| Previous changeset 39:432bb619c079 (2018-03-15) Next changeset 41:4fdf606153df (2018-05-24) |
|
Commit message:
planemo upload for repository https://github.com/bardin-lab/readtagger/tree/master/galaxy commit 2e991a52c828b0234020e89748eafe1028e44a7d |
|
modified:
add_matesequence.xml allow_dovetailing.xml bam_readtagger.xml filter_insertions.xml findcluster.xml plot_coverage.xml test-data/a_pasteurianus_tagged_with_dm6.bam test-data/a_pasteurianus_tagged_with_dm6_discarded.bam test-data/a_pasteurianus_tagged_with_dm6_verified.bam test-data/all_control_insertions.gff test-data/all_treatment_insertions.gff test-data/confirmed_insertions.gff test-data/dm6.bam test-data/dm6_mate_annotated.bam test-data/dm6_tagged_with_a_pasteurianus.bam test-data/dm6_tagged_with_a_pasteurianus_discarded.bam test-data/dm6_tagged_with_a_pasteurianus_verified.bam test-data/proper_pair_discard_out.bam test-data/proper_pair_discard_verified_empty.bam test-data/proper_pair_out_suboptimal_tags.bam test-data/putative_insertions.gff test-data/three_cluster_out.bam test-data/three_cluster_out.gff test-data/three_cluster_plot.pdf update_mapq.xml write_supplementary_fastq.xml |
|
added:
test-data/three_cluster_out.vcf |
| b |
| diff -r 432bb619c079 -r 4b1ebfcd0f46 add_matesequence.xml --- a/add_matesequence.xml Thu Mar 15 07:20:58 2018 -0400 +++ b/add_matesequence.xml Sun Apr 01 03:53:15 2018 -0400 |
| [ |
| @@ -1,7 +1,7 @@ -<tool id="add_matesequence" name="Add matesequence" version="0.4.9"> +<tool id="add_matesequence" name="Add matesequence" version="0.4.10"> <description>into tag field</description> <requirements> - <requirement type="package" version="0.4.9">readtagger</requirement> + <requirement type="package" version="0.4.10">readtagger</requirement> </requirements> <version_command>add_matesequence --version</version_command> <command detect_errors="aggressive"><![CDATA[ |
| b |
| diff -r 432bb619c079 -r 4b1ebfcd0f46 allow_dovetailing.xml --- a/allow_dovetailing.xml Thu Mar 15 07:20:58 2018 -0400 +++ b/allow_dovetailing.xml Sun Apr 01 03:53:15 2018 -0400 |
| [ |
| @@ -1,7 +1,7 @@ -<tool id="allow_dovetailing" name="Allow dovetailing" version="0.4.9"> +<tool id="allow_dovetailing" name="Allow dovetailing" version="0.4.10"> <description>modifies proper_pair flag in bam files</description> <requirements> - <requirement type="package" version="0.4.9">readtagger</requirement> + <requirement type="package" version="0.4.10">readtagger</requirement> </requirements> <command detect_errors="aggressive"><![CDATA[ allow_dovetailing -i '$input' -o '$output' |
| b |
| diff -r 432bb619c079 -r 4b1ebfcd0f46 bam_readtagger.xml --- a/bam_readtagger.xml Thu Mar 15 07:20:58 2018 -0400 +++ b/bam_readtagger.xml Sun Apr 01 03:53:15 2018 -0400 |
| [ |
| @@ -1,10 +1,10 @@ -<tool id="bam_readtagger" name="Tag alignment files" version="0.4.9"> +<tool id="bam_readtagger" name="Tag alignment files" version="0.4.10"> <description>from multiple bam files</description> <macros> <import>macros.xml</import> </macros> <requirements> - <requirement type="package" version="0.4.9">readtagger</requirement> + <requirement type="package" version="0.4.10">readtagger</requirement> </requirements> <command detect_errors="aggressive"><![CDATA[ readtagger -t '$tag_file' -s |
| b |
