Add AlignedSegment.query_qualities_str and fix sequence and qualities caching #1341
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
These deprecated properties forward to corresponding query_alignment_XYZ properties which are all read-only as they are derived from query_XYZ.
Rewrite query_qualities directly, and have query_alignment_qualities trim that's final value rather than computing its own similarly. Clear caches in __set__ et al and populate them only in __get__ routines. Previously the input value was cached rather than the canonical one reconverted from the raw data, and setting to None did not clear the previously cached value.
The existing query_qualities property provides QUAL as a Python array (and in fact has long allowed it to be set from most iterables other than strings and tuples). This new query_qualities_str property enables QUAL to be accessed as the usual ASCII-encoded base quality string (and now query_qualities also allows it to be set from such a string). Also add (read-only) query_alignment_qualities_str paralleling query_alignment_qualities similarly.
Updating query_sequence did not invalidate cache_query_alignment_sequence previously. Clear caches in __set__ et al and populate them only in __get__ routines.
jmarshall
force-pushed
the
query_qualities_str
branch
from
173a128 to
1082aa2
Compare
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Outdated suggestions cannot be applied.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.
On PR #1324 @nh13 requested being able to set
AlignedSegment.query_qualitiesvia a SAM/FASTQ-style base quality string. This expands that to be able to retrieve QUAL as a string too.Add a
query_qualities_strproperty implemented directly against the underlyingbam1_tdata structure rather than translating to an array first viaqualitystring_to_array()/array_to_qualitystring(). Recodequery_qualitiesto work more obviously directly against thebam1_ttoo, and fix several bugs in its caching layer. (See #121 for why this caching is important.) Enable settingquery_qualitiesto use a string too, by delegating to the new property.Fix some similar caching bugs in
query_sequencetoo.