test: validate one/zero based coords #181
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Pull Request Overview
This PR validates coordinate systems in the conversion functions by adding tests with micro BAM/SAM files and updating documentation.
- Added new pytest fixtures for micro BAM/SAM and reference file paths in tests/process/conftest.py.
- Introduced a new test (test_bam_to_fastq_handle_indels_micro) in tests/process/test_convert.py to verify conversion behavior with a micro BAM file.
- Inserted a TODO comment in src/sr2silo/process/convert.py regarding coordinate numbering and added a notebook for generating test reads.
Reviewed Changes
Copilot reviewed 9 out of 17 changed files in this pull request and generated 3 comments.
| File | Description |
|---|---|
| tests/process/conftest.py | Added fixtures for micro BAM/SAM and micro reference files. |
| tests/process/test_convert.py | Added a test for bam_to_fastq_handle_indels using the micro BAM file. |
| src/sr2silo/process/convert.py | Added a TODO comment regarding coordinate system verification. |
| notebooks/Make_Test_Reads.ipynb | Added a notebook for generating test data used in the test suite. |
Files not reviewed (8)
- notebooks/micro.sam: Language not supported
- notebooks/micro_ref.fasta: Language not supported
- notebooks/out.sam: Language not supported
- notebooks/translate.txt: Language not supported
- tests/data/bam/micro/insertions.txt: Language not supported
- tests/data/bam/micro/micro.sam: Language not supported
- tests/data/bam/micro/micro_ref.fasta: Language not supported
- tests/data/bam/micro/output.fastq: Language not supported
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Pull Request Overview
This PR introduces a micro BAM file generator to support tests that verify the correct handling of one‐based versus zero‐based coordinate systems in the SAM/BAM conversion process. Key changes include:
- Adding a new micro BAM generator script (make_test_bam.py) with representative SAM records.
- Enhancing tests (test_convert.py and conftest.py) to use the micro BAM file and associated fixtures.
- Updating the bam_to_fastq_handle_indels function in convert.py with additional logging and handling for skipped regions and soft clipping.
Reviewed Changes
Copilot reviewed 9 out of 17 changed files in this pull request and generated 1 comment.
| File | Description |
|---|---|
| tests/data/bam/micro/make_test_bam.py | Adds a script to generate a test BAM file with specific records. |
| tests/process/test_convert.py | Introduces a new test using the micro BAM file for conversion. |
| tests/process/conftest.py | Adds fixtures for the micro BAM, SAM and reference files. |
| src/sr2silo/process/convert.py | Updates the conversion function with additional logging and handling for extra CIGAR operations. |
Files not reviewed (8)
- notebooks/micro.sam: Language not supported
- notebooks/micro_ref.fasta: Language not supported
- notebooks/out.sam: Language not supported
- notebooks/translate.txt: Language not supported
- tests/data/bam/micro/expected_clear_nucs.fastq: Language not supported
- tests/data/bam/micro/expected_nuc_insertions.txt: Language not supported
- tests/data/bam/micro/micro.sam: Language not supported
- tests/data/bam/micro/micro_ref.fasta: Language not supported
Comments suppressed due to low confidence (1)
tests/data/bam/micro/make_test_bam.py:6
- The reference sequence contains double asterisks, which might be unintentional. Please verify that this sequence is correct as per SAM/BAM specifications.
# ref AGCATGTTAGATAA**GATAGCTGTGCTAGTAGGCAGTCAGCGCCAT
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Nucleotide Coordinates are correctly 1-based. I have manually asserted Nuclitide cleartext reads and insertions and implemented a sufficient test. |
added 2 commits
March 21, 2025 15:08
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I just tested, and I can run diamond on a sequence that is 15 AA characters long. This means I can probably design main acids. It works if I just choose one reading frame. |
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TODO:
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gordonkoehn
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Mar 27, 2025
get insertions form Nextclade get insertions form Nextclade get insertions form Nextclade WIP get nuc sequence WIP: parsesd nextclade to read objects remove trash WIP: failing tests Fix: indexing of bam black formating WIP - got the results to compare WIP all __eq__ adding Nuc comparison WIP making Nextclade use the reference from sr2silo WIP changed sr2silo ref to nextclade - still not workign add sorting by coordinate config feature: add paired read merging on alignments (#125) * copy over the script * update by manual copy * WIP * ignore .bai index files - should be freshly generated * add smallgenomutils conda package * add read pair merger * add sam * WIP * WIP: adding checks * move to temp * move to temp * move constants * Reset wokrflows * fix test * add proper test with check fo sorting * add test coverage * up test coverage * Update workflow to conditionally run coverage tests based on PR or push to main/dev branch * Add check for changed files before running coverage * remove template / badge * lower the test coverage * lower the test coverage --------- Co-authored-by: Gordon J. Köhn <gordon.koehn@dbsse.ethz.ch> test: fix in CI for test coverage (#153) * test: test coverage in CI (#152) * Update workflow to conditionally run coverage tests based on PR or push to main/dev branch * Add check for changed files before running coverage * remove template / badge * Update .github/workflows/test.yml praying this is correct. Co-authored-by: Copilot <175728472+Copilot@users.noreply.github.com> --------- Co-authored-by: Gordon J. Köhn <gordon.koehn@dbsse.ethz.ch> Co-authored-by: Copilot <175728472+Copilot@users.noreply.github.com> * fixing CI --------- Co-authored-by: Gordon J. Köhn <gordon.koehn@dbsse.ethz.ch> Co-authored-by: Copilot <175728472+Copilot@users.noreply.github.com> fixing CI test: test coverage in CI (#152) (#154) * Update workflow to conditionally run coverage tests based on PR or push to main/dev branch * Add check for changed files before running coverage * remove template / badge * Update .github/workflows/test.yml praying this is correct. --------- Co-authored-by: Gordon J. Köhn <gordon.koehn@dbsse.ethz.ch> Co-authored-by: Copilot <175728472+Copilot@users.noreply.github.com> fix CI test coverage (#155) Co-authored-by: Gordon J. Köhn <gordon.koehn@dbsse.ethz.ch> backtack: the CI issues are bad (#156) * fix CI test coverage * fix aciton * backtrack on code coverage --------- Co-authored-by: Gordon J. Köhn <gordon.koehn@dbsse.ethz.ch> test: adjusting pytest coverage in CI (#159) * fix CI test coverage * fix aciton * backtrack on code coverage * fixing format of pipeline * fixing format of pipeline * fixing format of pipeline --------- Co-authored-by: Gordon J. Köhn <gordon.koehn@dbsse.ethz.ch> feature: integrate paired-end read merging into CLI (#160) * adding sam_to_bam * add conversion tests * remove comments * specify sorting * rought workflow * add sorting by coordinate * WIP move aux functions to convert * working start-to-end with merging * black it * fix workflwotest * fix workflwotest * fix ruff * ruff ruff --------- Co-authored-by: Gordon J. Köhn <gordon.koehn@dbsse.ethz.ch> test: test coverage in CI (#152) * Update workflow to conditionally run coverage tests based on PR or push to main/dev branch * Add check for changed files before running coverage * remove template / badge * Update .github/workflows/test.yml praying this is correct. Co-authored-by: Copilot <175728472+Copilot@users.noreply.github.com> --------- Co-authored-by: Gordon J. Köhn <gordon.koehn@dbsse.ethz.ch> Co-authored-by: Copilot <175728472+Copilot@users.noreply.github.com> history cleanup for dev --------- Co-authored-by: Gordon J. Köhn <gordon.koehn@dbsse.ethz.ch> Co-authored-by: Copilot <175728472+Copilot@users.noreply.github.com> fixing CI test: test coverage in CI (#152) (#154) * Update workflow to conditionally run coverage tests based on PR or push to main/dev branch * Add check for changed files before running coverage * remove template / badge * Update .github/workflows/test.yml praying this is correct. --------- Co-authored-by: Gordon J. Köhn <gordon.koehn@dbsse.ethz.ch> Co-authored-by: Copilot <175728472+Copilot@users.noreply.github.com> fix CI test coverage (#155) Co-authored-by: Gordon J. Köhn <gordon.koehn@dbsse.ethz.ch> backtack: the CI issues are bad (#156) * fix CI test coverage * fix aciton * backtrack on code coverage --------- Co-authored-by: Gordon J. Köhn <gordon.koehn@dbsse.ethz.ch> test: adjusting pytest coverage in CI (#159) * fix CI test coverage * fix aciton * backtrack on code coverage * fixing format of pipeline * fixing format of pipeline * fixing format of pipeline --------- Co-authored-by: Gordon J. Köhn <gordon.koehn@dbsse.ethz.ch> test: test coverage in CI (#152) * Update workflow to conditionally run coverage tests based on PR or push to main/dev branch * Add check for changed files before running coverage * remove template / badge Co-authored-by: Copilot <175728472+Copilot@users.noreply.github.com> --------- Co-authored-by: Gordon J. Köhn <gordon.koehn@dbsse.ethz.ch> Co-authored-by: Copilot <175728472+Copilot@users.noreply.github.com> fix test to temp dir declutter temp dir handling in main (#166) Co-authored-by: Gordon J. Köhn <gordon.koehn@dbsse.ethz.ch> add sr2silo in namespace for workflow setup (#165) Co-authored-by: Gordon J. Köhn <gordon.koehn@dbsse.ethz.ch> centralize workflow config (#167) feature / fix: temporary directory handling for amino acid aligment (#179) * Introduces TMPDIR support in both main and translate_align modules * Refactors enrich_read_with_metadata into curry_read_with_metadata and updates related tests * Updates documentation and configuration files for resource requirements and CI environment handling --------- Co-authored-by: Gordon J. Köhn <gordon.koehn@dbsse.ethz.ch> Co-authored-by: Copilot <175728472+Copilot@users.noreply.github.com> test: validate one/zero based coords (#181) * WUP * WIP tests * support for skipped char * add support for soft clipping * add support for hardclipping * adding Padding support * fix test read 02 * fix last read * move to script * note on coord system * fix black * cleanup test to tmp_path * remove trash * bam_to_fasta_query - support for soft clippings + validation * add test for create index and move test_bam_to_fasta_query to temp * update parse_translate_align text fixture after corrections * reformat ruff --------- Co-authored-by: Gordon J. Köhn <gordon.koehn@dbsse.ethz.ch> resolve changing base issues ram ref nextclade change ref to same as V-Pipe fix: Insertions JSON format (#183) * change insertion strings * add validator to pydantic model * update front to end tests * Update src/sr2silo/silo_read_schema.py Co-authored-by: Copilot <175728472+Copilot@users.noreply.github.com> * satisfy ruff --------- Co-authored-by: Gordon J. Köhn <gordon.koehn@dbsse.ethz.ch> Co-authored-by: Copilot <175728472+Copilot@users.noreply.github.com> reformat black nextclade test cannot work skip
gordonkoehn
added a commit
that referenced
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Mar 27, 2025
* layout orthogonal test * Salvage Nextclade Orth Test Changes get insertions form Nextclade get insertions form Nextclade get insertions form Nextclade WIP get nuc sequence WIP: parsesd nextclade to read objects remove trash WIP: failing tests Fix: indexing of bam black formating WIP - got the results to compare WIP all __eq__ adding Nuc comparison WIP making Nextclade use the reference from sr2silo WIP changed sr2silo ref to nextclade - still not workign add sorting by coordinate config feature: add paired read merging on alignments (#125) * copy over the script * update by manual copy * WIP * ignore .bai index files - should be freshly generated * add smallgenomutils conda package * add read pair merger * add sam * WIP * WIP: adding checks * move to temp * move to temp * move constants * Reset wokrflows * fix test * add proper test with check fo sorting * add test coverage * up test coverage * Update workflow to conditionally run coverage tests based on PR or push to main/dev branch * Add check for changed files before running coverage * remove template / badge * lower the test coverage * lower the test coverage --------- Co-authored-by: Gordon J. Köhn <gordon.koehn@dbsse.ethz.ch> test: fix in CI for test coverage (#153) * test: test coverage in CI (#152) * Update workflow to conditionally run coverage tests based on PR or push to main/dev branch * Add check for changed files before running coverage * remove template / badge * Update .github/workflows/test.yml praying this is correct. Co-authored-by: