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Merged
Snicker7 merged 4 commits into from
Aug 10, 2026
Merged

Sam/allele search #104

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4a5c36f
Update tests
Snicker7 Aug 7, 2026
15d07f8
Merge branch 'master' of https://github.com/edilytics/CRISPResso2_tes…
Snicker7 Aug 7, 2026
636b14e
Update for new fig layout
Snicker7 Aug 8, 2026
952c93d
expected results
Snicker7 Aug 8, 2026
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753 changes: 745 additions & 8 deletions ...ected_results_pro/CRISPRessoBatch_on_FANC/CRISPResso_on_Cas9/Cas9.CRISPResso2_report.html
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753 changes: 745 additions & 8 deletions ...lts_pro/CRISPRessoBatch_on_FANC/CRISPResso_on_Untreated/Untreated.CRISPResso2_report.html
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751 changes: 744 additions & 7 deletions ...ts_pro/CRISPRessoPooled_on_Both.Cas9/CRISPResso_on_FAN_+-C_asdf_-/CRISPResso2_report.html
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751 changes: 744 additions & 7 deletions ...cted_results_pro/CRISPRessoPooled_on_Both.Cas9/CRISPResso_on_HEK3/CRISPResso2_report.html
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751 changes: 744 additions & 7 deletions ...essoPooled_on_pooled-mixed-mode-genome-demux/CRISPResso_on_GENOME/CRISPResso2_report.html
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751 changes: 744 additions & 7 deletions ...ults_pro/CRISPRessoPooled_on_pooled-mixed-mode/CRISPResso_on_FANC/CRISPResso2_report.html
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751 changes: 744 additions & 7 deletions ...ts_pro/CRISPRessoPooled_on_pooled-mixed-mode/CRISPResso_on_GENOME/CRISPResso2_report.html
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751 changes: 744 additions & 7 deletions ...ults_pro/CRISPRessoPooled_on_pooled-mixed-mode/CRISPResso_on_HEK3/CRISPResso2_report.html
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5 changes: 2 additions & 3 deletions ...s_pro/CRISPRessoPooled_on_pooled-paired-sim/CRISPResso_on_Trimmed/CRISPResso2_report.html
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Expand Up @@ -795,10 +795,10 @@ <h5 class="text-center mb-3">Trimmed</h5>

<div class="text-start screen-only" id="log_params">
<p><strong>CRISPResso version:</strong> 2.3.4</p>
<p><strong>Run completed:</strong> 2026-06-09 16:43:56</p>
<p><strong>Run completed:</strong> 2026-08-07 17:48:34</p>
<p><strong>Amplicon sequence:</strong> <pre class='pre-scrollable'>TCCAATCAGTACGCAGAGAGTCGCCGTCTCCAAGGTGAAAGCGGAAGTAGGGCCTTCGCGCACCTCATGGAATCCCTTCTGCAGCACCTGGATCGCTTTTCCGAGCTTCTGGCGGTCTCAAGCACTACCTACGTCAGCACCTGGGACCCCGCCACCGTGCGCCGGGCCTTGCAGTGGGCGCGCTACCTGCGCCACATCCATCGGCGCTT</pre></p>

<p><strong>Command used:</strong> <pre class='pre-scrollable'>/Users/mckaybowcut/Edilytics/CRISPResso2/.pixi/envs/test-pro/bin/CRISPResso --fastq_r1 CRISPRessoPooled_on_pooled-paired-sim/AMPL_Trimmed.fastq.gz --amplicon_seq TCCAATCAGTACGCAGAGAGTCGCCGTCTCCAAGGTGAAAGCGGAAGTAGGGCCTTCGCGCACCTCATGGAATCCCTTCTGCAGCACCTGGATCGCTTTTCCGAGCTTCTGGCGGTCTCAAGCACTACCTACGTCAGCACCTGGGACCCCGCCACCGTGCGCCGGGCCTTGCAGTGGGCGCGCTACCTGCGCCACATCCATCGGCGCTT --name Trimmed --display_name Trimmed --output_folder CRISPRessoPooled_on_pooled-paired-sim --trim_sequences --fastp_options_string --detect_adapter_for_pe --keep_intermediate --place_report_in_output_folder --debug --halt_on_plot_fail</pre></p>
<p><strong>Command used:</strong> <pre class='pre-scrollable'>/mnt/c/Users/Snic9/Edilytics/CRISPResso2/.pixi/envs/test-pro/bin/CRISPResso --fastq_r1 CRISPRessoPooled_on_pooled-paired-sim/AMPL_Trimmed.fastq.gz --amplicon_seq TCCAATCAGTACGCAGAGAGTCGCCGTCTCCAAGGTGAAAGCGGAAGTAGGGCCTTCGCGCACCTCATGGAATCCCTTCTGCAGCACCTGGATCGCTTTTCCGAGCTTCTGGCGGTCTCAAGCACTACCTACGTCAGCACCTGGGACCCCGCCACCGTGCGCCGGGCCTTGCAGTGGGCGCGCTACCTGCGCCACATCCATCGGCGCTT --name Trimmed --display_name Trimmed --output_folder CRISPRessoPooled_on_pooled-paired-sim --trim_sequences --fastp_options_string --detect_adapter_for_pe --keep_intermediate --place_report_in_output_folder --debug --halt_on_plot_fail</pre></p>
<p><strong>Parameters:</strong> <pre class='pre-scrollable'>allele_plot_pcts_only_for_assigned_reference: False
aln_seed_count: 5
aln_seed_len: 10
Expand Down Expand Up @@ -1792,7 +1792,6 @@ <h5 class="text-center mb-3">Trimmed</h5>
</script>