| diff -r 432bb619c079 -r 4b1ebfcd0f46 filter_insertions.xml --- a/filter_insertions.xml Thu Mar 15 07:20:58 2018 -0400 +++ b/filter_insertions.xml Sun Apr 01 03:53:15 2018 -0400 |
| [ |
| @@ -1,7 +1,7 @@ -<tool id="confirm_insertions" name="Confirm or discard insertions" version="0.4.9"> +<tool id="confirm_insertions" name="Confirm or discard insertions" version="0.4.10"> <description>based on softclips in control files</description> <requirements> - <requirement type="package" version="0.4.9">readtagger</requirement> + <requirement type="package" version="0.4.10">readtagger</requirement> </requirements> <version_command>confirm_insertions --version</version_command> <command detect_errors="aggressive"><![CDATA[ |
| b |
| diff -r 432bb619c079 -r 4b1ebfcd0f46 findcluster.xml --- a/findcluster.xml Thu Mar 15 07:20:58 2018 -0400 +++ b/findcluster.xml Sun Apr 01 03:53:15 2018 -0400 |
| [ |
| @@ -1,10 +1,10 @@ -<tool id="findcluster" name="Find clusters of reads" version="0.4.9"> +<tool id="findcluster" name="Find clusters of reads" version="0.4.10"> <description>in bam files</description> <macros> <import>macros.xml</import> </macros> <requirements> - <requirement type="package" version="0.4.9">readtagger</requirement> + <requirement type="package" version="0.4.10">readtagger</requirement> </requirements> <version_command>findcluster --version</version_command> <command detect_errors="aggressive"><![CDATA[ @@ -28,33 +28,57 @@ --genome_bwa_index '$genome_source.ref_file.fields.path' #end if #end if - --output_bam '$output_bam' - --output_gff '$output_gff' - --output_fasta '$output_fasta' + #if str($make_bam) == 'True': + --output_bam '$output_bam' + #end if + #if str($make_vcf) == 'True' + --output_vcf '$output_vcf' + #end if + #if str($make_gff) == 'True' + --output_gff '$output_gff' + #end if + #if str($make_fasta) == 'True' + --output_fasta '$output_fasta' + #end if --sample_name '$sample_name' --threads "\${GALAXY_SLOTS:-2}" ]]></command> <inputs> <param name="input" argument="--input_path" type="data" format="bam"/> - + <param name="make_bam" type="boolean" truevalue="True" checked="true" label="Produce an alignment file containing evidence for insertions."/> + <param name="make_vcf" type="boolean" truevalue="True" checked="true" label="Produce a VCF file describing the insertion that have been found."/> + <param name="make_gff" type="boolean" truevalue="True" checked="false" label="produce a GFF file describing the insertions that have been found."/> + <param name="make_fasta" type="boolean" checked="True" truevalue="True" label="Produce a fasta file containing assembled contigs."/> <expand macro="reference_source_conditional" reference_type="transposon"/> <expand macro="reference_source_conditional" reference_type="genome"/> </inputs> <outputs> - <data name="output_bam" format="bam" label="findcluster BAM on $on_string"/> - <data name="output_fasta" format="fasta" label="findcluster contigs on $on_string"/> - <data name="output_gff" format="gff3" label="findcluster GFF on $on_string"/> + <data name="output_bam" format="bam" label="findcluster BAM on $on_string"> + <filter>make_bam</filter> + </data> + <data name="output_fasta" format="fasta" label="findcluster contigs on $on_string"> + <filter>make_fasta</filter> + </data> + <data name="output_vcf" format="vcf" label="findcluster VCF on $on_string"> + <filter>make_vcf</filter> + </data> + <data