374676	1	+	.	ID=SOFTCLIP_2520711244791099460;consensus=TGGCAAAACATATGCAAAGTGCA;max_mapq=60
+3R	findcluster	TE	13374595	13374709	2	+	.	ID=extended_and_annotated_roi.bam_3;genotype=homozygous;genotype_likelihoods=0.010684606252473288,0.32977179791584227,0.6595435958316845;insert_reference_name=None;left_inserts=GTTCACCCGCGTCCGAGTTCCTGCTCCACTACTCCCTGGCTGCTGACTCACTGTTGTTATAGGGGTGGCTTCCCCTCTGTTCTTCCTGGGGGAATGCTGCATCTTCCCCAGCTCCAAAATGGCGG;left_mate_count=2;max_mapq=60;nref=0;right_inserts=;right_mate_count=0;softclip_clusters=;total_left_count=2;total_right_count=0;valid_TSD=False
+3R	find_softclip	5p_clip	13374677	13374676	1	+	.	ID=SOFTCLIP_extended_and_annotated_roi.bam_ad5ab08ae7f225f452b4e79bb9ab8425;consensus=TGGCAAAACATATGCAAAGTGCA;max_mapq=60
diff -r 16eba798cbc6 -r e675e6d349bd test-data/three_cluster_out.vcf
--- a/test-data/three_cluster_out.vcf	Sat Aug 31 09:48:36 2019 -0400
+++ b/test-data/three_cluster_out.vcf	Sun Sep 01 12:03:42 2019 -0400
@@ -1,7 +1,7 @@
 ##fileformat=VCFv4.1
 ##FILTER=<ID=PASS,Description="All filters passed">
-##fileDate=2018-03-30 15:24:43.667621
-##source=readtagger-v1.2.3
+##fileDate=2019-09-01 16:54:39.264420
+##source=readtagger-v0.5.9
 ##contig=<ID=2L,length=23513712>
 ##contig=<ID=2R,length=25286936>
 ##contig=<ID=3L,length=28110227>
@@ -1878,6 +1878,7 @@
 ##INFO=<ID=EVENT,Number=1,Type=String,Description="ID of event associated to breakend">
 ##INFO=<ID=MATEID,Number=.,Type=String,Description="ID of mate breakends">
 ##INFO=<ID=MQ,Number=1,Type=Integer,Description="Maximum MAPQ of evidence supporting the variant">
+##INFO=<ID=VALID_TSD,Number=0,Type=Flag,Description="Insertion is flanked by a Target Site Duplication.">
 ##ALT=<ID=DEL,Description="Deletion">
 ##ALT=<ID=DEL:ME,Description="Deletion of mobile element present in reference">
 ##ALT=<ID=INS,Description="Insertion of novel sequence">
@@ -1907,10 +1908,10 @@
 ##FORMAT=<ID=MSP,Number=1,Type=Integer,Description="Number of fragments supporting insertion with both mates. Indicates short insertions.">
 ##FORMAT=<ID=CLIP_CONSENSUS,Number=1,Type=String,Description="Consensus sequence for SOFTCLIP event. The consensus is listed in the 5p to 3p direction relative to the alignment.">
 #CHROM	POS	ID	REF	ALT	QUAL	FILTER	INFO	FORMAT	extended_and_annotated_roi.bam
-3R	13373206	INS_2444456283915041025	N	<INS:ME>	.	.	END=13373207;SVTYPE=INS:ME;SVLEN=.;MQ=60;EVENT=INS_2444456283915041025;MATEID	GT:GL:AD:DP:SU:SU5:SU3:SR:SR5:SR3:MSP:MENAME:MESTART:MEEND:MEASSEMBLY5:MEASSEMBLY3	1/1:0.0106846,0.329772,0.659544:0,2:2:2:2:0:0:0:0:0::.:.::
