| Previous changeset 62:16eba798cbc6 (2019-08-31) Next changeset 64:190d64e5e32b (2019-09-01) |
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Commit message:
"planemo upload for repository https://github.com/bardin-lab/readtagger/tree/master/galaxy commit 8ed4215b007a3f552e1b1964907a505858822fb4" |
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modified:
add_matesequence.xml allow_dovetailing.xml bam_readtagger.xml extract_variants.xml filter_insertions.xml findcluster.xml plot_coverage.xml test-data/confirmed_insertions.gff test-data/three_cluster_out.gff test-data/three_cluster_out.vcf update_mapq.xml write_supplementary_fastq.xml |
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| 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 |
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| @@ -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[ |
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| 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 |
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| @@ -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' |
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| 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 |
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| @@ -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 |
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| 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 |
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| @@ -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[ |
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| 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 |
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| @@ -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[ |
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| 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 |
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| @@ -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[ |
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| 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 |
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| @@ -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 |
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| 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 |
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| @@ -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 |
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| 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 |
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| @@ -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 |
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| 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 |
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| @@ -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 |
| b |
| 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[ |
| b |
| 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[ |