GitLab

Initialize the bins differently for different binning methods.

lightweight flag when creating objects for binning.

binning work again.

_remap() is a method, not a subroutine.

For now, throw in _remap() if it is expected to actually do something.

RepeatFeature as the test case for now.  Won't do anything useful just
yet.

featurecollection-dev'.

Sprout from master 2008-02-07 11:53:09 UTC Andreas Kusalananda Kähäri <ak4@sanger.ac.uk> 'Fixup POD for method translation().'
Delete:
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    modules/t/test-genome-DBs/homo_sapiens/core/oligo_probe.sql
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    modules/t/test-genome-DBs/homo_sapiens/core/peptide_archive.sql
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    modules/t/test-genome-DBs/homo_sapiens/core/prediction_exon.sql
    modules/t/test-genome-DBs/homo_sapiens/core/prediction_exon.txt
    modules/t/test-genome-DBs/homo_sapiens/core/prediction_transcript.sql
    modules/t/test-genome-DBs/homo_sapiens/core/prediction_transcript.txt
    modules/t/test-genome-DBs/homo_sapiens/core/protein_align_feature.sql
    modules/t/test-genome-DBs/homo_sapiens/core/protein_align_feature.txt
    modules/t/test-genome-DBs/homo_sapiens/core/protein_feature.sql
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    modules/t/test-genome-DBs/homo_sapiens/core/qtl.sql
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    modules/t/test-genome-DBs/homo_sapiens/core/xref.sql
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fetchrow_arrayref().

decrease the amount of code (slightly) in most of the feature-specific
sub-classes.

slowest method, about 100 times slower than the most basic 'count'
binning method, but it now only uses 0.5 seconds to bin 2360 repeat
features into 100 bins instead of 6-9 seconds...

inefficiently implemented.

  Returns an array of bins, each bin containing the fraction of the bin
  that is coverage by any feature.

The current implementation is correct but inefficient.

  Returns an array of bins, each bin containing the sum of the fractions
  of features overlapping that bin.  A feature fully inside a bin will
  contribute 1 to the sum while a feature spanning exactly three bins
  (from the very start of the first to the very end of the third) will
  contribute 1/3 to the sum of each bin.

object creation time:

  Rename method lightweight() as is_lightweight().

  Remove -light argument from method populate().

Add example to SYNOPSIS of how to restrict by analysis.logic_name.

Further small modifications of POD.

analysis.logic_name by using -analysis in the constructor, e.g.
"-analysis => 'Dust'" (for a feature collection of repeat features).

Each Collection sub-class needs to specialize the _has_analysis() method
so that it returns true if there is an analysis_id in the main feature
table for that feature type.

implem'ted.

Do some argument checking in get_bins().

Move some code around.

  Flushes (deletes) all cached data not associated with the current
  slice.

Also store the projection segments and the mapping from seq_region_ids
to the projection segments in the class.

lines shorter.

Add documentation on binning methods.

Still need to implement the 'coverage' binning method.

the private methods, yet.

new(), lightweight().