Native CRISPResso Paired End Read Merging#537
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kclem merged 1 commit intopinellolab:masterfrom May 16, 2025
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* Implement crispresso_merge * Add new crispresso_merge to args * Update test_env.yml * Parallel * Fastq_out with single process only * Native merge tests * Remove unused aln_matrix * Fix get consensus from pairs stubs * Fix unit tests, upack 5 vasl * Update score * Update integration_tests.yml * Update tests, remove insertions beyond amplicon * Update tests, new score * Update for deletions * Update for deletions * Update scores * Update scores * Update scores * Fix fastq_output * f-string fix * CRISPResso_merge for core only * Comments * Unpin numpy<2 * Pin cython 3.0.12 * Pip install no isolation * numpy fix * Fix workflows * Write and read slots during parallelization * Delete unused test * Add run native merge test to github actions * Update c files with cython=3.1.0 * Remove import for ResultsSlotsDict * Repoint tests at master --------- Co-authored-by: mbowcut2 <mbowcut@gmail.com>
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* Implement crispresso_merge * Add new crispresso_merge to args * Update test_env.yml * Parallel * Fastq_out with single process only * Native merge tests * Remove unused aln_matrix * Fix get consensus from pairs stubs * Fix unit tests, upack 5 vasl * Update score * Update integration_tests.yml * Update tests, remove insertions beyond amplicon * Update tests, new score * Update for deletions * Update for deletions * Update scores * Update scores * Update scores * Fix fastq_output * f-string fix * CRISPResso_merge for core only * Comments * Unpin numpy<2 * Pin cython 3.0.12 * Pip install no isolation * numpy fix * Fix workflows * Write and read slots during parallelization * Delete unused test * Add run native merge test to github actions * Update c files with cython=3.1.0 * Remove import for ResultsSlotsDict * Repoint tests at master --------- Co-authored-by: Samuel Nichols <Snic9004@gmail.com> Co-authored-by: mbowcut2 <mbowcut@gmail.com>
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* Implement crispresso_merge * Add new crispresso_merge to args * Update test_env.yml * Parallel * Fastq_out with single process only * Native merge tests * Remove unused aln_matrix * Fix get consensus from pairs stubs * Fix unit tests, upack 5 vasl * Update score * Update integration_tests.yml * Update tests, remove insertions beyond amplicon * Update tests, new score * Update for deletions * Update for deletions * Update scores * Update scores * Update scores * Fix fastq_output * f-string fix * CRISPResso_merge for core only * Comments * Unpin numpy<2 * Pin cython 3.0.12 * Pip install no isolation * numpy fix * Fix workflows * Write and read slots during parallelization * Delete unused test * Add run native merge test to github actions * Update c files with cython=3.1.0 * Remove import for ResultsSlotsDict * Repoint tests at master --------- Co-authored-by: Samuel Nichols <Snic9004@gmail.com> Co-authored-by: mbowcut2 <mbowcut@gmail.com>
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* Implement crispresso_merge * Add new crispresso_merge to args * Update test_env.yml * Parallel * Fastq_out with single process only * Native merge tests * Remove unused aln_matrix * Fix get consensus from pairs stubs * Fix unit tests, upack 5 vasl * Update score * Update integration_tests.yml * Update tests, remove insertions beyond amplicon * Update tests, new score * Update for deletions * Update for deletions * Update scores * Update scores * Update scores * Fix fastq_output * f-string fix * CRISPResso_merge for core only * Comments * Unpin numpy<2 * Pin cython 3.0.12 * Pip install no isolation * numpy fix * Fix workflows * Write and read slots during parallelization * Delete unused test * Add run native merge test to github actions * Update c files with cython=3.1.0 * Remove import for ResultsSlotsDict * Repoint tests at master --------- Co-authored-by: Samuel Nichols <Snic9004@gmail.com> Co-authored-by: mbowcut2 <mbowcut@gmail.com>
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* Implement crispresso_merge * Add new crispresso_merge to args * Update test_env.yml * Parallel * Fastq_out with single process only * Native merge tests * Remove unused aln_matrix * Fix get consensus from pairs stubs * Fix unit tests, upack 5 vasl * Update score * Update integration_tests.yml * Update tests, remove insertions beyond amplicon * Update tests, new score * Update for deletions * Update for deletions * Update scores * Update scores * Update scores * Fix fastq_output * f-string fix * CRISPResso_merge for core only * Comments * Unpin numpy<2 * Pin cython 3.0.12 * Pip install no isolation * numpy fix * Fix workflows * Write and read slots during parallelization * Delete unused test * Add run native merge test to github actions * Update c files with cython=3.1.0 * Remove import for ResultsSlotsDict * Repoint tests at master --------- Co-authored-by: Samuel Nichols <Snic9004@gmail.com> Co-authored-by: mbowcut2 <mbowcut@gmail.com>
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This PR introduces the
--crispresso_mergeparameter, which allows for paired end read merging to be performed using the CRISPResso alignment algorithm. It works by aligning r1 and r2 to the amplicon, computing the overlap, and merging the reads accordingly. In the overlap region, if there is a discrepancy between r1 and r2, the base with the higher quality score is chosen.This PR also includes a fix for the breaking change in Cython where
longis no longer supported. This fix works with both3.0.12and3.1.0.