Copilot <175728472+Copilot@users.noreply.github.com> --------- Co-authored-by: Gordon J. Köhn <gordon.koehn@dbsse.ethz.ch> Co-authored-by: Copilot <175728472+Copilot@users.noreply.github.com> * fixing CI --------- Co-authored-by: Gordon J. Köhn <gordon.koehn@dbsse.ethz.ch> Co-authored-by: Copilot <175728472+Copilot@users.noreply.github.com> fixing CI test: test coverage in CI (#152) (#154) * Update workflow to conditionally run coverage tests based on PR or push to main/dev branch * Add check for changed files before running coverage * remove template / badge * Update .github/workflows/test.yml praying this is correct. --------- Co-authored-by: Gordon J. Köhn <gordon.koehn@dbsse.ethz.ch> Co-authored-by: Copilot <175728472+Copilot@users.noreply.github.com> fix CI test coverage (#155) Co-authored-by: Gordon J. Köhn <gordon.koehn@dbsse.ethz.ch> backtack: the CI issues are bad (#156) * fix CI test coverage * fix aciton * backtrack on code coverage --------- Co-authored-by: Gordon J. Köhn <gordon.koehn@dbsse.ethz.ch> test: adjusting pytest coverage in CI (#159) * fix CI test coverage * fix aciton * backtrack on code coverage * fixing format of pipeline * fixing format of pipeline * fixing format of pipeline --------- Co-authored-by: Gordon J. Köhn <gordon.koehn@dbsse.ethz.ch> feature: integrate paired-end read merging into CLI (#160) * adding sam_to_bam * add conversion tests * remove comments * specify sorting * rought workflow * add sorting by coordinate * WIP move aux functions to convert * working start-to-end with merging * black it * fix workflwotest * fix workflwotest * fix ruff * ruff ruff --------- Co-authored-by: Gordon J. Köhn <gordon.koehn@dbsse.ethz.ch> test: test coverage in CI (#152) * Update workflow to conditionally run coverage tests based on PR or push to main/dev branch * Add check for changed files before running coverage * remove template / badge * Update .github/workflows/test.yml praying this is correct. Co-authored-by: Copilot <175728472+Copilot@users.noreply.github.com> --------- Co-authored-by: Gordon J. Köhn <gordon.koehn@dbsse.ethz.ch> Co-authored-by: Copilot <175728472+Copilot@users.noreply.github.com> history cleanup for dev --------- Co-authored-by: Gordon J. Köhn <gordon.koehn@dbsse.ethz.ch> Co-authored-by: Copilot <175728472+Copilot@users.noreply.github.com> fixing CI test: test coverage in CI (#152) (#154) * Update workflow to conditionally run coverage tests based on PR or push to main/dev branch * Add check for changed files before running coverage * remove template / badge * Update .github/workflows/test.yml praying this is correct. --------- Co-authored-by: Gordon J. Köhn <gordon.koehn@dbsse.ethz.ch> Co-authored-by: Copilot <175728472+Copilot@users.noreply.github.com> fix CI test coverage (#155) Co-authored-by: Gordon J. Köhn <gordon.koehn@dbsse.ethz.ch> backtack: the CI issues are bad (#156) * fix CI test coverage * fix aciton * backtrack on code coverage --------- Co-authored-by: Gordon J. Köhn <gordon.koehn@dbsse.ethz.ch> test: adjusting pytest coverage in CI (#159) * fix CI test coverage * fix aciton * backtrack on code coverage * fixing format of pipeline * fixing format of pipeline * fixing format of pipeline --------- Co-authored-by: Gordon J. Köhn <gordon.koehn@dbsse.ethz.ch> test: test coverage in CI (#152) * Update workflow to conditionally run coverage tests based on PR or push to main/dev branch * Add check for changed files before running coverage * remove template / badge Co-authored-by: Copilot <175728472+Copilot@users.noreply.github.com> --------- Co-authored-by: Gordon J. Köhn <gordon.koehn@dbsse.ethz.ch> Co-authored-by: Copilot <175728472+Copilot@users.noreply.github.com> fix test to temp dir declutter temp dir handling in main (#166) Co-authored-by: Gordon J. Köhn <gordon.koehn@dbsse.ethz.ch> add sr2silo in namespace for workflow setup (#165) Co-authored-by: Gordon J. Köhn <gordon.koehn@dbsse.ethz.ch> centralize workflow config (#167) feature / fix: temporary directory handling for amino acid aligment (#179) * Introduces TMPDIR support in both main and translate_align modules * Refactors enrich_read_with_metadata into curry_read_with_metadata and updates related tests * Updates documentation and configuration files for resource requirements and CI environment handling --------- Co-authored-by: Gordon J. Köhn <gordon.koehn@dbsse.ethz.ch> Co-authored-by: Copilot <175728472+Copilot@users.noreply.github.com> test: validate one/zero based coords (#181) * WUP * WIP tests * support for skipped char * add support for soft clipping * add support for hardclipping * adding Padding support * fix test read 02 * fix last read * move to script * note on coord system * fix black * cleanup test to tmp_path * remove trash * bam_to_fasta_query - support for soft clippings + validation * add test for create index and move test_bam_to_fasta_query to temp * update parse_translate_align text fixture after corrections * reformat ruff --------- Co-authored-by: Gordon J. Köhn <gordon.koehn@dbsse.ethz.ch> resolve changing base issues ram ref nextclade change ref to same as V-Pipe fix: Insertions JSON format (#183) * change insertion strings * add validator to pydantic model * update front to end tests * Update src/sr2silo/silo_read_schema.py Co-authored-by: Copilot <175728472+Copilot@users.noreply.github.com> * satisfy ruff --------- Co-authored-by: Gordon J. Köhn <gordon.koehn@dbsse.ethz.ch> Co-authored-by: Copilot <175728472+Copilot@users.noreply.github.com> reformat black nextclade test cannot work skip * remove nextclade add tests for insertions Update tests/conftest.py Co-authored-by: Copilot <175728472+Copilot@users.noreply.github.com> * format black * double code bug * accidental removal * accidental removal --------- Co-authored-by: Gordon J. Köhn <gordon.koehn@dbsse.ethz.ch> Co-authored-by: Copilot <175728472+Copilot@users.noreply.github.com>
gordonkoehn
added a commit
that referenced
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Mar 28, 2025
