Add alignment position info and read length to RAD format#9

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ygao61 wants to merge 27 commits intodevfrom

Commits on Dec 10, 2025

Add alignment-level position info to RAD output and record read length at file level
ygao61
committed

Commits on Dec 11, 2025

add changes to make recording positions optional; not yet tested
rob-p
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optional positional info
rob-p
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Commits on Dec 18, 2025

specific atacseq bug on program terminate
rob-p
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Commits on Dec 19, 2025

update to fixed libradicl
Rob Patro
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don't fill strings with bed info when we aren't writing bed output
Rob Patro
committed

Commits on Jan 9, 2026

switch from zlib-cloudflare to zlib-ng
Rob Patro
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Commits on Jan 29, 2026

Initial plan
Copilot
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Add memory pre-allocation optimizations to mapping_cache_info

Copilot
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rob-p
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Improve code maintainability by using member variables for reserve sizes

Copilot
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rob-p
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FQFeeder updates
Rob Patro
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Commits on Jan 30, 2026

Merge branch 'dev-pos' into copilot/optimize-memory-allocation
Rob Patro
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Phase 1: Replace phmap::flat_hash_map with ankerl::unordered_dense::map in mapping hot path

Copilot
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rob-p
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Add comprehensive summary of hash map replacement exploration and implementation

Copilot
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rob-p
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Add detailed code changes visualization and finalize documentation

Copilot
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rob-p
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Merge pull request #10 from COMBINE-lab/copilot/optimize-memory-allocation
rob-p
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notes
Rob Patro
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update unordered dense
Rob Patro
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tweak params
Rob Patro
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fix missing variable in condition
Rob Patro
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set chunk size in single-read case as well
Rob Patro
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Commits on Jan 31, 2026

use system dependent lib path
Rob Patro
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Commits on Feb 14, 2026

fix subtle shifting bug in _has_homopolymer_prefix()
rob-p
committed

Commits on May 4, 2026

update sshash submodule from v4.0.0 to v5.1.1

rob-p
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claude
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fix set_remaining_contig_bases() undercount and add streaming lookup benchmark

rob-p
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claude
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Commits on May 5, 2026

Add lean_read_iterator with independent rolling k-mer state

rob-p
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claude
committed

Commits on May 6, 2026

Optimize hit processing and fix canonical lean iterator

rob-p
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claude
committed