Code

pad the target when aligning#312

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ekg merged 108 commits intomainwaveygang/wfmash:mainfrom target-padwaveygang/wfmash:target-padCopy head branch name to clipboardJan 27, 2025

+1,027-83

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Commits on Dec 2, 2024

• feat: Add target padding option for sequence alignment

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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 Jan 22, 2025

• Merge branch 'main' of github.com:waveygang/wfmash into target-pad

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• Merge branch 'main' of github.com:waveygang/wfmash into target-pad

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• feat: Add chain metadata parsing to MappingBoundaryRow

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• refactor: Remove duplicate MappingBoundaryRow struct and add chain metadata

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• feat: Add indel swizzling functions for CIGAR alignment optimization

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• feat: Add wflign_swizzle.cpp to CMakeLists.txt source files

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• feat: Add CIGAR conversion and swizzling for internal chain chunks

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• fix: Add missing WFA header and edit_cigar_t type definition

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• refactor: Update include paths and function signatures in wflign files

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• fix: Update WFA CIGAR handling and include paths in wflign module

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• fix: Resolve WFA2 library compilation issues in wflign module

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• fix: Resolve include path and type definition errors in wflign module

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• refactor: Remove align_types.hpp dependency and simplify chain metadata handling

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• fix: Add missing header and update biWFA alignment call parameters

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• fix: Update CIGAR conversion functions to use wflign_cigar_t

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• fix: Define wflign_cigar_t and fix CIGAR conversion functions

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Commits on Jan 23, 2025

• fix: Resolve namespace and function declaration conflicts in wflign_swizzle.hpp

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• fix: Resolve namespace and type compatibility issues in wflign CIGAR handling

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• fix: Resolve namespace and compilation issues in wflign module

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• fix: Resolve duplicate function definitions and namespace issues in wflign

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• fix: Resolve namespace and type resolution issues in wflign CIGAR conversion

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• refactor: Remove duplicate wflign_cigar_t definition and include wflign_alignment.hpp

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• fix: Resolve typedef and function declaration issues in wflign_swizzle

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• fix: Update do_biwfa_alignment call with correct chain parameters

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• fix: Remove static from wflign namespace functions to resolve linker errors

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• fix: Resolve conflicting function declarations in wflign_swizzle.hpp

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• refactor: Add debug logging for CIGAR swizzling in internal chain chunks

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• feat: Add debug logging for chain swizzling in wflign alignment

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• feat: Add debug logging to track swizzling conditions in wflign alignment

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• feat: Add chain information tracking in mapping generation

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• ok

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• feat: Add CIGAR conversion and swizzling for internal chain chunks

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• fix: Implement alignment_end_coords in wflign_swizzle.hpp

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• fix: Resolve redefinition of alignment_end_coords function

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• fix: Remove redundant namespace qualifier in wflign_swizzle.cpp

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• feat: Enhance chain mapping output with position and length information

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• feat: Update chain parsing and target padding logic in wfmash

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• refactor: Always attempt CIGAR swizzling for all alignment chunks

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• refactor: Update target padding logic to apply to all segments

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• feat: Add debug logging for chain info parsing in computeAlignments.hpp

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• fix: Correct chain info parsing index in wfmash alignment

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• refactor: Remove debug print statements from wflign and computeAlignments

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• refactor: Improve indel swizzling robustness with enhanced debug logging and boundary checks

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• fix: Add missing iostream and resolve function declaration ambiguity

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• fix: Remove default arguments from function implementations in wflign_swizzle.cpp

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• feat: Add debug logging for CIGAR string swizzling in wflign

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• feat: Add detailed debug logging for CIGAR string swizzling

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• fix: Convert CIGAR 'M' to '=' for exact matches in wflign

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• The commit message for this change would be:

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• refactor: Reduce debug output to 100 characters for better readability

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• fix: Adjust target sequence coordinates in swizzle to use 0-based indexing

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• the target and query offset are 0 and 0 in global alignment

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• feat: Add functionality to trim leading and trailing deletions from alignments

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• feat: Add trim_deletions method to handle CIGAR string trimming

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• refactor: Write alignments directly to stderr instead of using queue

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• feat: Add debug logging for coordinate changes during deletion trimming

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• feat: Add debug logging and coordinate validation in mashmap row parsing

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• feat: Add debug logging for initial alignment and pre-trimming coordinates

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Commits on Jan 24, 2025

• less debug

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• Revert "refactor: Write alignments directly to stderr instead of using queue"

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• fix: Correctly calculate reference end coordinate in trim_deletions()

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• refactor: Adjust target start coordinate when swapping deletion in CIGAR string

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• sort of fixed

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• fix: Update trim_deletions to adjust both query and reference coordinates

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• feat: Add debug prints to track matches and alignment lengths in CIGAR and PAF output

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• correctly process =/M

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• fix: Initialize alignment counters to zero in wfa_alignment_to_cigar()

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• refactor: Modify identity computation logic using direct edit_cigar processing

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• fix: Replace non-existent wfa_edit_cigar_to_string with custom CIGAR conversion

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• fix: Add debug logging for CIGAR operations and alignment statistics

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• fix: Properly trim CIGAR string when removing leading/trailing indels

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• refactor: Remove debug print statement in write_alignment_paf function

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• refactor: Modify write_alignment functions to accept optional CIGAR string parameter

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• refactor: Optimize CIGAR string processing with compressed metrics computation

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• The changes look good. This modification will ensure that the metrics (matches, mismatches, etc.) are calculated directly from the compressed CIGAR string, which should resolve the discrepancy betw…

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• feat: Add debug logging to process_compressed_cigar for detailed CIGAR parsing

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• feat: Add debug logging for CIGAR string processing

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Commits on Jan 26, 2025

• fix: Add debug logging for CIGAR string comparison

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• refactor: Move trim_deletions to wflign namespace and update alignment metrics

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• refactor: Remove trim_deletions function and related code from computeAlignments

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• I'll help you remove the debug statements. Here's a concise commit message for these changes:

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• refactor: Remove debug print statements from wflign_patch.cpp

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• feat: Remove parse-debug messages from computeAlignments.hpp

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• refactor: Remove commented-out code and update alignment writing logic

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• feat: Remove wflign debug logging messages

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• refactor: Simplify wfa_edit_cigar_to_string function by removing unnecessary blank line

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• refactor: Remove debug print statements from wflign_swizzle.cpp

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• chore: Remove debug print statements from wflign_swizzle.cpp

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• refactor: Remove debug print statements from alignment and swizzle code

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• refactor: Remove debug print statements from wflign_swizzle.cpp

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• refactor: Remove debug logging in sequences_match function

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• feat: Set default target_padding to 100bp

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• hmmm, forgot these

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Commits on Jan 27, 2025

• Merge branch 'main' of github.com:waveygang/wfmash into target-pad

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• correct the start swizzle

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• lil debug cleanup

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• refactor: Replace file comparisons with coverage threshold checks in tests

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• test: Replace short-read tests with pafcheck validation test

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• feat: Add wgatools MAF validity check and install pafcheck in CI workflow

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• chore: Remove duplicate cargo install lines in workflow file

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• feat: Add MAF alignment length validation in tests

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• ci: Simplify GitHub Actions workflow to use ctest for testing

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• fix: Remove invalid wgatools maf-check command from test

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