* feature: add paired read merging on alignments (#125) * copy over the script * update by manual copy * WIP * ignore .bai index files - should be freshly generated * add smallgenomutils conda package * add read pair merger * add sam * WIP * WIP: adding checks * move to temp * move to temp * move constants * Reset wokrflows * fix test * add proper test with check fo sorting * add test coverage * up test coverage * Update workflow to conditionally run coverage tests based on PR or push to main/dev branch * Add check for changed files before running coverage * remove template / badge * lower the test coverage * lower the test coverage --------- Co-authored-by: Gordon J. Köhn <gordon.koehn@dbsse.ethz.ch> * test: fix in CI for test coverage (#153) * test: test coverage in CI (#152) * Update workflow to conditionally run coverage tests based on PR or push to main/dev branch * Add check for changed files before running coverage * remove template / badge * Update .github/workflows/test.yml praying this is correct. Co-authored-by: Copilot <175728472+Copilot@users.noreply.github.com> --------- Co-authored-by: Gordon J. Köhn <gordon.koehn@dbsse.ethz.ch> Co-authored-by: Copilot <175728472+Copilot@users.noreply.github.com> * fixing CI --------- Co-authored-by: Gordon J. Köhn <gordon.koehn@dbsse.ethz.ch> Co-authored-by: Copilot <175728472+Copilot@users.noreply.github.com> * fixing CI * test: test coverage in CI (#152) (#154) * Update workflow to conditionally run coverage tests based on PR or push to main/dev branch * Add check for changed files before running coverage * remove template / badge * Update .github/workflows/test.yml praying this is correct. --------- Co-authored-by: Gordon J. Köhn <gordon.koehn@dbsse.ethz.ch> Co-authored-by: Copilot <175728472+Copilot@users.noreply.github.com> * fix CI test coverage (#155) Co-authored-by: Gordon J. Köhn <gordon.koehn@dbsse.ethz.ch> * backtack: the CI issues are bad (#156) * fix CI test coverage * fix aciton * backtrack on code coverage --------- Co-authored-by: Gordon J. Köhn <gordon.koehn@dbsse.ethz.ch> * test: adjusting pytest coverage in CI (#159) * fix CI test coverage * fix aciton * backtrack on code coverage * fixing format of pipeline * fixing format of pipeline * fixing format of pipeline --------- Co-authored-by: Gordon J. Köhn <gordon.koehn@dbsse.ethz.ch> * feature: integrate paired-end read merging into CLI (#160) * adding sam_to_bam * add conversion tests * remove comments * specify sorting * rought workflow * add sorting by coordinate * WIP move aux functions to convert * working start-to-end with merging * black it * fix workflwotest * fix workflwotest * fix ruff * ruff ruff --------- Co-authored-by: Gordon J. Köhn <gordon.koehn@dbsse.ethz.ch> * history cleanup for dev --------- Co-authored-by: Gordon J. Köhn <gordon.koehn@dbsse.ethz.ch> Co-authored-by: Copilot <175728472+Copilot@users.noreply.github.com> fixing CI test: test coverage in CI (#152) (#154) * Update workflow to conditionally run coverage tests based on PR or push to main/dev branch * Add check for changed files before running coverage * remove template / badge * Update .github/workflows/test.yml praying this is correct. --------- Co-authored-by: Gordon J. Köhn <gordon.koehn@dbsse.ethz.ch> Co-authored-by: Copilot <175728472+Copilot@users.noreply.github.com> fix CI test coverage (#155) Co-authored-by: Gordon J. Köhn <gordon.koehn@dbsse.ethz.ch> backtack: the CI issues are bad (#156) * fix CI test coverage * fix aciton * backtrack on code coverage --------- Co-authored-by: Gordon J. Köhn <gordon.koehn@dbsse.ethz.ch> test: adjusting pytest coverage in CI (#159) * fix CI test coverage * fix aciton * backtrack on code coverage * fixing format of pipeline * fixing format of pipeline * fixing format of pipeline --------- Co-authored-by: Gordon J. Köhn <gordon.koehn@dbsse.ethz.ch> * test: test coverage in CI (#152) * Update workflow to conditionally run coverage tests based on PR or push to main/dev branch * Add check for changed files before running coverage * remove template / badge Co-authored-by: Copilot <175728472+Copilot@users.noreply.github.com> --------- Co-authored-by: Gordon J. Köhn <gordon.koehn@dbsse.ethz.ch> Co-authored-by: Copilot <175728472+Copilot@users.noreply.github.com> fix test to temp dir * declutter temp dir handling in main (#166) Co-authored-by: Gordon J. Köhn <gordon.koehn@dbsse.ethz.ch> * add sr2silo in namespace for workflow setup (#165) Co-authored-by: Gordon J. Köhn <gordon.koehn@dbsse.ethz.ch> * centralize workflow config (#167) * feature / fix: temporary directory handling for amino acid aligment (#179) * Introduces TMPDIR support in both main and translate_align modules * Refactors enrich_read_with_metadata into curry_read_with_metadata and updates related tests * Updates documentation and configuration files for resource requirements and CI environment handling --------- Co-authored-by: Gordon J. Köhn <gordon.koehn@dbsse.ethz.ch> Co-authored-by: Copilot <175728472+Copilot@users.noreply.github.com> * test: validate one/zero based coords (#181) * WUP * WIP tests * support for skipped char * add support for soft clipping * add support for hardclipping * adding Padding support * fix test read 02 * fix last read * move to script * note on coord system * fix black * cleanup test to tmp_path * remove trash * bam_to_fasta_query - support for soft clippings + validation * add test for create index and move test_bam_to_fasta_query to temp * update parse_translate_align text fixture after corrections * reformat ruff --------- Co-authored-by: Gordon J. Köhn <gordon.koehn@dbsse.ethz.ch> * fix: Insertions JSON format (#183) * change insertion strings * add validator to pydantic model * update front to end tests * Update src/sr2silo/silo_read_schema.py Co-authored-by: Copilot <175728472+Copilot@users.noreply.github.com> * satisfy ruff --------- Co-authored-by: Gordon J. Köhn <gordon.koehn@dbsse.ethz.ch> Co-authored-by: Copilot <175728472+Copilot@users.noreply.github.com> * refactor/feature: remove nextclade | add eqn to reads (#187) * layout orthogonal test * Salvage Nextclade Orth Test Changes get insertions form Nextclade get insertions form Nextclade get insertions form Nextclade WIP get nuc sequence WIP: parsesd nextclade to read objects remove trash WIP: failing tests Fix: indexing of bam black formating WIP - got the results to compare WIP all __eq__ adding Nuc comparison WIP making Nextclade use the reference from sr2silo WIP changed sr2silo ref to nextclade - still not workign add sorting by coordinate config feature: add paired read merging on alignments (#125) * copy over the script * update by manual copy * WIP * ignore .bai index files - should be freshly generated * add smallgenomutils conda package * add read pair merger * add sam * WIP * WIP: adding checks * move to temp * move to temp * move constants * Reset wokrflows * fix test * add proper