Add bespoke classes for accessing SEQ and QUAL #1347
Draft
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Outdated suggestions cannot be applied.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.
Inspired by the request in #1346, “Faster Single-Base Access for Long Reads”:—
Instead of accessing
SEQ
(and eventuallyQUAL
) via astr
property, add classes that implement__getitem__
,__str__
, etc directly from the internal BAM representation. These classes can then be used to access subsequences and do other useful things that you would do with astr
:without decoding the unrequested parts of the sequence data.
This demonstrates the idea. We will likely rename this and position it to become the principal way to access SEQ, deprecating
query_sequence
, and similarly for base qualities.