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1. Commits on Jan 29, 2026

   • Merge pull request #344 from MontgomeryLab/issue-343

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   • Updated setup.sh to address installation issues related to Apple Silicon–based systems.

     

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2. Commits on Jun 4, 2025

   • Merge pull request #341 from MontgomeryLab/issue-340

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   • Merge pull request #337 from MontgomeryLab/issue-336

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3. Commits on May 2, 2025

   • If pipefail isn't set, then non-zero exit codes from `shasum` are masked.

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4. Commits on Apr 29, 2025

   • Minor consistency and spelling corrections

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   • Minor formatting changes for final messages and updating miniconda_version to the latest

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   • Updating Miniconda installation routine to use new helper functions

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   • Misc. improvements to function hygiene:

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   • Updating setup_environment(). Mamba doesn't emit "Executing transaction: ...working... done" on success, so instead we check if the environment name is listed by `conda env list`. This is vastly le…

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   • Adding helper functions that handle differences in usage between conda and mamba:

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   • Bugfix: the list of Miniconda installer hashes was recently moved to a new URL, and the structure of the new page is an HTML table rather than RST.

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   • Improved platform and shell checks.

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5. Commits on Jul 8, 2024

   • Adding a sanity check for the unlikely case that an alignment is missing a CIGAR string

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   • Minor fix, renaming a variable whose name was misleading

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   • These changes landed on the wrong changelist. This commit restores query sequence handling to the former approach. The query sequence, its start position, and its length are once again determined f…

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6. Commits on Jun 10, 2024

   • The MD string is now reported in the Mismatches column of diagnostic alignment tables when a mismatch pattern is specified.

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   • Corrected handling of the line_num cdef attribute from Python space

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   • Minor optimization in AdarEditMatch. The character "0" is very abundant in MD strings. If it isn't preceded by another digit, skip the unnecessary work of parsing it into an int and incrementing th…

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   • Minor consistency change to have AlignmentReader throw the same exception type as AlignmentIter when checking the first alignment for missing NM tag

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   • Adding a check for incompatible CIGAR operators (soft clip, hard clip, skip, and pad). If found, the exception includes the offending record number and the basename of the file.

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7. Commits on May 31, 2024

   • Updating documentation to reflect the new mismatch pattern parameter, and the temporary removal of mismatch calculation from the cigar string

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   • Adding missing @SQ headers to identity_choice_test.sam to appease Pysam since this otherwise isn't a target for tests.

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   • Making NumericalMatch more robust by removing leading, trailing, and delimiter-surrounding whitespace from definitions before parsing. This allows more flexibility for definitions like "1 - 2" or "…

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   • Adding a dummy class that inherits from two argparse formatters that are required for the tiny-count help string.

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   • Minor style change. Makes more sense for the default case to be next to the lookup method

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   • Minor changes to the AlignmentIter class. The detailed_mismatch argument now defaults to False. Since we are temporarily removing mismatch calculation from the CIGAR string, missing NM tags are now…

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8. Commits on May 29, 2024

   • Adding unit tests for AdarEditMatch and TutEditMatch

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   • Minor changes to the NumericalMatch class. This class has been used for more than just length selection for a while now...

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   • Adding the command line parameter to tiny-count, Run Configs, and CWL for specifying edit pattern.

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   • Adding the new *EditMatch classes to FeatureSelector.build_selectors(). Stage 2 alignment now passes the entire alignment dictionary to *EditMatch classes so that edit pattern can be evaluated usin…

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   • Adding 3 new selector classes:

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   • Updating the AlignmentReader class to handle the new mismatch_pattern command line argument, and the new arguments for AlignmentIter.

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   • AlignmentIter now returns the MD tag in alignment dictionaries when detailed_mismatch is True.

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9. Commits on May 8, 2024

   • Merge pull request #335 from MontgomeryLab/issue-334

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