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5 changes: 2 additions & 3 deletions .../CRISPRessoWGS_on_Both.Cas9.fastq.smallGenome/CRISPResso_on_FANCF/CRISPResso2_report.html
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Expand Up @@ -801,10 +801,10 @@ <h5 class="text-center mb-3">FANCF</h5>

<div class="text-start screen-only" id="log_params">
<p><strong>CRISPResso version:</strong> 2.3.4</p>
<p><strong>Run completed:</strong> 2026-06-09 16:43:58</p>
<p><strong>Run completed:</strong> 2026-08-07 17:47:39</p>
<p><strong>Amplicon sequence:</strong> <pre class='pre-scrollable'>AGAGCCGTGCGAATGGGGCCATGCCGACCAAAGCGCCGATGGATGTGGCGCAGGTAGCGCGCCCACTGCAAGGCCCGGCGCACGGTGGCGGGGTCCCAGGTGCTGACGTAGGTAGTGCTTGAGACCGCCAGAAGCTCGGAAAAGCGATCCAGGTGCTGCAGAAGGGATTCCATGAGGTGCGCGAAGGCCCTACTTCCGCTTTCACCTTGGAGACGGCGACTCTCTGCGTACTGATTGGAACATCCGCGAA</pre></p>

<p><strong>Command used:</strong> <pre class='pre-scrollable'>/Users/mckaybowcut/Edilytics/CRISPResso2/.pixi/envs/test-pro/bin/CRISPResso --fastq_r1 CRISPRessoWGS_on_Both.Cas9.fastq.smallGenome/ANALYZED_REGIONS/REGION_FANCF.fastq.gz --amplicon_seq AGAGCCGTGCGAATGGGGCCATGCCGACCAAAGCGCCGATGGATGTGGCGCAGGTAGCGCGCCCACTGCAAGGCCCGGCGCACGGTGGCGGGGTCCCAGGTGCTGACGTAGGTAGTGCTTGAGACCGCCAGAAGCTCGGAAAAGCGATCCAGGTGCTGCAGAAGGGATTCCATGAGGTGCGCGAAGGCCCTACTTCCGCTTTCACCTTGGAGACGGCGACTCTCTGCGTACTGATTGGAACATCCGCGAA --name FANCF --output_folder CRISPRessoWGS_on_Both.Cas9.fastq.smallGenome --place_report_in_output_folder --debug --halt_on_plot_fail</pre></p>
<p><strong>Command used:</strong> <pre class='pre-scrollable'>/mnt/c/Users/Snic9/Edilytics/CRISPResso2/.pixi/envs/test-pro/bin/CRISPResso --fastq_r1 CRISPRessoWGS_on_Both.Cas9.fastq.smallGenome/ANALYZED_REGIONS/REGION_FANCF.fastq.gz --amplicon_seq AGAGCCGTGCGAATGGGGCCATGCCGACCAAAGCGCCGATGGATGTGGCGCAGGTAGCGCGCCCACTGCAAGGCCCGGCGCACGGTGGCGGGGTCCCAGGTGCTGACGTAGGTAGTGCTTGAGACCGCCAGAAGCTCGGAAAAGCGATCCAGGTGCTGCAGAAGGGATTCCATGAGGTGCGCGAAGGCCCTACTTCCGCTTTCACCTTGGAGACGGCGACTCTCTGCGTACTGATTGGAACATCCGCGAA --name FANCF --output_folder CRISPRessoWGS_on_Both.Cas9.fastq.smallGenome --place_report_in_output_folder --debug --halt_on_plot_fail</pre></p>
<p><strong>Parameters:</strong> <pre class='pre-scrollable'>allele_plot_pcts_only_for_assigned_reference: False
aln_seed_count: 5
aln_seed_len: 10
Expand Down Expand Up @@ -1798,7 +1798,6 @@ <h5 class="text-center mb-3">FANCF</h5>
</script>




