Major fix and feature expansion #24
Merged
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
Fetch was not filtering out reads that were *before* the region, just the ones after.
This should be the first steps towards fully supporting BAM output mentioned in #5
There was a deleterious flaw in the random access algorithm that was causing the file cursor to start way to the right of regions if interest.
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Outdated suggestions cannot be applied.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 fixed #3 and #5. CSI support should be relatively seamless. Format is determined based on index file magic. BAM output is implemented, but not fully documented or fully featured.
However, the most important part of this PR is fixing a major random access issue. Previously, queries against the index returned the first chunk offset that ended past the linear offset calculated by
reg_beg >> 14. The issue is, bins are not ordered within the index. Therefore, it could potentially return a starting virtual offset beyond the region of interest.Additionally,
fetchwas failing to return reads that spanned the entire region of interest. This is fixed by this PR.