test with check fo sorting * add test coverage * up test coverage * Update workflow to conditionally run coverage tests based on PR or push to main/dev branch * Add check for changed files before running coverage * remove template / badge * lower the test coverage * lower the test coverage --------- Co-authored-by: Gordon J. Köhn <gordon.koehn@dbsse.ethz.ch> test: fix in CI for test coverage (#153) * test: test coverage in CI (#152) * Update workflow to conditionally run coverage tests based on PR or push to main/dev branch * Add check for changed files before running coverage * remove template / badge * Update .github/workflows/test.yml praying this is correct. Co-authored-by: Copilot <175728472+Copilot@users.noreply.github.com> --------- Co-authored-by: Gordon J. Köhn <gordon.koehn@dbsse.ethz.ch> Co-authored-by: Copilot <175728472+Copilot@users.noreply.github.com> * fixing CI --------- Co-authored-by: Gordon J. Köhn <gordon.koehn@dbsse.ethz.ch> Co-authored-by: Copilot <175728472+Copilot@users.noreply.github.com> fixing CI test: test coverage in CI (#152) (#154) * Update workflow to conditionally run coverage tests based on PR or push to main/dev branch * Add check for changed files before running coverage * remove template / badge * Update .github/workflows/test.yml praying this is correct. --------- Co-authored-by: Gordon J. Köhn <gordon.koehn@dbsse.ethz.ch> Co-authored-by: Copilot <175728472+Copilot@users.noreply.github.com> fix CI test coverage (#155) Co-authored-by: Gordon J. Köhn <gordon.koehn@dbsse.ethz.ch> backtack: the CI issues are bad (#156) * fix CI test coverage * fix aciton * backtrack on code coverage --------- Co-authored-by: Gordon J. Köhn <gordon.koehn@dbsse.ethz.ch> test: adjusting pytest coverage in CI (#159) * fix CI test coverage * fix aciton * backtrack on code coverage * fixing format of pipeline * fixing format of pipeline * fixing format of pipeline --------- Co-authored-by: Gordon J. Köhn <gordon.koehn@dbsse.ethz.ch> feature: integrate paired-end read merging into CLI (#160) * adding sam_to_bam * add conversion tests * remove comments * specify sorting * rought workflow * add sorting by coordinate * WIP move aux functions to convert * working start-to-end with merging * black it * fix workflwotest * fix workflwotest * fix ruff * ruff ruff --------- Co-authored-by: Gordon J. Köhn <gordon.koehn@dbsse.ethz.ch> test: test coverage in CI (#152) * Update workflow to conditionally run coverage tests based on PR or push to main/dev branch * Add check for changed files before running coverage * remove template / badge * Update .github/workflows/test.yml praying this is correct. Co-authored-by: Copilot <175728472+Copilot@users.noreply.github.com> --------- Co-authored-by: Gordon J. Köhn <gordon.koehn@dbsse.ethz.ch> Co-authored-by: Copilot <175728472+Copilot@users.noreply.github.com> history cleanup for dev --------- Co-authored-by: Gordon J. Köhn <gordon.koehn@dbsse.ethz.ch> Co-authored-by: Copilot <175728472+Copilot@users.noreply.github.com> fixing CI test: test coverage in CI (#152) (#154) * Update workflow to conditionally run coverage tests based on PR or push to main/dev branch * Add check for changed files before running coverage * remove template / badge * Update .github/workflows/test.yml praying this is correct. --------- Co-authored-by: Gordon J. Köhn <gordon.koehn@dbsse.ethz.ch> Co-authored-by: Copilot <175728472+Copilot@users.noreply.github.com> fix CI test coverage (#155) Co-authored-by: Gordon J. Köhn <gordon.koehn@dbsse.ethz.ch> backtack: the CI issues are bad (#156) * fix CI test coverage * fix aciton * backtrack on code coverage --------- Co-authored-by: Gordon J. Köhn <gordon.koehn@dbsse.ethz.ch> test: adjusting pytest coverage in CI (#159) * fix CI test coverage * fix aciton * backtrack on code coverage * fixing format of pipeline * fixing format of pipeline * fixing format of pipeline --------- Co-authored-by: Gordon J. Köhn <gordon.koehn@dbsse.ethz.ch> test: test coverage in CI (#152) * Update workflow to conditionally run coverage tests based on PR or push to main/dev branch * Add check for changed files before running coverage * remove template / badge Co-authored-by: Copilot <175728472+Copilot@users.noreply.github.com> --------- Co-authored-by: Gordon J. Köhn <gordon.koehn@dbsse.ethz.ch> Co-authored-by: Copilot <175728472+Copilot@users.noreply.github.com> fix test to temp dir declutter temp dir handling in main (#166) Co-authored-by: Gordon J. Köhn <gordon.koehn@dbsse.ethz.ch> add sr2silo in namespace for workflow setup (#165) Co-authored-by: Gordon J. Köhn <gordon.koehn@dbsse.ethz.ch> centralize workflow config (#167) feature / fix: temporary directory handling for amino acid aligment (#179) * Introduces TMPDIR support in both main and translate_align modules * Refactors enrich_read_with_metadata into curry_read_with_metadata and updates related tests * Updates documentation and configuration files for resource requirements and CI environment handling --------- Co-authored-by: Gordon J. Köhn <gordon.koehn@dbsse.ethz.ch> Co-authored-by: Copilot <175728472+Copilot@users.noreply.github.com> test: validate one/zero based coords (#181) * WUP * WIP tests * support for skipped char * add support for soft clipping * add support for hardclipping * adding Padding support * fix test read 02 * fix last read * move to script * note on coord system * fix black * cleanup test to tmp_path * remove trash * bam_to_fasta_query - support for soft clippings + validation * add test for create index and move test_bam_to_fasta_query to temp * update parse_translate_align text fixture after corrections * reformat ruff --------- Co-authored-by: Gordon J. Köhn <gordon.koehn@dbsse.ethz.ch> resolve changing base issues ram ref nextclade change ref to same as V-Pipe fix: Insertions JSON format (#183) * change insertion strings * add validator to pydantic model * update front to end tests * Update src/sr2silo/silo_read_schema.py Co-authored-by: Copilot <175728472+Copilot@users.noreply.github.com> * satisfy ruff --------- Co-authored-by: Gordon J. Köhn <gordon.koehn@dbsse.ethz.ch> Co-authored-by: Copilot <175728472+Copilot@users.noreply.github.com> reformat black nextclade test cannot work skip * remove nextclade add tests for insertions Update tests/conftest.py Co-authored-by: Copilot <175728472+Copilot@users.noreply.github.com> * format black * double code bug * accidental removal * accidental removal --------- Co-authored-by: Gordon J. Köhn <gordon.koehn@dbsse.ethz.ch> Co-authored-by: Copilot <175728472+Copilot@users.noreply.github.com> * Update resources/sars-cov-2/README.md Co-authored-by: Copilot <175728472+Copilot@users.noreply.github.com> * remove notebooks * add option to skip paired-end read merging `skip_merge` and tests (#189) Co-authored-by: Gordon J. Köhn <gordon.koehn@dbsse.ethz.ch> * Add conda packaging and GitHub Actions workflows (#191) Co-authored-by: Gordon J. Köhn <gordon.koehn@dbsse.ethz.ch> * remove brnach protection (#188) Co-authored-by: Gordon J. Köhn <gordon.koehn@dbsse.ethz.ch> * Update version to 0.0.4 and prepare for conda packaging * Fix version handling in GitHub release workflow --------- Co-authored-by: Gordon J. Köhn <gordon.koehn@dbsse.ethz.ch> Co-authored-by: Copilot <175728472+Copilot@users.noreply.github.com>
