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Flagtastrophe#290

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ekg merged 96 commits intomainwaveygang/wfmash:mainfrom flagtastrophewaveygang/wfmash:flagtastropheCopy head branch name to clipboardNov 8, 2024

+421-414

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Commits on Nov 1, 2024

• fix: Update CLI interface for wfmash

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• fix: feat: Add missing variable declarations and remove duplicate option declarations in parse_args.hpp

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• feat: remove duplicate no_merge flag declaration in parse_args.hpp

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• fix: remove duplicate approx_mapping flag and declare kmer_size

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• fix: Add approx_mapping flag to parse_args.hpp

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• fix: change short option for approx_mapping to -m

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

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• feat: add num_mappings_for_short_seq, lower_triangular, and skip_self flags

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• fix: Remove unused CLI arguments and set default values directly

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• fix: Fix SEARCH/REPLACE block to exactly match src/interface/parse_args.hpp

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• feat: change short option for --one-to-one from -4 to -o

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• fix: remove drop-low-id parameter

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• feat: add default parameter for keep_low_pct_id

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• fix: Update help text formatting

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• feat: Reorganize help text in parse_args.hpp

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• fix: Add missing options_group to argument parser

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• feat: Add improved argument parser formatting

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• fix: remove invalid usageindent parameter from parse_args.hpp

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• feat: Add version and help flags to system options group

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• feat: Remove unnecessary indentation from wfmash help output

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

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• fix: remove duplicate "Options:" header

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• feat: Improve help text conciseness

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• fix: remove extra "wfmash" line from help output

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• feat: Add lower triangular option to mapping parameters

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• feat: compress query prefix option text

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• fix: Update default group prefix and help text

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• feat: add default group prefix character to help text

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• feat: use shorter param name for WFA scoring

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• feat: update hypergeometric filter help text

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• feat: Update hypergeometric filter parameter names in help text

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

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

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• feat: Add -W short option for --write-index

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• feat: Improve help text formatting for sequence files

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• clarify fasta input usage

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Commits on Nov 4, 2024

• feat: Replace --index with --read-index for symmetry with --write-index

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• feat: add input-mapping option to alignment section

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• feat: Add validation for segment length, block length, and max mapping length parameters

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Commits on Nov 5, 2024

• test: add input mapping functionality test

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

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• fix: Enforce required target.fa argument in wfmash

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• feat: update mashmap version to 3.5.0

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• build: update mapping test command

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• feat: add compact parameter display format

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• more options cleanup

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• fix: replace all '[mashmap]' with '[wfmash]'

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• refactor: Separate mapping and alignment checks in test workflow

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• fix: Move version flag handling before argument validation

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• feat: Add WFMASH_GIT_VERSION to SAM header

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

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• feat: Add wflign directory to git version generation script

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• fix: add command line tag to SAM header version

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• fix: Update SAM header version string

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• fix: replace WFMASH_GIT_VERSION with WFLIGN_GIT_VERSION in wflign_patch.cpp

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• feat: Update SAM header version in computeAlignments.hpp

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

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

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• refactor: replace 'mashmap::skch' with 'wfmash::mashmap'

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

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• fix: replace instances of mashmap::mapQuery with wfmash::mashmap

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• fix: replace 'wfmash::map' with 'wfmash::mashmap'

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

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

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• fix: replace remaining 'mashmap::skch' with 'wfmash::mashmap'

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• fix: update SEARCH/REPLACE block to match existing lines in src/map/include/winSketch.hpp

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• chore: remove initialization messages

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• feat: combine sequence and hash/window stats, simplify index computation timing

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• feat: Update README to reflect current MashMap 3.5 and WFA usage

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• feat: Update README with concise and clear description

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• feat: Add explanation for mapping length limits in README

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

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• fix: add debug output to track sequence size metrics

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• build: Fix compilation error in parse_args.hpp

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• fix: Update reference size calculation in parse_args.hpp

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• chore: comment out debugging output in parse_args.hpp

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• feat: Add target sequence information to log output

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• fix: Move logging information before mapping indexing

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• feat: Add logging of target sequence information before indexing

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• unaider

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• feat: Compute and display query and target lengths separately

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• fix: initialize sequence names before calculating lengths

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• feat: Move sequence length reporting to after sequence manager initialization

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• build: Initialize sequence names and calculate lengths in constructor

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• build: Improve output conciseness and remove duplicate line

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• fix: Replace "seqs" with "queries" in output messages

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• chore: remove detailed statistics line

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• fix: Set default group prefix delimiter to '#'

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• fix: Remove warning about single file all-vs-all mapping

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• fix: Set default group prefix delimiter to '#' and enable prefix skipping

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• feat: add group information to query and target count output

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• refactor: split long log message into multiple lines

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Commits on Nov 6, 2024

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

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Commits on Nov 7, 2024

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

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• feat: Add parallel index building to improve performance

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