docs: refresh README for bounded whole-genome variants --index - #20
Merged
Conversation
Foregrounds the now-real flagship capability (Phase B4): bounded whole-genome germline calling from a portable index + a coordinate-sorted BAM, with a verifiable memory receipt. Adds an accessible plain-language lead (what it is, why it matters, who it's for), the index->sort->variants --index flagship workflow, an accurate single-contig vs whole-genome scope section, and an updated roadmap (Phase A+B done; C = budget enforcement / plan / verify; aligner-over-index + sublinear-space construction later). Corrects the stale 'wiring variants is a later phase' text. Co-Authored-By: Claude Opus 4.7 (1M context) <noreply@anthropic.com>
This file contains hidden or bidirectional Unicode text that may be interpreted or compiled differently than what appears below. To review, open the file in an editor that reveals hidden Unicode characters.
Learn more about bidirectional Unicode characters
Sign up for free
to join this conversation on GitHub.
Already have an account?
Sign in to comment
1 participant
Add this suggestion to a batch that can be applied as a single commit.This suggestion is invalid because no changes were made to the code.Suggestions cannot be applied while the pull request is closed.Suggestions cannot be applied while viewing a subset of changes.Only one suggestion per line can be applied in a batch.Add this suggestion to a batch that can be applied as a single commit.Applying suggestions on deleted lines is not supported.You must change the existing code in this line in order to create a valid suggestion.Outdated suggestions cannot be applied.This suggestion has been applied or marked resolved.Suggestions cannot be applied from pending reviews.Suggestions cannot be applied on multi-line comments.Suggestions cannot be applied while the pull request is queued to merge.Suggestion cannot be applied right now. Please check back later.
Summary
Refreshes the README to clearly and accurately reflect the current system after Phase B4 (PR #19), and to make the high-level story accessible to builders.
index → sort → variants --indexworkflow up top.align/variantsis a later phase" —variants --indexhas landed. Adds an honest single-contig (aligner /--reference) vs. whole-genome (variants --index,index/locate) scope section.rosalind plan/verify; aligner-over-the-index and sublinear-space construction later. Notes--memory-budget-mbis record-only today (does not yet enforce).variants_indextest target to the test list and a note on thecall_germline_whole_genomelibrary entry point.Docs-only; all claims verified against the live CLI (
--help), the manifest naming (<output>.manifest.json), and the present test targets / example data.🤖 Generated with Claude Code