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target padding during alignment#303

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ekg wants to merge 76 commits intomainwaveygang/wfmash:mainfrom tiny-patchwaveygang/wfmash:tiny-patchCopy head branch name to clipboard

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Commits on Dec 2, 2024

• feat: Add target padding option for sequence alignment

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  7c95af9

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• refactor: Add target padding with bounds checking during mapping record parsing

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• refactor: Remove target_padding from sequence record padding calculation

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• fix: Modify parseMashmapRow to accept target_padding as parameter

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• fix: Update parseMashmapRow call with target_padding parameter

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Commits on Dec 9, 2024

• feat: Adjust CIGAR string based on sequence comparison in alignment process

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• feat: Add logging for original CIGAR string before adjustment

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• fix: Adjust end deletions in adjust_cigar_string to move right instead of left

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• fix: Adjust left-shifting of initial deletions in CIGAR string alignment

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• fix: Declare variable 'idx' before using it in adjust_cigar_string function

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• fix: Correct match representation in CIGAR string after alignment adjustments

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• feat: Implement adjust_cigar_string function to shift deletions correctly

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• refactor: Optimize CIGAR string adjustment by directly manipulating operations

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• fix: Correct deletion adjustment in CIGAR string processing function

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• feat: Update adjust_cigar_string to merge successive CIGAR operations

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• feat: Add functions to trim CIGAR string and recompute identity metrics

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  172c5ae

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• fix: Adjust CIGAR string and positions in alignment output processing

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• fix: Replace identity metrics tags and correct scaling in alignment output

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• chore: Remove debugging output from processAlignment function

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• fix: Prevent extra newline in updated_output in processAlignment function

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• feat: Set default target_padding to 100bp and update help message

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• feat: Add CIGAR alignment verification to catch mismatches early

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Commits on Dec 10, 2024

• fix: Handle sequence boundary conditions in alignment processing

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Commits on Dec 11, 2024

• feat: Add debugging print statements to processAlignment function

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• feat: Add debug output for alignment modifications in processAlignment function

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• feat: Add detailed debugging output for mismatch errors in alignment validation

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• fix: Resolve type mismatch in std::min calls in verify_cigar_alignment function

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• fix: Update position adjustments in CIGAR trimming and alignment verification

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  28bfb43

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• feat: Add debug statements to trace CIGAR trimming and alignment processing

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• feat: Validate sequence matches before adjusting CIGAR string operations

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• feat: Update adjust_cigar_string to handle query and target end positions

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• fix: Correct variable usage in CIGAR string adjustment logic

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  ef161f2

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• feat: Implement alignment adjustment functions for leading/trailing deletions

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• feat: Allow deletion shifts up to target_padding in alignment functions

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• fix: Update function signatures and calls to include max_shift parameter

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  9e182cd

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• refactor: Remove trimming functionality and update CIGAR adjustment logic

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  b33eb8f

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• fix: Correct function call and remove unused position adjustment logic

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• fix: Fix SEARCH block to match existing lines in computeAlignments.hpp

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• fix: Replace undeclared variables with currentRecord references in debug output

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Commits on Dec 12, 2024

• refactor: Improve sequence verification for CIGAR operation swapping

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• refactor: Fix CIGAR operation swap sequence verification logic

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• fix: Prevent CIGAR operation swap when sequence mismatch occurs

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• fix: Replace undefined original_cigar with input cigar in adjust_cigar_string

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• refactor: Optimize CIGAR string manipulation by direct string processing

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• fix: Correct sequence matching in CIGAR string adjustment

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• feat: Add CIGAR operation merging function to simplify alignment representation

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• feat: Add function to trim leading/trailing deletions from CIGAR string

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• feat: Add debugging messages to track alignment validation steps

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• almost there

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• correctness

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• refactor: Remove debugging statements while preserving validity checks

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• refactor: Remove extra blank line in CIGAR string extraction

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• refactor: Remove debug print statement for CIGAR string

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• remove double adjustment

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• refactor: Optimize CIGAR string merging with more efficient parsing

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• refactor: Optimize CIGAR string parsing in trim_leading_trailing_deletions

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• refactor: Add macro to control CIGAR validation checks

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• feat: Enable CIGAR validation checks by setting VALIDATE_CIGAR to 1

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• feat: Add detailed debug logging for CIGAR validation and alignment process

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• feat: Add CIGAR validation after adjust_cigar_string

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• feat: Add debug output for alignment record details in worker thread

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• refactor: Enhance CIGAR string swap validation with comprehensive sequence matching checks

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• feat: Add detailed debugging for CIGAR string adjustment character comparisons

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  69f9d3d

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• fix: Correct position calculation in leading deletion swap validation

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• fix: Remove duplicate variable declarations in adjust_cigar_string

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• refactor: Add detailed debug logging for CIGAR alignment verification

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• fix: Improve CIGAR alignment verification with detailed position tracking

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• fix: Improve CIGAR alignment verification with better position tracking

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• fix: Cast int64_t to size_t in std::min calls to resolve type mismatch

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• fix: Correct CIGAR string handling for leading mismatched operations

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• refactor: Simplify CIGAR validation and error reporting

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• refactor: Remove debug output for character comparison in alignment

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• refactor: Remove debug logging from alignment processing

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• refactor: Remove debug logging from CIGAR alignment verification

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• style: Comment out debug messages in adjust_cigar_string function

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• chore: Comment out debug messages in adjust_cigar_string function

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