CSIv2

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#148 opened on Nov 13, 2014 5 comments 0 reactions 0 assignees View on GitHub

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Assessment

Difficulty: 5/5
Estimated time: Over a week
Newbie friendliness: 25/100

Issue type: Feature
Clarity: Needs clarification
Activity status: Stale
Tech stack: c
Domain: bioinformatics

Research direction

Start by reviewing the linked CSIv2 implementation branch and hts-specs change, then inspect the existing indexing and query APIs and the tabix entry point. Clarify whether to support record-range queries, chunk generation, or both, including their proposed syntax. Done means an agreed API and command-line behavior with tests covering the selected use cases.

Written by the indexing model from the issue text.

Description

I created a new branch (https://github.com/samtools/htslib/commit/9b117953a312e7abca55a9820f8c0bc656522e9d) which supports reading and writing of the CSIv2 index (https://github.com/samtools/hts-specs/commit/b131ffc8b905e4e1c147134dc04912e0e72af4d2). There is currently no API to use it. The motivation for the extension was to allow queries like:

get N-th to M-th record
create a list of regions with N records each (possibly with optional overlaps). This is useful in pipelines which split BCF/BAM in smaller chunks and process them in parallel

Shane suggested that the first type could be easily integrated with existing tools by using "::" instead of ":". Then chr::N-M would be interpreted as record indexes, while chr:from-to as genomic coordinates.

For the second, I was thinking of adding a new switch to tabix, one could do something like:
tabix --new-switch CHUNK_SIZE[,OVERLAP_SIZE] file.bcf [REGION]

What do you think? Comments and feedback is welcome.

Dominant language: C
Stars: 950
Forks: 475
Avg merge: 3d 13h
Merged PRs (30d): 11

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