Merging changes on develop #1874
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[NEW] implemented using slots, so it takes less memory
than the dict it replaces. It supports dictionary
style indexing, so old code will work. It also
aliases certain old keys.
[CHANGED] updated return type hints to reflect the new class
[CHANGED] updated tests to reflect these changes
[CHANGED] this frees parser from having to always start at
the top of a file to figure out the format version.
[CHANGED] previously, this was reversed if a feature was on the minus
strand.
[CHANGED] this was a private method on GffAnnotationDb but has been
made a function to facilitate chunked reading of Gff files.
[CHANGED] iter_line_blocks() now supports num_lines=None, which results
in all lines being returned.
[CHANGED] just calls bound sqlitedb's close method
[CHANGED] incomplete records in a GFF database can be updated
…tations
[CHANGED] we achieve a ~75% reduction in RAM for creating a GffAnnotationDb
for the human genome by combining iter_line_blocks(), which uses
iter_splitlines(), merged_gff_records() and
GffAnnotationDb.update_record_spans(). The
load_annotations(lines_per_block=500_000) argument controls how many lines
are read before the insert is done. We track all record name's that have
been inserted and update their existing spans.
[NEW] builds indexes for standard columns, biotype, seqid, start, etc..
[NEW] thanks to comment in code review by khiron, added
# codacy:ignore[sql-injection] - limited SQL injection exposure
to silence this codacy warning. As this is purely in a test,
it doesn't seem to have much risk.
[CHANGED] seems comment ws incorrect
[CHANGED] this is from the bandit tool, which indicates B608
as the error for hardcoded_sql_expressions
Improve performance of annotation db creation, querying
NEW: abstract base class for views, fixes #1865
[NEW] MolType.is_compatible_alphabet() checks that the characters
in an alphabet match those in one of the members of the
MolType.alphabets. The argument strict=False (the default)
means the exact ordering of elements must match.
[NEW] AlphabetGroup.iter_alphabets() yields individual alphabets
from the group.
Revert "Merge branch 'seq-collections-refactor' into develop"
Pull Request Test Coverage Report for Build 9200124195Details
💛 - Coveralls |
DOC: Add IndelMap param docstring
GavinHuttley
merged commit b832dd4
into
seq-collections-refactor
31 of 33 checks passed
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