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Flagtastrophe #290

Merged
merged 96 commits into from
Nov 8, 2024
Merged

Flagtastrophe #290

merged 96 commits into from
Nov 8, 2024

Commits on Nov 1, 2024

  1. fix: Update CLI interface for wfmash

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  2. fix: feat: Add missing variable declarations and remove duplicate opt… 

    …ion declarations in parse_args.hpp
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  3. feat: remove duplicate no_merge flag declaration in parse_args.hpp

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  4. fix: remove duplicate approx_mapping flag and declare kmer_size

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  5. fix: Add approx_mapping flag to parse_args.hpp

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  6. fix: change short option for approx_mapping to -m

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  7. feat: Add short option -k for kmer-size and -w for sketch-size

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  8. Here is the one-line commit message based on the provided diffs: 

    chore: remove unused WFA/WFlign options from parse_args.hpp
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  9. feat: add num_mappings_for_short_seq, lower_triangular, and skip_self… 

    … flags
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  10. fix: Remove unused CLI arguments and set default values directly

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  11. fix: Fix SEARCH/REPLACE block to exactly match src/interface/parse_ar… 

    …gs.hpp
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  12. feat: change short option for --one-to-one from -4 to -o

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  13. fix: remove drop-low-id parameter

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  14. feat: add default parameter for keep_low_pct_id

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  15. fix: Update help text formatting

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  16. feat: Reorganize help text in parse_args.hpp

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  17. fix: Add missing options_group to argument parser

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  18. feat: Add improved argument parser formatting

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  19. fix: remove invalid usageindent parameter from parse_args.hpp

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  20. feat: Add version and help flags to system options group

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  21. feat: Remove unnecessary indentation from wfmash help output

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  22. feat: Adjust help text formatting to match minimap2's style

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  23. fix: remove duplicate "Options:" header

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  24. feat: Improve help text conciseness

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  25. fix: remove extra "wfmash" line from help output

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  26. feat: Add lower triangular option to mapping parameters

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  27. feat: compress query prefix option text

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  28. fix: Update default group prefix and help text

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  29. feat: add default group prefix character to help text

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  30. feat: use shorter param name for WFA scoring

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  31. feat: update hypergeometric filter help text

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  32. feat: Update hypergeometric filter parameter names in help text

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  33. feat: update parameter name to "ani-Δ" in help text

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  34. feat: update help text for group prefix option to be concise

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  35. feat: Add -W short option for --write-index

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  36. feat: Improve help text formatting for sequence files

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  37. clarify fasta input usage

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Commits on Nov 4, 2024

  1. feat: Replace --index with --read-index for symmetry with --write-index

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  2. feat: add input-mapping option to alignment section

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  3. feat: Add validation for segment length, block length, and max mappin… 

    …g length parameters
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Commits on Nov 5, 2024

  1. test: add input mapping functionality test

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  2. feat: restrict mapping to S288C and SK1 strains to speed up test

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  3. fix: Enforce required target.fa argument in wfmash

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  4. feat: update mashmap version to 3.5.0

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  5. build: update mapping test command

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  6. feat: add compact parameter display format

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  7. more options cleanup

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  8. fix: replace all '[mashmap]' with '[wfmash]'

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  9. refactor: Separate mapping and alignment checks in test workflow

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  10. fix: Move version flag handling before argument validation

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  11. feat: Add WFMASH_GIT_VERSION to SAM header

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  12. feat: Add wflign_git_version.hpp and update generate_dataset.sh

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  13. feat: Add wflign directory to git version generation script

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  14. fix: add command line tag to SAM header version

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  15. fix: Update SAM header version string

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  16. fix: replace WFMASH_GIT_VERSION with WFLIGN_GIT_VERSION in wflign_pat… 

    …ch.cpp
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  17. feat: Update SAM header version in computeAlignments.hpp

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  18. fix: Update logging messages to consistently use '[wfmash::mashmap]'

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  19. chore: update logging messages to use '[wfmash::mashmap]' prefix

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  20. refactor: replace 'mashmap::skch' with 'wfmash::mashmap'

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  21. fix: replace search/replace blocks in src/map/include/computeMap.hpp

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  22. fix: replace instances of mashmap::mapQuery with wfmash::mashmap

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  23. fix: replace 'wfmash::map' with 'wfmash::mashmap'

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  24. fix: compress logging messages in winsketch and main.cpp

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  25. fix: correct SEARCH/REPLACE block in winSketch.hpp

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  26. fix: replace remaining 'mashmap::skch' with 'wfmash::mashmap'

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  27. fix: update SEARCH/REPLACE block to match existing lines in src/map/i… 

    …nclude/winSketch.hpp
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  28. chore: remove initialization messages

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  29. feat: combine sequence and hash/window stats, simplify index computat… 

    …ion timing
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  30. feat: Update README to reflect current MashMap 3.5 and WFA usage

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  31. feat: Update README with concise and clear description

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  32. feat: Add explanation for mapping length limits in README

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  33. feat: Add length of target subsets in base pairs to output

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  34. fix: add debug output to track sequence size metrics

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  35. build: Fix compilation error in parse_args.hpp

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  36. fix: Update reference size calculation in parse_args.hpp

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  37. chore: comment out debugging output in parse_args.hpp

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  38. feat: Add target sequence information to log output

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  39. fix: Move logging information before mapping indexing

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  40. feat: Add logging of target sequence information before indexing

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  41. unaider

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  42. feat: Compute and display query and target lengths separately

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  43. fix: initialize sequence names before calculating lengths

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  44. feat: Move sequence length reporting to after sequence manager initia… 

    …lization
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  45. build: Initialize sequence names and calculate lengths in constructor

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  46. build: Improve output conciseness and remove duplicate line

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  47. fix: Replace "seqs" with "queries" in output messages

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  48. chore: remove detailed statistics line

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  49. fix: Set default group prefix delimiter to '#'

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  50. fix: Remove warning about single file all-vs-all mapping

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  51. fix: Set default group prefix delimiter to '#' and enable prefix skip… 

    …ping
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  52. feat: add group information to query and target count output

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  53. refactor: split long log message into multiple lines

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Commits on Nov 6, 2024

  1. fix: Add check for .fai index files before parameter validation

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Commits on Nov 7, 2024

  1. Revert "fix: Add check for .fai index files before parameter validation" 

    This reverts commit dedb843.
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  2. feat: Add parallel index building to improve performance

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