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751 changes: 744 additions & 7 deletions cli_integration_tests/expected_results_pro/CRISPResso_on_FANC.Cas9/CRISPResso2_report.html
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751 changes: 744 additions & 7 deletions cli_integration_tests/expected_results_pro/CRISPResso_on_asym_both/CRISPResso2_report.html
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751 changes: 744 additions & 7 deletions cli_integration_tests/expected_results_pro/CRISPResso_on_asym_left/CRISPResso2_report.html
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751 changes: 744 additions & 7 deletions cli_integration_tests/expected_results_pro/CRISPResso_on_asym_right/CRISPResso2_report.html
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5 changes: 2 additions & 3 deletions ...tegration_tests/expected_results_pro/CRISPResso_on_bam-out-genome/CRISPResso2_report.html
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Expand Up @@ -803,10 +803,10 @@ <h5 class="text-center mb-3">bam-out-genome</h5>

<div class="text-start screen-only" id="log_params">
<p><strong>CRISPResso version:</strong> 2.3.4</p>
<p><strong>Run completed:</strong> 2026-06-09 16:44:28</p>
<p><strong>Run completed:</strong> 2026-08-07 17:46:21</p>
<p><strong>Amplicon sequence:</strong> <pre class='pre-scrollable'>CGGATGTTCCAATCAGTACGCAGAGAGTCGCCGTCTCCAAGGTGAAAGCGGAAGTAGGGCCTTCGCGCACCTCATGGAATCCCTTC,GGAAACGCCCATGCAATTAGTCTATTTCTGCTGCAAGTAAGCATGCATTTGTAGGCTTGATGCTTTTTTTCTGCTTCTCCAGCCCT</pre></p>

<p><strong>Command used:</strong> <pre class='pre-scrollable'>/Users/mckaybowcut/Edilytics/CRISPResso2/.pixi/envs/test-pro/bin/CRISPResso -r1 inputs/bam_test.fq -a CGGATGTTCCAATCAGTACGCAGAGAGTCGCCGTCTCCAAGGTGAAAGCGGAAGTAGGGCCTTCGCGCACCTCATGGAATCCCTTC,GGAAACGCCCATGCAATTAGTCTATTTCTGCTGCAAGTAAGCATGCATTTGTAGGCTTGATGCTTTTTTTCTGCTTCTCCAGCCCT --bam_output -n bam-out-genome -x inputs/small_genome/smallGenome --place_report_in_output_folder --halt_on_plot_fail --debug</pre></p>
<p><strong>Command used:</strong> <pre class='pre-scrollable'>/mnt/c/Users/Snic9/Edilytics/CRISPResso2/.pixi/envs/test-pro/bin/CRISPResso -r1 inputs/bam_test.fq -a CGGATGTTCCAATCAGTACGCAGAGAGTCGCCGTCTCCAAGGTGAAAGCGGAAGTAGGGCCTTCGCGCACCTCATGGAATCCCTTC,GGAAACGCCCATGCAATTAGTCTATTTCTGCTGCAAGTAAGCATGCATTTGTAGGCTTGATGCTTTTTTTCTGCTTCTCCAGCCCT --bam_output -n bam-out-genome -x inputs/small_genome/smallGenome --place_report_in_output_folder --halt_on_plot_fail --debug</pre></p>
<p><strong>Parameters:</strong> <pre class='pre-scrollable'>allele_plot_pcts_only_for_assigned_reference: False
aln_seed_count: 5
aln_seed_len: 10
Expand Down Expand Up @@ -2171,7 +2171,6 @@ <h5>Indel Characterization for Amplicon1</h5>
</script>




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5 changes: 2 additions & 3 deletions ...gration_tests/expected_results_pro/CRISPResso_on_bam-out-parallel/CRISPResso2_report.html
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Expand Up @@ -803,10 +803,10 @@ <h5 class="text-center mb-3">bam-out-parallel</h5>

<div class="text-start screen-only" id="log_params">
<p><strong>CRISPResso version:</strong> 2.3.4</p>
<p><strong>Run completed:</strong> 2026-06-09 16:44:25</p>
<p><strong>Run completed:</strong> 2026-08-07 17:45:38</p>
<p><strong>Amplicon sequence:</strong> <pre class='pre-scrollable'>CGGATGTTCCAATCAGTACGCAGAGAGTCGCCGTCTCCAAGGTGAAAGCGGAAGTAGGGCCTTCGCGCACCTCATGGAATCCCTTC,GGAAACGCCCATGCAATTAGTCTATTTCTGCTGCAAGTAAGCATGCATTTGTAGGCTTGATGCTTTTTTTCTGCTTCTCCAGCCCT</pre></p>