name="output_gff" format="gff3" label="findcluster GFF on $on_string"> + <filter>make_gff</filter> + </data> </outputs> <tests> <test> <param name="input" value="extended_and_annotated_roi.bam" ftype="bam"/> + <param name="make_gff" value="true"/> <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" sort="True"/> + <output name="output_gff" file="three_cluster_out.gff" ftype="gff3" compare="sim_size"/> + <output name="output_vcf" file="three_cluster_out.vcf" ftype="vcf" compare="sim_size"/> </test> <test> <param name="input" value="extended_and_annotated_roi.bam" ftype="bam"/> <param name="transposon_source|reference_source_selector" value="history"/> <param name="transposon_source|ref_file" value="reference.fasta" ftype="fasta"/> + <param name="make_gff" value="true"/> <output name="output_bam" file="three_cluster_out.bam" ftype="bam" lines_diff="2"/> <output name="output_gff"> <assert_contents> |
| b |
| diff -r 432bb619c079 -r 4b1ebfcd0f46 plot_coverage.xml --- a/plot_coverage.xml Thu Mar 15 07:20:58 2018 -0400 +++ b/plot_coverage.xml Sun Apr 01 03:53:15 2018 -0400 |
| [ |
| @@ -1,7 +1,7 @@ -<tool id="plot_coverage" name="Plot coverage" version="0.4.9"> +<tool id="plot_coverage" name="Plot coverage" version="0.4.10"> <description>as area plot between BAM files</description> <requirements> - <requirement type="package" version="0.4.9">readtagger</requirement> + <requirement type="package" version="0.4.10">readtagger</requirement> </requirements> <command detect_errors="aggressive"><![CDATA[ #import re |
| b |
| diff -r 432bb619c079 -r 4b1ebfcd0f46 test-data/a_pasteurianus_tagged_with_dm6.bam |
| b |
| Binary file test-data/a_pasteurianus_tagged_with_dm6.bam has changed |
| b |
| diff -r 432bb619c079 -r 4b1ebfcd0f46 test-data/a_pasteurianus_tagged_with_dm6_discarded.bam |
| b |
| Binary file test-data/a_pasteurianus_tagged_with_dm6_discarded.bam has changed |
| b |
| diff -r 432bb619c079 -r 4b1ebfcd0f46 test-data/a_pasteurianus_tagged_with_dm6_verified.bam |
| b |
| Binary file test-data/a_pasteurianus_tagged_with_dm6_verified.bam has changed |
| b |
| diff -r 432bb619c079 -r 4b1ebfcd0f46 test-data/all_control_insertions.gff --- a/test-data/all_control_insertions.gff Thu Mar 15 07:20:58 2018 -0400 +++ b/test-data/all_control_insertions.gff Sun Apr 01 03:53:15 2018 -0400 |
| b |
| @@ -1,2 +1,3 @@ -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 +TEST find_softclip 5p_clip 16727068 16727111 6 + . ID=softclip_test2;consensus=TTTTTTT +X find_softclip 5p_clip 16727068 16727067 3 + . ID=softclip_0;consensus=ACTTAATA;max_mapq=25 +X find_softclip 3p_clip 16727112 16727111 4 + . ID=softclip_1;consensus=TTTAATAAAATTAAAGGACAACTAAACGGAAGGAAAATATCGTGAGCAG;max_mapq=28 |
| b |
| diff -r 432bb619c079 -r 4b1ebfcd0f46 test-data/all_treatment_insertions.gff --- a/test-data/all_treatment_insertions.gff Thu Mar 15 07:20:58 2018 -0400 +++ b/test-data/all_treatment_insertions.gff Sun Apr 01 03:53:15 2018 -0400 |
| b |
