Support for reading alignments in specific region without CRAI index file #311
Conversation
This file contains 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
Codecov ReportAttention: Patch coverage is
Additional details and impacted files@@ Coverage Diff @@
## master #311 +/- ##
=======================================
Coverage 88.49% 88.50%
=======================================
Files 95 95
Lines 8173 8214 +41
Branches 506 506
=======================================
+ Hits 7233 7270 +37
- Misses 434 438 +4
Partials 506 506 ☔ View full report in Codecov by Sentry. |
alumi
reviewed
May 15, 2024
| (is (not (cram/indexed? cram-rdr'))) | ||
| (are [?region ?count] (= ?count | ||
| (count (cram/read-alignments cram-rdr ?region)) | ||
| (count (cram/read-alignments cram-rdr' ?region))) |
There was a problem hiding this comment.
This test fails in my environment.
Maybe we need to reset the position of the mapped buffer before calling next read-alignments
There was a problem hiding this comment.
Thank you for pointing that out! Yeah, I'm just looking into it right now. I wasn't aware that I didn't run these tests on my local environment at all 😂
alumi
approved these changes
May 15, 2024
Sign up for free
to join this conversation on GitHub.
Already have an account?
Sign in to comment
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Outdated suggestions cannot be applied.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.
This PR allows the CRAM reader to read alignments from a specified region within a CRAM file without requiring an index file.
CRAM readers can instantly check if each container or slice overlaps with the specified region by examining their headers. This makes it much more efficient to read alignments by skipping non-overlapping containers or slices, rather than performing a linear scan of the entire CRAM file.
This PR also adds a new test file
medium_without_index.cram, which is identical tomedium.cramexcept that it does not come with its corresponding index file.