<p><strong>Command used:</strong> <pre class='pre-scrollable'>/Users/mckaybowcut/Edilytics/CRISPResso2/.pixi/envs/test-pro/bin/CRISPResso -r1 inputs/bam_test.fq -a CGGATGTTCCAATCAGTACGCAGAGAGTCGCCGTCTCCAAGGTGAAAGCGGAAGTAGGGCCTTCGCGCACCTCATGGAATCCCTTC,GGAAACGCCCATGCAATTAGTCTATTTCTGCTGCAAGTAAGCATGCATTTGTAGGCTTGATGCTTTTTTTCTGCTTCTCCAGCCCT --bam_output -n bam-out-parallel --n_processes max --place_report_in_output_folder --halt_on_plot_fail --debug</pre></p>
<p><strong>Command used:</strong> <pre class='pre-scrollable'>/mnt/c/Users/Snic9/Edilytics/CRISPResso2/.pixi/envs/test-pro/bin/CRISPResso -r1 inputs/bam_test.fq -a CGGATGTTCCAATCAGTACGCAGAGAGTCGCCGTCTCCAAGGTGAAAGCGGAAGTAGGGCCTTCGCGCACCTCATGGAATCCCTTC,GGAAACGCCCATGCAATTAGTCTATTTCTGCTGCAAGTAAGCATGCATTTGTAGGCTTGATGCTTTTTTTCTGCTTCTCCAGCCCT --bam_output -n bam-out-parallel --n_processes max --place_report_in_output_folder --halt_on_plot_fail --debug</pre></p>
<p><strong>Parameters:</strong> <pre class='pre-scrollable'>allele_plot_pcts_only_for_assigned_reference: False
aln_seed_count: 5
aln_seed_len: 10
Expand Down Expand Up @@ -2171,7 +2171,6 @@ <h5>Indel Characterization for Amplicon1</h5>
</script>




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5 changes: 2 additions & 3 deletions cli_integration_tests/expected_results_pro/CRISPResso_on_bam-out/CRISPResso2_report.html
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Expand Up @@ -803,10 +803,10 @@ <h5 class="text-center mb-3">bam-out</h5>

<div class="text-start screen-only" id="log_params">
<p><strong>CRISPResso version:</strong> 2.3.4</p>
<p><strong>Run completed:</strong> 2026-06-09 16:43:41</p>
<p><strong>Run completed:</strong> 2026-08-07 17:45:23</p>
<p><strong>Amplicon sequence:</strong> <pre class='pre-scrollable'>CGGATGTTCCAATCAGTACGCAGAGAGTCGCCGTCTCCAAGGTGAAAGCGGAAGTAGGGCCTTCGCGCACCTCATGGAATCCCTTC,GGAAACGCCCATGCAATTAGTCTATTTCTGCTGCAAGTAAGCATGCATTTGTAGGCTTGATGCTTTTTTTCTGCTTCTCCAGCCCT</pre></p>

<p><strong>Command used:</strong> <pre class='pre-scrollable'>/Users/mckaybowcut/Edilytics/CRISPResso2/.pixi/envs/test-pro/bin/CRISPResso -r1 inputs/bam_test.fq -a CGGATGTTCCAATCAGTACGCAGAGAGTCGCCGTCTCCAAGGTGAAAGCGGAAGTAGGGCCTTCGCGCACCTCATGGAATCCCTTC,GGAAACGCCCATGCAATTAGTCTATTTCTGCTGCAAGTAAGCATGCATTTGTAGGCTTGATGCTTTTTTTCTGCTTCTCCAGCCCT --bam_output -n bam-out --place_report_in_output_folder --halt_on_plot_fail --debug</pre></p>
<p><strong>Command used:</strong> <pre class='pre-scrollable'>/mnt/c/Users/Snic9/Edilytics/CRISPResso2/.pixi/envs/test-pro/bin/CRISPResso -r1 inputs/bam_test.fq -a CGGATGTTCCAATCAGTACGCAGAGAGTCGCCGTCTCCAAGGTGAAAGCGGAAGTAGGGCCTTCGCGCACCTCATGGAATCCCTTC,GGAAACGCCCATGCAATTAGTCTATTTCTGCTGCAAGTAAGCATGCATTTGTAGGCTTGATGCTTTTTTTCTGCTTCTCCAGCCCT --bam_output -n bam-out --place_report_in_output_folder --halt_on_plot_fail --debug</pre></p>
<p><strong>Parameters:</strong> <pre class='pre-scrollable'>allele_plot_pcts_only_for_assigned_reference: False
aln_seed_count: 5
aln_seed_len: 10
Expand Down Expand Up @@ -2171,7 +2171,6 @@ <h5>Indel Characterization for Amplicon1</h5>
</script>




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