| @@ -1,12 +1,13 @@ +TEST find_softclip 5p_clip 16727068 16727111 6 + . ID=softclip_test1;consensus=AAAAAA 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 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;softclip_clusters=;total_left_count=6;total_right_count=18;valid_TSD=True +X find_softclip 5p_clip 10766937 10766936 6 + . ID=softclip_0;consensus=GGCGTTGATCTTAGTCAAACGACGGATCATTTGTTCGACTCGAATAGTAAAATACGTAAG;max_mapq=60 +X find_softclip 3p_clip 10766943 10766942 3 + . ID=softclip_1;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 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;softclip_clusters=;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 +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 +X find_softclip 3p_clip 16727068 16727111 6 + . ID=softclip_2;consensus=TTTAATAAAATTAAAGGAC;max_mapq=34 +X find_softclip 5p_clip 16727068 16727111 5 + . ID=softclip_3;consensus=GAATTTAATATTTAAAAAGGTGGACTGAATACTTAATA;max_mapq=34 +X find_softclip 3p_clip 16727110 16727109 1 + . ID=softclip_4;consensus=CCTTTAATAAAATTAAAGGACAACTAAACGGAAGGAAAATATCGTGAGCAGAAAATAATATTAAGTCTTTAAAAG;max_mapq=34 |
| b |
| diff -r 432bb619c079 -r 4b1ebfcd0f46 test-data/confirmed_insertions.gff --- a/test-data/confirmed_insertions.gff Thu Mar 15 07:20:58 2018 -0400 +++ b/test-data/confirmed_insertions.gff Sun Apr 01 03:53:15 2018 -0400 |
| b |
| @@ -1,3 +1,4 @@ -TEST 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 +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;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_in_control |
| b |
| diff -r 432bb619c079 -r 4b1ebfcd0f46 test-data/dm6.bam |
| b |
| Binary file test-data/dm6.bam has changed |
| b |
| diff -r 432bb619c079 -r 4b1ebfcd0f46 test-data/dm6_mate_annotated.bam |
| b |
| Binary file test-data/dm6_mate_annotated.bam has changed |
| b |
| diff -r 432bb619c079 -r 4b1ebfcd0f46 test-data/dm6_tagged_with_a_pasteurianus.bam |
| b |
| Binary file test-data/dm6_tagged_with_a_pasteurianus.bam has changed |
| b |
| diff -r 432bb619c079 -r 4b1ebfcd0f46 test-data/dm6_tagged_with_a_pasteurianus_discarded.bam |
| b |
| Binary file test-data/dm6_tagged_with_a_pasteurianus_discarded.bam has changed |
| b |
| diff -r 432bb619c079 -r 4b1ebfcd0f46 test-data/dm6_tagged_with_a_pasteurianus_verified.bam |
| b |
| Binary file test-data/dm6_tagged_with_a_pasteurianus_verified.bam has changed |
| b |
| diff -r 432bb619c079 -r 4b1ebfcd0f46 test-data/proper_pair_discard_out.bam |
| b |
| Binary file test-data/proper_pair_discard_out.bam has changed |
| b |
| diff -r 432bb619c079 -r 4b1ebfcd0f46 test-data/proper_pair_discard_verified_empty.bam |
| b |
| Binary file test-data/proper_pair_discard_verified_empty.bam has changed |
| b |
| diff -r 432bb619c079 -r 4b1ebfcd0f46 test-data/proper_pair_out_suboptimal_tags.bam |
| b |
| Binary file test-data/proper_pair_out_suboptimal_tags.bam has changed |
| b |
| diff -r 432bb619c079 -r 4b1ebfcd0f46 test-data/putative_insertions.gff --- a/test-data/putative_insertions.gff Thu Mar 15 07:20:58 2018 -0400 +++ b/test-data/putative_insertions.gff Sun Apr 01 03:53:15 2018 -0400 |
| b |
| @@ -1,3 +1,4 @@ -TEST 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 +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;total_left_count=3;total_right_count=4;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 |
| b |
| diff -r 432bb619c079 -r 4b1ebfcd0f46 test-data/three_cluster_out.bam |
| b |
| Binary file test-data/three_cluster_out.bam has changed |
| b |
| diff -r 432bb619c079 -r 4b1ebfcd0f46 test-data/three_cluster_out.gff --- a/test-data/three_cluster_out.gff Thu Mar 15 07:20:58 2018 -0400 +++ b/test-data/three_cluster_out.gff Sun Apr 01 03:53:15 2018 -0400 |
| b |
