v0.2.0

This major release introduces several updates to nailpolish, including workflow improvements, dependency management, feature additions, and updates to the documentation and CLI.

Warning: files will need to be reindexed and the consensus called output format has been modified

Index

• Use a new index format which is faster and more memory efficient + stores a hashmap in zero-copy form leading to faster load times at the slight cost of higher disk storage use
• Indexing now no longer requires the user to specify the location of the index file; this is generated automatically from the file path

Extract

• Replaced the Group command with a new Extract command in the CLI, allowing users to filter reads by group IDs, regex patterns, or group size.
• Added support for specifying output formats (fastq, fasta) in the Extract command, particularly useful for manual verification

Summary

• Updated the summary file to report a table of all groups and summary statistics (mean length and quality)
• Change the graph format to be clearer and more readable

Consensus

• Implemented clustering to detect false duplicates
• Allow for stdout or file output
• Provide flags for extra header information (--extra-stats, --report-original-headers)

Dependency management:

• Moved spoa dependency to submodule deps/spoa-rs for local dependency management
• Supports SIMD compilation in SPOA with SISD fallback
• Add nonative feature for x86_64 compilation on ARM (SISD)

Bugfixes

Fixes #2, #6