Index perf - #2
Merged
Merged
Conversation
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Outdated suggestions cannot be applied.This suggestion has been applied or marked resolved.Suggestions cannot be applied from pending reviews.Suggestions cannot be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.
Speeds up mafutils index ~2× end-to-end by replacing the per-line TextIOWrapper.tell() call with binary-mode reading plus a simple byte counter for none/gz input. Profiling on a 1.5GB real MAF showed tell() was ~60% of runtime, it must snapshot the incremental UTF-8 decoder state to build a seekable cookie, costing ~4.6× more than the readline() beside it. Scan-only throughput improves 8.6× (11.89s → 1.38s); end-to-end index goes 23.82s → 11.63s. Output is byte-identical, verified across all three compression types on both fixtures and 1.5GB of real production data. bgzip deliberately stays on the tell() path, since its virtual offsets aren't additive. Also drops a redundant join→split round-trip and per-line strip() on sequence lines.
Adds a --version flag to the CLI, accepting --version, -version, -v, and -V. Reads from installed package metadata via importlib.metadata and exposes version on the mafutils package.
New tests (tests/test_cli.py): all four version spellings, plus regressions guarding that -version isn't mis-parsed as grouped short flags and that the new top-level callback doesn't break subcommand dispatch. Full suite: 72 passing.