{"categories":[{"label":"Scientific/Engineering","url":"https://skillfed.io/packages/category/scientific-engineering/8"}],"enrichment":{"capability":"NCLS provides a fast interval overlap query data structure implemented in C, designed to find which intervals overlap with a given range much faster than traditional interval trees.","skillfed_tags":["genomics","interval-queries","performance-critical"],"use_cases":["Finding all genomic features that overlap a given region in a genome annotation database.","Batch-querying multiple query intervals against a large reference set of intervals to identify all pairwise overlaps.","Building interval indices for read alignment or variant annotation pipelines where speed is critical.","Detecting overlaps in time-series or coordinate-based data where traditional tree structures are too slow.","Memory-constrained environments where interval tree memory overhead is prohibitive."],"what_it_does":"NCLS is a Nested Containment List data structure for interval overlap queries, originally from the defunct PyGr library and revived as a standalone tool. It builds on the algorithm described in the original paper and is optimized for speed and memory efficiency compared to traditional interval trees. The package wraps a C implementation with Python bindings and depends only on numpy.\n\nYou use NCLS by constructing an index from arrays of interval start and end positions, then query it to find overlaps with new intervals. It supports both single-query (slower, Python-based) and batch-query (faster, C-based) modes. The package is designed for genomic and bioinformatics workflows but works for any interval overlap problem.","worth_installing":"Yes, if you need fast interval overlap queries and are comfortable with a compiled dependency. The package is stable, has no known vulnerabilities, and offers significant speed and memory advantages. However, note the deprecation notice recommending an alternative for new projects and the aging maintenance status\u2014evaluate whether that better suits your long-term needs."},"id":"ncls","links":{"html":"https://skillfed.io/packages/ncls","md":"https://skillfed.io/packages/ncls.md","pypi":"https://pypi.org/project/ncls/"},"maintenance":{"status":"aging"},"meta":{"latest_release":"2025-07-04","license_spdx":null,"license_treatment":"permissive","name":"ncls","python_support":"unspecified","summary":"A fast interval tree-like implementation in C, wrapped for the Python ecosystem."},"popularity":{"monthly_downloads":104335,"position":12753,"tier":"top_15000"},"security":{"n_vulnerabilities":0},"version":"0.0.70"}