| @@ -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;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 +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 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 |
| b |
| diff -r 432bb619c079 -r 4b1ebfcd0f46 test-data/three_cluster_out.vcf --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/three_cluster_out.vcf Sun Apr 01 03:53:15 2018 -0400 |
| b |
| b'@@ -0,0 +1,1916 @@\n+##fileformat=VCFv4.1\n+##FILTER=<ID=PASS,Description="All filters passed">\n+##fileDate=2018-03-30 15:24:43.667621\n+##source=readtagger-v1.2.3\n+##contig=<ID=2L,length=23513712>\n+##contig=<ID=2R,length=25286936>\n+##contig=<ID=3L,length=28110227>\n+##contig=<ID=3R,length=32079331>\n+##contig=<ID=4,length=1348131>\n+##contig=<ID=X,length=23542271>\n+##contig=<ID=Y,length=3667352>\n+##contig=<ID=2Cen_mapped_Scaffold_10_D1684,length=19956>\n+##contig=<ID=2Cen_mapped_Scaffold_43_D1668,length=44411>\n+##contig=<ID=2R2_mapped_Scaffold_56_D1828,length=13157>\n+##contig=<ID=3Cen_mapped_Scaffold_1_D1896_D1895,length=76224>\n+##contig=<ID=3Cen_mapped_Scaffold_27_D1777,length=11983>\n+##contig=<ID=3Cen_mapped_Scaffold_31_D1643_D1653_D1791,length=87365>\n+##contig=<ID=3Cen_mapped_Scaffold_36_D1605,length=36913>\n+##contig=<ID=3Cen_mapped_Scaffold_41_D1641,length=22604>\n+##contig=<ID=3Cen_mapped_Scaffold_50_D1686,length=23238>\n+##contig=<ID=Unmapped_Scaffold_4_D1555_D1692,length=86267>\n+##contig=<ID=Unmapped_Scaffold_8_D1580_D1567,length=88768>\n+##contig=<ID=Unmapped_Scaffold_11_D1754,length=36482>\n+##contig=<ID=Unmapped_Scaffold_13_D1782,length=25537>\n+##contig=<ID=Unmapped_Scaffold_17_D1756_D1775,length=62570>\n+##contig=<ID=Unmapped_Scaffold_22_D1753,length=45120>\n+##contig=<ID=Unmapped_Scaffold_24_D1707,length=22882>\n+##contig=<ID=Unmapped_Scaffold_28_D1723,length=46986>\n+##contig=<ID=Unmapped_Scaffold_29_D1705,length=37106>\n+##contig=<ID=Unmapped_Scaffold_32_D1773,length=16157>\n+##contig=<ID=Unmapped_Scaffold_35_D1599,length=57785>\n+##contig=<ID=Unmapped_Scaffold_37_D1608,length=20763>\n+##contig=<ID=Unmapped_Scaffold_38_D1625,length=28305>\n+##contig=<ID=Unmapped_Scaffold_44_D1670,length=25698>\n+##contig=<ID=Unmapped_Scaffold_45_D1673,length=29583>\n+##contig=<ID=Unmapped_Scaffold_46_D1675,length=25560>\n+##contig=<ID=Unmapped_Scaffold_48_D1678,length=26115>\n+##contig=<ID=Unmapped_Scaffold_51_D1697,length=13455>\n+##contig=<ID=Unmapped_Scaffold_52_D1739,length=43383>\n+##contig=<ID=Unmapped_Scaffold_54_D1776,length=12632>\n+##contig=<ID=Unmapped_Scaffold_58_D1862,length=10091>\n+##contig=<ID=Unmapped_Scaffold_60_D1601,length=24503>\n+##contig=<ID=211000022278279,length=12714>\n+##contig=<ID=X3X4_mapped_Scaffold_6_D1712,length=33320>\n+##contig=<ID=X3X4_mapped_Scaffold_14_D1732,length=27447>\n+##contig=<ID=XY_mapped_Scaffold_42_D1648,length=47411>\n+##contig=<ID=Y_mapped_Scaffold_5_D1748_D1610,length=73091>\n+##contig=<ID=Y_mapped_Scaffold_9_D1573,length=66731>\n+##contig=<ID=Y_mapped_Scaffold_12_D1771,length=66439>\n+##contig=<ID=Y_mapped_Scaffold_15_D1727,length=33316>\n+##contig=<ID=Y_mapped_Scaffold_18_D1698,length=34521>\n+##contig=<ID=Y_mapped_Scaffold_20_D1762_D1719,length=39041>\n+##contig=<ID=Y_mapped_Scaffold_21_D1683_D1693,length=34359>\n+##contig=<ID=Y_mapped_Scaffold_23_D1638,length=31460>\n+##contig=<ID=Y_mapped_Scaffold_26_D1717,length=21921>\n+##contig=<ID=Y_mapped_Scaffold_30_D1720,length=25805>\n+##contig=<ID=Y_mapped_Scaffold_34_D1584,length=24380>\n+##contig=<ID=Y_mapped_Scaffold_53_D1765,length=44104>\n+##contig=<ID=211000022279762,length=11498>\n+##contig=<ID=rDNA,length=76973>\n+##contig=<ID=211000022278033,length=1143>\n+##contig=<ID=211000022278089,length=4222>\n+##contig=<ID=211000022278170,length=1160>\n+##contig=<ID=211000022278224,length=1650>\n+##contig=<ID=211000022278269,length=11430>\n+##contig=<ID=211000022278354,length=21074>\n+##contig=<ID=211000022278391,length=1152>\n+##contig=<ID=211000022278415,length=25840>\n+##contig=<ID=211000022278678,length=1966>\n+##contig=<ID=211000022278894,length=1303>\n+##contig=<ID=211000022278978,length=12424>\n+##contig=<ID=211000022279018,length=6860>\n+##contig=<ID=211000022279130,length=1990>\n+##contig=<ID=211000022279169,length=3120>\n+##contig=<ID=211000022279344,length=4573>\n+##contig=<ID=211000022279387,length=1044>\n+##contig=<ID=211000022279450,length=1719>\n+##contig=<ID=211000022279594,length=12148>\n+##contig=<ID=211000022279735,length=7722>\n+##contig=<ID=211000022280087,length=4986>\n+##conti'..b'MAT=<ID=DP,Number=1,Type=Integer,Description="Approximate read depth (reads with MQ=255 or with bad mates are filtered)">\n+##FORMAT=<ID=SU,Number=1,Type=Integer,Description="Number of pieces of evidence supporting the variant">\n+##FORMAT=<ID=SU5,Number=1,Type=Integer,Description="Number of pieces of evidence supporting the variant from the 5p side">\n+##FORMAT=<ID=SU3,Number=1,Type=Integer,Description="Number of pieces of evidence supporting the variant form the 3p side">\n+##FORMAT=<ID=PE,Number=1,Type=Integer,Description="Number of paired-end reads supporting the variant">\n+##FORMAT=<ID=PE5,Number=1,Type=Integer,Description="Number of paired-end reads supporting the variant from the 5p side">\n+##FORMAT=<ID=PE3,Number=1,Type=Integer,Description="Number of paired-end reads supporting the variant from the 3p side">\n+##FORMAT=<ID=SR,Number=1,Type=Integer,Description="Number of split reads supporting the variant">\n+##FORMAT=<ID=SR5,Number=1,Type=Integer,Description="Number of split reads supporting the variant from the 5p side">\n+##FORMAT=<ID=SR3,Number=1,Type=Integer,Description="Number of split reads supporting the variant from the 3p side">\n+##FORMAT=<ID=MSP,Number=1,Type=Integer,Description="Number of fragments supporting insertion with both mates. Indicates short insertions.">\n+##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.">\n+#CHROM\tPOS\tID\tREF\tALT\tQUAL\tFILTER\tINFO\tFORMAT\textended_and_annotated_roi.bam\n+3R\t13373206\tINS_2444456283915041025\tN\t<INS:ME>\t.\t.\tEND=13373207;SVTYPE=INS:ME;SVLEN=.;MQ=60;EVENT=INS_2444456283915041025;MATEID\tGT:GL:AD:DP:SU:SU5:SU3:SR:SR5:SR3:MSP:MENAME:MESTART:MEEND:MEASSEMBLY5:MEASSEMBLY3\t1/1:0.0106846,0.329772,0.659544:0,2:2:2:2:0:0:0:0:0::.:.::\n+3R\t13373515\tINS_630831370416389201\tN\t<INS:ME>\t.\t.