| Previous changeset 37:93f7962a3e19 (2018-01-06) Next changeset 39:432bb619c079 (2018-03-15) |
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Commit message:
planemo upload for repository https://github.com/bardin-lab/readtagger/tree/master/galaxy commit 6ac744bd9d610990d1d54a2c36ddfca671b15205-dirty |
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modified:
add_matesequence.xml allow_dovetailing.xml bam_readtagger.xml deploy.sh 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/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/three_cluster_out.bam test-data/three_cluster_out.gff test-data/three_cluster_plot.pdf update_mapq.xml write_supplementary_fastq.xml |
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added:
filter_insertions.xml test-data/all_control_insertions.gff test-data/all_treatment_insertions.gff test-data/confirmed_insertions.gff test-data/putative_insertions.gff |
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| 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 |
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| @@ -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[ |
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| 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 |
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| @@ -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' |
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| 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 |
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| @@ -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 '$tag_file' -s |
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| diff -r 93f7962a3e19 -r f6311a04a6c9 filter_insertions.xml --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/filter_insertions.xml Thu Mar 15 05:13:22 2018 -0400 |
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| @@ -0,0 +1,56 @@ +<tool id="confirm_insertions" name="Confirm or discard insertions" version="0.4.9"> + <description>based on softclips in control files</description> + <requirements> + <requirement type="package" version="0.4.9">readtagger</requirement> + </requirements> + <version_command>confirm_insertions --version</version_command> + <command detect_errors="aggressive"><![CDATA[ + confirm_insertions + --putative_insertions_path '$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> |
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| 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 |
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| @@ -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"/> |
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| 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 |
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| @@ -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> |
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| diff -r 93f7962a3e19 -r f6311a04a6c9 test-data/a_pasteurianus_tagged_with_dm6.bam |
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| Binary file test-data/a_pasteurianus_tagged_with_dm6.bam has changed |
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| diff -r 93f7962a3e19 -r f6311a04a6c9 test-data/a_pasteurianus_tagged_with_dm6_discarded.bam |
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| Binary file test-data/a_pasteurianus_tagged_with_dm6_discarded.bam has changed |
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| diff -r 93f7962a3e19 -r f6311a04a6c9 test-data/a_pasteurianus_tagged_with_dm6_verified.bam |
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| Binary file test-data/a_pasteurianus_tagged_with_dm6_verified.bam has changed |
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| 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 |
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| @@ -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 |
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| 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 |
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| @@ -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 |
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| 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 |
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| @@ -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 |
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| diff -r 93f7962a3e19 -r f6311a04a6c9 test-data/dm6_mate_annotated.bam |
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| Binary file test-data/dm6_mate_annotated.bam has changed |
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| diff -r 93f7962a3e19 -r f6311a04a6c9 test-data/dm6_tagged_with_a_pasteurianus.bam |
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| Binary file test-data/dm6_tagged_with_a_pasteurianus.bam has changed |
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| diff -r 93f7962a3e19 -r f6311a04a6c9 test-data/dm6_tagged_with_a_pasteurianus_discarded.bam |
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| Binary file test-data/dm6_tagged_with_a_pasteurianus_discarded.bam has changed |
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| diff -r 93f7962a3e19 -r f6311a04a6c9 test-data/dm6_tagged_with_a_pasteurianus_verified.bam |
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| Binary file test-data/dm6_tagged_with_a_pasteurianus_verified.bam has changed |
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| diff -r 93f7962a3e19 -r f6311a04a6c9 test-data/proper_pair_discard_out.bam |
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| Binary file test-data/proper_pair_discard_out.bam has changed |
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| diff -r 93f7962a3e19 -r f6311a04a6c9 test-data/proper_pair_discard_verified_empty.bam |
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| Binary file test-data/proper_pair_discard_verified_empty.bam has changed |
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| diff -r 93f7962a3e19 -r f6311a04a6c9 test-data/proper_pair_out_suboptimal_tags.bam |
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| Binary file test-data/proper_pair_out_suboptimal_tags.bam has changed |
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| 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 |
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| @@ -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 |
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| diff -r 93f7962a3e19 -r f6311a04a6c9 test-data/three_cluster_out.bam |
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| Binary file test-data/three_cluster_out.bam has changed |
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| 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 |
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| @@ -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 |
| b |
| diff -r 93f7962a3e19 -r f6311a04a6c9 test-data/three_cluster_plot.pdf |
| b |
| Binary file test-data/three_cluster_plot.pdf has changed |
| b |
| 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[ |
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| 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[ |