-3R	13373515	INS_630831370416389201	N	<INS:ME>	.	.	END=13373525;SVTYPE=INS:ME;SVLEN=.;MQ=60;EVENT=INS_630831370416389201;MATEID=SOFTCLIP_8392192716115976782,SOFTCLIP_3495167510329773485,SOFTCLIP_8392192716115976782,SOFTCLIP_3495167510329773485	GT:GL:AD:DP:SU:SU5:SU3:SR:SR5:SR3:MSP:MENAME:MESTART:MEEND:MEASSEMBLY5:MEASSEMBLY3	1/1:6.2762e-30,1.90734e-06,0.999998:0,20:20:20:9:11:8:3:5:0::.:.:GGAAAAATAACGGTATGGATGCACAACAAATCATGCGCTTAAGTGTAAGTAAAAATGTAAGCTGGTTTGATGTGTTTATGCATGTGCAAGATTGTATGTACAATTAGTGTAAGTATGTAAACGTAATATGAGAAGCATATTATGTTACTATATGTATATGTCCATATGTCCATATGCATACGAATTGGCGCACTTGCTTATATTTGATATGAGTTTGTTAGTTAGATACATTCCGAG:GACAACGAAGAAATAAAGATCCAAACTAAAAAAATACCTCGTGTTGATTCTGAAACTTCTTTAAAGGCGTTGATCTTAGTCAAACGACGGATCATTTGTTCGACTCGAATAGTAAAATACGTAAGTATATAGATAGTCTATATTAATTTTAAAAGCTCAAAGGGGCGCAAGTCTCTCTCATCAGTTGTGTCTTTAGTTTTTTTGATTTGGTTTGGTG
-3R	13373515	SOFTCLIP_8392192716115976782	N	<SOFTCLIP:3P>	.	.	END=13373514;SVTYPE=<SOFTCLIP:3P>;MQ=60;EVENT=INS_630831370416389201;MATEID=INS_630831370416389201	CLIP_CONSENSUS:AD:SU	ACATATAGTAACATAATATGCTTCTCATATTACGTTTACATACTTACACTAATTGTAC:0,7:7
-3R	13373525	SOFTCLIP_3495167510329773485	N	<SOFTCLIP:5P>	.	.	END=13373524;SVTYPE=<SOFTCLIP:5P>;MQ=60;EVENT=INS_630831370416389201;MATEID=INS_630831370416389201	CLIP_CONSENSUS:AD:SU	CTTAGTCAAACGACGGATCATTTGTTCGACTCGAATAGTAAAATACGTAAGT:0,6:6
-3R	13374539	INS_2520711244791099460	N	<INS:ME>	.	.	END=13374677;SVTYPE=INS:ME;SVLEN=.;MQ=60;EVENT=INS_2520711244791099460;MATEID	GT:GL:AD:DP:SU:SU5:SU3:SR:SR5:SR3:MSP:MENAME:MESTART:MEEND:MEASSEMBLY5:MEASSEMBLY3	1/1:0.212598,0.393701,0.393701:0,1:1:1:0:1:0:0:0:0::.:.::
-3R	13374595	INS_7083183827793206730	N	<INS:ME>	.	.	END=13374710;SVTYPE=INS:ME;SVLEN=.;MQ=60;EVENT=INS_7083183827793206730;MATEID	GT:GL:AD:DP:SU:SU5:SU3:SR:SR5:SR3:MSP:MENAME:MESTART:MEEND:MEASSEMBLY5:MEASSEMBLY3	1/1:0.0106846,0.329772,0.659544:0,2:2:2:2:0:0:0:0:0::.:.:GTTCACCCGCGTCCGAGTTCCTGCTCCACTACTCCCTGGCTGCTGACTCACTGTTGTTATAGGGGTGGCTTCCCCTCTGTTCTTCCTGGGGGAATGCTGCATCTTCCCCAGCTCCAAAATGGCGG:
-3R	13374677	SOFTCLIP_2520711244791099460	N	<SOFTCLIP:5P>	.	.	END=13374676;SVTYPE=<SOFTCLIP:5P>;MQ=60;EVENT;MATEID	CLIP_CONSENSUS:AD:SU	TGGCAAAACATATGCAAAGTGCA:0,1:1
+3R	13373206	INS_5bfddbc5f7f1e5f2fadb46bd3089d5a3	N	<INS:ME>	.	.	END=13373207;SVTYPE=INS:ME;SVLEN=.;MQ=60;EVENT=INS_5bfddbc5f7f1e5f2fadb46bd3089d5a3;MATEID	GT:GL:AD:DP:SU:SU5:SU3:PE:PE5:PE3:SR:SR5:SR3:MSP:MENAME:MESTART:MEEND:MEASSEMBLY5:MEASSEMBLY3	1/1:0.0106846,0.329772,0.659544:0,2:2:2:2:0:2:2:0:0:0:0:0::.:.::
+3R	13373515	INS_cc8163f20ac949c35cc556ed447ebff9	N	<INS:ME>	.	.	END=13373525;SVTYPE=INS:ME;SVLEN=.;MQ=60;EVENT=INS_cc8163f20ac949c35cc556ed447ebff9;MATEID=SOFTCLIP_extended_and_annotated_roi.bam_3398f19a848a55cfd7c2bd0a378f055a,SOFTCLIP_extended_and_annotated_roi.bam_32b958679d37cf982d968bf395ce0801	GT:GL:AD:DP:SU:SU5:SU3:PE:PE5:PE3:SR:SR5:SR3:MSP:MENAME:MESTART:MEEND:MEASSEMBLY5:MEASSEMBLY3	1/1:6.2762e-30,1.90734e-06,0.999998:0,20:20:20:9:11:12:6:6:8:3:5:0::.:.:GGAAAAATAACGGTATGGATGCACAACAAATCATGCGCTTAAGTGTAAGTAAAAATGTAAGCTGGTTTGATGTGTTTATGCATGTGCAAGATTGTATGTACAATTAGTGTAAGTATGTAAACGTAATATGAGAAGCATATTATGTTACTATATGTATATGTCCATATGTCCATATGCATACGAATTGGCGCACTTGCTTATATTTGATATGAGTTTGTTAGTTAGATACATTCCGAG:GACAACGAAGAAATAAAGATCCAAACTAAAAAAATACCTCGTGTTGATTCTGAAACTTCTTTAAAGGCGTTGATCTTAGTCAAACGACGGATCATTTGTTCGACTCGAATAGTAAAATACGTAAGTATATAGATAGTCTATATTAATTTTAAAAGCTCAAAGGGGCGCAAGTCTCTCTCATCAGTTGTGTCTTTAGTTTTTTTGATTTGGTTTGGTG