\tEND=13373525;SVTYPE=INS:ME;SVLEN=.;MQ=60;EVENT=INS_630831370416389201;MATEID=SOFTCLIP_8392192716115976782,SOFTCLIP_3495167510329773485,SOFTCLIP_8392192716115976782,SOFTCLIP_3495167510329773485\tGT:GL:AD:DP:SU:SU5:SU3:SR:SR5:SR3:MSP:MENAME:MESTART:MEEND:MEASSEMBLY5:MEASSEMBLY3\t1/1:6.2762e-30,1.90734e-06,0.999998:0,20:20:20:9:11:8:3:5:0::.:.:GGAAAAATAACGGTATGGATGCACAACAAATCATGCGCTTAAGTGTAAGTAAAAATGTAAGCTGGTTTGATGTGTTTATGCATGTGCAAGATTGTATGTACAATTAGTGTAAGTATGTAAACGTAATATGAGAAGCATATTATGTTACTATATGTATATGTCCATATGTCCATATGCATACGAATTGGCGCACTTGCTTATATTTGATATGAGTTTGTTAGTTAGATACATTCCGAG:GACAACGAAGAAATAAAGATCCAAACTAAAAAAATACCTCGTGTTGATTCTGAAACTTCTTTAAAGGCGTTGATCTTAGTCAAACGACGGATCATTTGTTCGACTCGAATAGTAAAATACGTAAGTATATAGATAGTCTATATTAATTTTAAAAGCTCAAAGGGGCGCAAGTCTCTCTCATCAGTTGTGTCTTTAGTTTTTTTGATTTGGTTTGGTG\n+3R\t13373515\tSOFTCLIP_8392192716115976782\tN\t<SOFTCLIP:3P>\t.\t.\tEND=13373514;SVTYPE=<SOFTCLIP:3P>;MQ=60;EVENT=INS_630831370416389201;MATEID=INS_630831370416389201\tCLIP_CONSENSUS:AD:SU\tACATATAGTAACATAATATGCTTCTCATATTACGTTTACATACTTACACTAATTGTAC:0,7:7\n+3R\t13373525\tSOFTCLIP_3495167510329773485\tN\t<SOFTCLIP:5P>\t.\t.\tEND=13373524;SVTYPE=<SOFTCLIP:5P>;MQ=60;EVENT=INS_630831370416389201;MATEID=INS_630831370416389201\tCLIP_CONSENSUS:AD:SU\tCTTAGTCAAACGACGGATCATTTGTTCGACTCGAATAGTAAAATACGTAAGT:0,6:6\n+3R\t13374539\tINS_2520711244791099460\tN\t<INS:ME>\t.\t.\tEND=13374677;SVTYPE=INS:ME;SVLEN=.;MQ=60;EVENT=INS_2520711244791099460;MATEID\tGT:GL:AD:DP:SU:SU5:SU3:SR:SR5:SR3:MSP:MENAME:MESTART:MEEND:MEASSEMBLY5:MEASSEMBLY3\t1/1:0.212598,0.393701,0.393701:0,1:1:1:0:1:0:0:0:0::.:.::\n+3R\t13374595\tINS_7083183827793206730\tN\t<INS:ME>\t.\t.\tEND=13374710;SVTYPE=INS:ME;SVLEN=.;MQ=60;EVENT=INS_7083183827793206730;MATEID\tGT:GL:AD:DP:SU:SU5:SU3:SR:SR5:SR3:MSP:MENAME:MESTART:MEEND:MEASSEMBLY5:MEASSEMBLY3\t1/1:0.0106846,0.329772,0.659544:0,2:2:2:2:0:0:0:0:0::.:.:GTTCACCCGCGTCCGAGTTCCTGCTCCACTACTCCCTGGCTGCTGACTCACTGTTGTTATAGGGGTGGCTTCCCCTCTGTTCTTCCTGGGGGAATGCTGCATCTTCCCCAGCTCCAAAATGGCGG:\n+3R\t13374677\tSOFTCLIP_2520711244791099460\tN\t<SOFTCLIP:5P>\t.\t.\tEND=13374676;SVTYPE=<SOFTCLIP:5P>;MQ=60;EVENT;MATEID\tCLIP_CONSENSUS:AD:SU\tTGGCAAAACATATGCAAAGTGCA:0,1:1\n' |
| b |
| diff -r 432bb619c079 -r 4b1ebfcd0f46 test-data/three_cluster_plot.pdf |
| b |
| Binary file test-data/three_cluster_plot.pdf has changed |
| b |
| diff -r 432bb619c079 -r 4b1ebfcd0f46 update_mapq.xml --- a/update_mapq.xml Thu Mar 15 07:20:58 2018 -0400 +++ b/update_mapq.xml Sun Apr 01 03:53:15 2018 -0400 |
| [ |
| @@ -1,7 +1,7 @@ -<tool id="update_mapq" name="Update MAPQ score" version="0.4.9"> +<tool id="update_mapq" name="Update MAPQ score" version="0.4.10"> <description>of supplementary alignments</description> <requirements> - <requirement type="package" version="0.4.9">readtagger</requirement> + <requirement type="package" version="0.4.10">readtagger</requirement> </requirements> <version_command>update_mapq --version</version_command> <command detect_errors="aggressive"><![CDATA[ |
| b |
| diff -r 432bb619c079 -r 4b1ebfcd0f46 write_supplementary_fastq.xml --- a/write_supplementary_fastq.xml Thu Mar 15 07:20:58 2018 -0400 +++ b/write_supplementary_fastq.xml Sun Apr 01 03:53:15 2018 -0400 |
| [ |
| @@ -1,7 +1,7 @@ -<tool id="write_supplementary_fastq" name="Extract supplementary alignments" version="0.4.9"> +<tool id="write_supplementary_fastq" name="Extract supplementary alignments" version="0.4.10"> <description>from SAM/BAM alignment files as FASTQ</description> <requirements> - <requirement type="package" version="0.4.9">readtagger</requirement> + <requirement type="package" version="0.4.10">readtagger</requirement> </requirements> <version_command>write_supplementary_fastq --version</version_command> <command detect_errors="aggressive"><![CDATA[ |