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* feature: add paired read merging on alignments (#125) * copy over the script * update by manual copy * WIP * ignore .bai index files - should be freshly generated * add smallgenomutils conda package * add read pair merger * add sam * WIP * WIP: adding checks * move to temp * move to temp * move constants * Reset wokrflows * fix test * add proper test with check fo sorting * add test coverage * up test coverage * Update workflow to conditionally run coverage tests based on PR or push to main/dev branch * Add check for changed files before running coverage * remove template / badge * lower the test coverage * lower the test coverage --------- Co-authored-by: Gordon J. Köhn <gordon.koehn@dbsse.ethz.ch> * test: fix in CI for test coverage (#153) * test: test coverage in CI (#152) * Update workflow to conditionally run coverage tests based on PR or push to main/dev branch * Add check for changed files before running coverage * remove template / badge * Update .github/workflows/test.yml praying this is correct. Co-authored-by: Copilot <175728472+Copilot@users.noreply.github.com> --------- Co-authored-by: Gordon J. Köhn <gordon.koehn@dbsse.ethz.ch> Co-authored-by: Copilot <175728472+Copilot@users.noreply.github.com> * fixing CI --------- Co-authored-by: Gordon J. Köhn <gordon.koehn@dbsse.ethz.ch> Co-authored-by: Copilot <175728472+Copilot@users.noreply.github.com> * fixing CI * test: test coverage in CI (#152) (#154) * Update workflow to conditionally run coverage tests based on PR or push to main/dev branch * Add check for changed files before running coverage * remove template / badge * Update .github/workflows/test.yml praying this is correct. --------- Co-authored-by: Gordon J. Köhn <gordon.koehn@dbsse.ethz.ch> Co-authored-by: Copilot <175728472+Copilot@users.noreply.github.com> * fix CI test coverage (#155) Co-authored-by: Gordon J. Köhn <gordon.koehn@dbsse.ethz.ch> * backtack: the CI issues are bad (#156) * fix CI test coverage * fix aciton * backtrack on code coverage --------- Co-authored-by: Gordon J. Köhn <gordon.koehn@dbsse.ethz.ch> * test: adjusting pytest coverage in CI (#159) * fix CI test coverage * fix aciton * backtrack on code coverage * fixing format of pipeline * fixing format of pipeline * fixing format of pipeline --------- Co-authored-by: Gordon J. Köhn <gordon.koehn@dbsse.ethz.ch> * feature: integrate paired-end read merging into CLI (#160) * adding sam_to_bam * add conversion tests * remove comments * specify sorting * rought workflow * add sorting by coordinate * WIP move aux functions to convert * working start-to-end with merging * black it * fix workflwotest * fix workflwotest * fix ruff * ruff ruff --------- Co-authored-by: Gordon J. Köhn <gordon.koehn@dbsse.ethz.ch> * history cleanup for dev --------- Co-authored-by: Gordon J. Köhn <gordon.koehn@dbsse.ethz.ch> Co-authored-by: Copilot <175728472+Copilot@users.noreply.github.com> fixing CI test: test coverage in CI (#152) (#154) * Update workflow to conditionally run coverage tests based on PR or push to main/dev branch * Add check for changed files before running coverage * remove template / badge * Update .github/workflows/test.yml praying this is correct. --------- Co-authored-by: Gordon J. Köhn <gordon.koehn@dbsse.ethz.ch> Co-authored-by: Copilot <175728472+Copilot@users.noreply.github.com> fix CI test coverage (#155) Co-authored-by: Gordon J. Köhn <gordon.koehn@dbsse.ethz.ch> backtack: the CI issues are bad (#156) * fix CI test coverage * fix aciton * backtrack on code coverage --------- Co-authored-by: Gordon J. Köhn <gordon.koehn@dbsse.ethz.ch> test: adjusting pytest coverage in CI (#159) * fix CI test coverage * fix aciton * backtrack on code coverage * fixing format of pipeline * fixing format of pipeline * fixing format of pipeline --------- Co-authored-by: Gordon J. Köhn <gordon.koehn@dbsse.ethz.ch> * test: test coverage in CI (#152) * Update workflow to conditionally run coverage tests based on PR or push to main/dev branch * Add check for changed files before running coverage * remove template / badge Co-authored-by: Copilot <175728472+Copilot@users.noreply.github.com> --------- Co-authored-by: Gordon J. Köhn <gordon.koehn@dbsse.ethz.ch> Co-authored-by: Copilot <175728472+Copilot@users.noreply.github.com> fix test to temp dir * declutter temp dir handling in main (#166) Co-authored-by: Gordon J. Köhn <gordon.koehn@dbsse.ethz.ch> * add sr2silo in namespace for workflow setup (#165) Co-authored-by: Gordon J. Köhn <gordon.koehn@dbsse.ethz.ch> * centralize workflow config (#167) * feature / fix: temporary directory handling for amino acid aligment (#179) * Introduces TMPDIR support in both main and translate_align modules * Refactors enrich_read_with_metadata into curry_read_with_metadata and updates related tests * Updates documentation and configuration files for resource requirements and CI environment handling --------- Co-authored-by: Gordon J. Köhn <gordon.koehn@dbsse.ethz.ch> Co-authored-by: Copilot <175728472+Copilot@users.noreply.github.com> * test: validate one/zero based coords (#181) * WUP * WIP tests * support for skipped char * add support for soft clipping * add support for hardclipping * adding Padding support * fix test read 02 * fix last read * move to script * note on coord system * fix black * cleanup test to tmp_path * remove trash * bam_to_fasta_query - support for soft clippings + validation * add test for create index and move test_bam_to_fasta_query to temp * update parse_translate_align text fixture after corrections * reformat ruff --------- Co-authored-by: Gordon J. Köhn <gordon.koehn@dbsse.ethz.ch> * fix: Insertions JSON format (#183) * change insertion strings * add validator to pydantic model * update front to end tests * Update src/sr2silo/silo_read_schema.py Co-authored-by: Copilot <175728472+Copilot@users.noreply.github.com> * satisfy ruff --------- Co-authored-by: Gordon J. Köhn <gordon.koehn@dbsse.ethz.ch> Co-authored-by: Copilot <175728472+Copilot@users.noreply.github.com> * refactor/feature: remove nextclade | add eqn to reads (#187) * layout orthogonal test * Salvage Nextclade Orth Test Changes get insertions form Nextclade get insertions form Nextclade get insertions form Nextclade WIP get nuc sequence WIP: parsesd nextclade to read objects remove trash WIP: failing tests Fix: indexing of bam black formating WIP - got the results to compare WIP all __eq__ adding Nuc comparison WIP making Nextclade use the reference from sr2silo WIP changed sr2silo ref to nextclade - still not workign add sorting by coordinate config feature: add paired read merging on alignments (#125) * copy over the script * update by manual copy * WIP * ignore .bai index files - should be freshly generated * add smallgenomutils conda package * add read pair merger * add sam * WIP * WIP: adding checks * move to temp * move to temp * move constants * Reset wokrflows * fix test * add proper test with check fo sorting * add test coverage * up test coverage * Update workflow to conditionally run coverage tests based on PR or push to main/dev branch * Add check for changed files before running coverage * remove template / badge * lower the test coverage * lower the test coverage --------- Co-authored-by: Gordon J. Köhn <gordon.koehn@dbsse.ethz.ch> test: fix in CI for test coverage (#153) * test: test coverage in CI (#152) * Update workflow to conditionally run coverage tests based on PR or push to main/dev branch * Add check for changed files before running coverage * remove template / badge * Update .github/workflows/test.yml praying this is correct. Co-authored-by: Copilot <175728472+Copilot@users.noreply.github.com> --------- Co-authored-by: Gordon J. Köhn <gordon.koehn@dbsse.ethz.ch> Co-authored-by: Copilot <175728472+Copilot@users.noreply.github.com> * fixing CI --------- Co-authored-by: Gordon J. Köhn <gordon.koehn@dbsse.ethz.ch> Co-authored-by: Copilot <175728472+Copilot@users.noreply.github.com> fixing CI test: test coverage in CI (#152) (#154) * Update workflow to conditionally run coverage tests based on PR or push to main/dev branch * Add check for changed files before running coverage * remove template / badge * Update .github/workflows/test.yml praying this is correct. --------- Co-authored-by: Gordon J. Köhn <gordon.koehn@dbsse.ethz.ch> Co-authored-by: Copilot <175728472+Copilot@users.noreply.github.com> fix CI test coverage (#155) Co-authored-by: Gordon J. Köhn <gordon.koehn@dbsse.ethz.ch> backtack: the CI issues are bad (#156) * fix CI test coverage * fix aciton * backtrack on code coverage --------- Co-authored-by: Gordon J. Köhn <gordon.koehn@dbsse.ethz.ch> test: adjusting pytest coverage in CI (#159) * fix CI test coverage * fix aciton * backtrack on code coverage * fixing format of pipeline * fixing format of pipeline * fixing format of pipeline --------- Co-authored-by: Gordon J. Köhn <gordon.koehn@dbsse.ethz.ch> feature: integrate paired-end read merging into CLI (#160) * adding sam_to_bam * add conversion tests * remove comments * specify sorting * rought workflow * add sorting by coordinate * WIP move aux functions to convert * working start-to-end with merging * black it * fix workflwotest * fix workflwotest * fix ruff * ruff ruff --------- Co-authored-by: Gordon J. Köhn <gordon.koehn@dbsse.ethz.ch> test: test coverage in CI (#152) * Update workflow to conditionally run coverage tests based on PR or push to main/dev branch * Add check for changed files before running coverage * remove template / badge * Update .github/workflows/test.yml praying this is correct. Co-authored-by: Copilot <175728472+Copilot@users.noreply.github.com> --------- Co-authored-by: Gordon J. Köhn <gordon.koehn@dbsse.ethz.ch> Co-authored-by: Copilot <175728472+Copilot@users.noreply.github.com> history cleanup for dev --------- Co-authored-by: Gordon J. Köhn <gordon.koehn@dbsse.ethz.ch> Co-authored-by: Copilot <175728472+Copilot@users.noreply.github.com> fixing CI test: test coverage in CI (#152) (#154) * Update workflow to conditionally run coverage tests based on PR or push to main/dev branch * Add check for changed files before running coverage * remove template / badge * Update .github/workflows/test.yml praying this is correct. --------- Co-authored-by: Gordon J. Köhn <gordon.koehn@dbsse.ethz.ch> Co-authored-by: Copilot <175728472+Copilot@users.noreply.github.com> fix CI test coverage (#155) Co-authored-by: Gordon J. Köhn <gordon.koehn@dbsse.ethz.ch> backtack: the CI issues are bad (#156) * fix CI test coverage * fix aciton * backtrack on code coverage --------- Co-authored-by: Gordon J. Köhn <gordon.koehn@dbsse.ethz.ch> test: adjusting pytest coverage in CI (#159) * fix CI test coverage * fix aciton * backtrack on code coverage * fixing format of pipeline * fixing format of pipeline * fixing format of pipeline --------- Co-authored-by: Gordon J. Köhn <gordon.koehn@dbsse.ethz.ch> test: test coverage in CI (#152) * Update workflow to conditionally run coverage tests based on PR or push to main/dev branch * Add check for changed files before running coverage * remove template / badge Co-authored-by: Copilot <175728472+Copilot@users.noreply.github.com> --------- Co-authored-by: Gordon J. Köhn <gordon.koehn@dbsse.ethz.ch> Co-authored-by: Copilot <175728472+Copilot@users.noreply.github.com> fix test to temp dir declutter temp dir handling in main (#166) Co-authored-by: Gordon J. Köhn <gordon.koehn@dbsse.ethz.ch> add sr2silo in namespace for workflow setup (#165) Co-authored-by: Gordon J. Köhn <gordon.koehn@dbsse.ethz.ch> centralize workflow config (#167) feature / fix: temporary directory handling for amino acid aligment (#179) * Introduces TMPDIR support in both main and translate_align modules * Refactors enrich_read_with_metadata into curry_read_with_metadata and updates related tests * Updates documentation and configuration files for resource requirements and CI environment handling --------- Co-authored-by: Gordon J. Köhn <gordon.koehn@dbsse.ethz.ch> Co-authored-by: Copilot <175728472+Copilot@users.noreply.github.com> test: validate one/zero based coords (#181) * WUP * WIP tests * support for skipped char * add support for soft clipping * add support for hardclipping * adding Padding support * fix test read 02 * fix last read * move to script * note on coord system * fix black * cleanup test to tmp_path * remove trash * bam_to_fasta_query - support for soft clippings + validation * add test for create index and move test_bam_to_fasta_query to temp * update parse_translate_align text fixture after corrections * reformat ruff --------- Co-authored-by: Gordon J. Köhn <gordon.koehn@dbsse.ethz.ch> resolve changing base issues ram ref nextclade change ref to same as V-Pipe fix: Insertions JSON format (#183) * change insertion strings * add validator to pydantic model * update front to end tests * Update src/sr2silo/silo_read_schema.py Co-authored-by: Copilot <175728472+Copilot@users.noreply.github.com> * satisfy ruff --------- Co-authored-by: Gordon J. Köhn <gordon.koehn@dbsse.ethz.ch> Co-authored-by: Copilot <175728472+Copilot@users.noreply.github.com> reformat black nextclade test cannot work skip * remove nextclade add tests for insertions Update tests/conftest.py Co-authored-by: Copilot <175728472+Copilot@users.noreply.github.com> * format black * double code bug * accidental removal * accidental removal --------- Co-authored-by: Gordon J. Köhn <gordon.koehn@dbsse.ethz.ch> Co-authored-by: Copilot <175728472+Copilot@users.noreply.github.com> * Update resources/sars-cov-2/README.md Co-authored-by: Copilot <175728472+Copilot@users.noreply.github.com> * remove notebooks * add option to skip paired-end read merging `skip_merge` and tests (#189) Co-authored-by: Gordon J. Köhn <gordon.koehn@dbsse.ethz.ch> * Add conda packaging and GitHub Actions workflows (#191) Co-authored-by: Gordon J. Köhn <gordon.koehn@dbsse.ethz.ch> * remove brnach protection (#188) Co-authored-by: Gordon J. Köhn <gordon.koehn@dbsse.ethz.ch> * Update version to 0.0.4 and prepare for conda packaging * Fix version handling in GitHub release workflow * GitHub Actions(deps): Bump actions/setup-python from 4 to 5 (#193) Bumps [actions/setup-python](https://github.com/actions/setup-python) from 4 to 5. - [Release notes](https://github.com/actions/setup-python/releases) - [Commits](actions/setup-python@v4...v5) --- updated-dependencies: - dependency-name: actions/setup-python dependency-type: direct:production update-type: version-update:semver-major ... Signed-off-by: dependabot[bot] <support@github.com> Co-authored-by: dependabot[bot] <49699333+dependabot[bot]@users.noreply.github.com> * GitHub Actions(deps): Bump actions/checkout from 3 to 4 (#192) Bumps [actions/checkout](https://github.com/actions/checkout) from 3 to 4. - [Release notes](https://github.com/actions/checkout/releases) - [Changelog](https://github.com/actions/checkout/blob/main/CHANGELOG.md) - [Commits](actions/checkout@v3...v4) --- updated-dependencies: - dependency-name: actions/checkout dependency-type: direct:production update-type: version-update:semver-major ... Signed-off-by: dependabot[bot] <support@github.com> Co-authored-by: dependabot[bot] <49699333+dependabot[bot]@users.noreply.github.com> * docs: specify usage of import-to-silo (#198) * validate silo insertions pydantic schema * add note to docs not to use untrimmed * add tests and allow N in insertiosn --------- Co-authored-by: Gordon J. Köhn <gordon.koehn@dbsse.ethz.ch> * fix: snakemake workflow / multiple batch ids clash (#202) * fix combination bug * fix multiple batch issue * fix config path * change path --------- Co-authored-by: Gordon J. Köhn <gordon.koehn@dbsse.ethz.ch> * fix: correct unknown / skipped char for amino acid padding (#200) * validate silo insertions pydantic schema * add note to docs not to use untrimmed * add tests and allow N in insertiosn * chang the Amio Acid Validation * changing unknown char for amino acid paddings * update expexte aligned reads fixture * fix test fixture aa insertions * Update src/sr2silo/silo_read_schema.py Co-authored-by: Copilot <175728472+Copilot@users.noreply.github.com> * update snakemake fixture --------- Co-authored-by: Gordon J. Köhn <gordon.koehn@dbsse.ethz.ch> Co-authored-by: Copilot <175728472+Copilot@users.noreply.github.com> * workflows: adding conda envs to rule (#194) * Adding conda rule support - (not tested) * remove redundant dependncies * adapt submission script --------- Co-authored-by: Gordon J. Köhn <gordon.koehn@dbsse.ethz.ch> * changing AA skipped chars in Readme (#205) Co-authored-by: Gordon J. Köhn <gordon.koehn@dbsse.ethz.ch> * update Readme with conda install (#206) Co-authored-by: Gordon J. Köhn <gordon.koehn@dbsse.ethz.ch> * feature : Add version tracking to 'import-to-loculus' metadata (#195) * WIP * make version info mandatory * adding version to all of test suits * update database config file * missing version * remove expected comparrions from smk rule * adjust test data * remove unused * generate index sr2silo_version * poetry dynamic versioning * adding transient dependency * install self-verisoning * adjust python version * remove brotli * adjsut * update fallback * simpligf --------- Co-authored-by: Gordon J. Köhn <gordon.koehn@dbsse.ethz.ch> --------- Signed-off-by: dependabot[bot] <support@github.com> Co-authored-by: Gordon J. Köhn <gordon.koehn@dbsse.ethz.ch> Co-authored-by: Copilot <175728472+Copilot@users.noreply.github.com> Co-authored-by: dependabot[bot] <49699333+dependabot[bot]@users.noreply.github.com>
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As bam and sam formats use different coordinates, it should be verified adequately that the coordinate systems are correct:
For Nuclotide Cleartext Sequence and Insertions:
this is done by function
bam_to_fastq_handle_indels.This has been extensively checked here, including the implementation of the SAMtools format specification example. We added support for soft clippings, skipped regions, and padding. This may already correct a lot of mistakes.
For Amino Acid Read Translation and Alignment and Insertions:
The
bam_to_fasta_query, formerlybam_to_fasta, now converts a BAM file to a FASTA file. Bluntly resolved the sam to fasta, removing soft clippings, keeping insertions and deletions, and ignoring skipped regions and padding. Outputs the sequence as it is read from the molecule. This is what is required for the input to Diamond.===
These are breaking changes, and final outputs differ !!!