+3R	13373515	SOFTCLIP_extended_and_annotated_roi.bam_3398f19a848a55cfd7c2bd0a378f055a	N	<SOFTCLIP:3P>	.	.	END=13373514;SVTYPE=SOFTCLIP:3P;MQ=60;EVENT;MATEID	AD:SU:CLIP_CONSENSUS	0,7:7:ACATATAGTAACATAATATGCTTCTCATATTACGTTTACATACTTACACTAATTGTAC
+3R	13373525	SOFTCLIP_extended_and_annotated_roi.bam_32b958679d37cf982d968bf395ce0801	N	<SOFTCLIP:5P>	.	.	END=13373524;SVTYPE=SOFTCLIP:5P;MQ=60;EVENT;MATEID	AD:SU:CLIP_CONSENSUS	0,6:6:CTTAGTCAAACGACGGATCATTTGTTCGACTCGAATAGTAAAATACGTAAGT
+3R	13374539	INS_a373d31185938bc1ac00a9cd96044b1a	N	<INS:ME>	.	.	END=13374677;SVTYPE=INS:ME;SVLEN=.;MQ=60;EVENT=INS_a373d31185938bc1ac00a9cd96044b1a;MATEID	GT:GL:AD:DP:SU:SU5:SU3:PE:PE5:PE3:SR:SR5:SR3:MSP:MENAME:MESTART:MEEND:MEASSEMBLY5:MEASSEMBLY3	1/1:0.212598,0.393701,0.393701:0,1:1:1:0:1:1:0:1:0:0:0:0::.:.::
+3R	13374595	INS_35bded4f750984db0fa2998261102019	N	<INS:ME>	.	.	END=13374710;SVTYPE=INS:ME;SVLEN=.;MQ=60;EVENT=INS_35bded4f750984db0fa2998261102019;MATEID	GT:GL:AD:DP:SU:SU5:SU3:PE:PE5:PE3:SR:SR5:SR3:MSP:MENAME:MESTART:MEEND:MEASSEMBLY5:MEASSEMBLY3	1/1:0.0106846,0.329772,0.659544:0,2:2:2:2:0:2:2:0:0:0:0:0::.:.:GTTCACCCGCGTCCGAGTTCCTGCTCCACTACTCCCTGGCTGCTGACTCACTGTTGTTATAGGGGTGGCTTCCCCTCTGTTCTTCCTGGGGGAATGCTGCATCTTCCCCAGCTCCAAAATGGCGG:
+3R	13374677	SOFTCLIP_extended_and_annotated_roi.bam_ad5ab08ae7f225f452b4e79bb9ab8425	N	<SOFTCLIP:5P>	.	.	END=13374676;SVTYPE=SOFTCLIP:5P;MQ=60;EVENT;MATEID	AD:SU:CLIP_CONSENSUS	0,1:1:TGGCAAAACATATGCAAAGTGCA
diff -r 16eba798cbc6 -r e675e6d349bd update_mapq.xml
--- a/update_mapq.xml	Sat Aug 31 09:48:36 2019 -0400
+++ b/update_mapq.xml	Sun Sep 01 12:03:42 2019 -0400
@@ -1,7 +1,7 @@
-<tool id="update_mapq" name="Update MAPQ score" version="0.5.9">
+<tool id="update_mapq" name="Update MAPQ score" version="0.5.10">
     <description>of supplementary alignments</description>
     <requirements>
-        <requirement type="package" version="0.5.9">readtagger</requirement>
+        <requirement type="package" version="0.5.10">readtagger</requirement>
     </requirements>
     <version_command>update_mapq --version</version_command>
     <command detect_errors="aggressive"><![CDATA[
diff -r 16eba798cbc6 -r e675e6d349bd write_supplementary_fastq.xml
--- a/write_supplementary_fastq.xml	Sat Aug 31 09:48:36 2019 -0400
+++ b/write_supplementary_fastq.xml	Sun Sep 01 12:03:42 2019 -0400
@@ -1,7 +1,7 @@
-<tool id="write_supplementary_fastq" name="Extract supplementary alignments" version="0.5.9">
+<tool id="write_supplementary_fastq" name="Extract supplementary alignments" version="0.5.10">
     <description>from SAM/BAM alignment files as FASTQ</description>
     <requirements>
-        <requirement type="package" version="0.5.9">readtagger</requirement>
+        <requirement type="package" version="0.5.10">readtagger</requirement>
     </requirements>
     <version_command>write_supplementary_fastq --version</version_command>
     <command detect_errors="aggressive"><![CDATA[