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Bug fix: fix bed start and end in bigwig_outlier_bed #6312

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merged 23 commits into from
Sep 15, 2024

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fubar2
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@fubar2 fubar2 commented Sep 9, 2024

  • This PR does something else (explain below)
    Fix bed coordinates and reran tests with new synthetic test bigwig

The test bed outputs now show correct start and half-open end positions for minwin of 10

New test data - a small bed converted to bigwig

chr1 	0 	10 	100 	100 	+ 						
chr1 	20 	30 	100 	100 	+ 						
chr1 	40 	50 	100 	100 	+ 						
chr1 	60 	70 	100 	100 	+ 						
chr1 	200 	300 	100 	100 	+ 						
chr1 	300 	400 	0 	0 	+ 						
chr1 	400 	1000 	100 	100 	+ 
test-data/bedouthi_qlo_notset_sample
::::::::::::::
chr1    0       10      fake.bigwig_1   1
chr1    20      30      fake.bigwig_1   1
chr1    40      50      fake.bigwig_1   1
chr1    60      70      fake.bigwig_1   1
chr1    200     1000    fake.bigwig_1   1

@fubar2 fubar2 changed the title fix bed segment end for bigwig_outlier_bed Bug fix: pad bed segment end by 1nt for bigwig_outlier_bed Sep 9, 2024
@fubar2 fubar2 closed this Sep 9, 2024
@fubar2 fubar2 reopened this Sep 9, 2024
chr1 	0 	10 	100 	100 	+
chr1 	20 	30 	100 	100 	+
chr1 	40 	50 	100 	100 	+
chr1 	60 	70 	100 	100 	+
chr1 	200 	300 	100 	100 	+
chr1 	300 	400 	0 	0 	+
chr1 	400 	1000 	100 	100 	+
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fubar2 commented Sep 10, 2024

@bernt-matthias: thanks for the suggestions.
A new test bigwig helps a lot I think.

Makes the tests outputs more informative...

The new fake.bigwig was made with this bed:

chr1 	0 	10 	100 	100 	+ 						
chr1 	20 	30 	100 	100 	+ 						
chr1 	40 	50 	100 	100 	+ 						
chr1 	60 	70 	100 	100 	+ 						
chr1 	200 	300 	100 	100 	+ 						
chr1 	300 	400 	0 	0 	+ 						
chr1 	400 	1000 	100 	100 	+ 

The score doesn't affect anything in the conversion so the last 700nt are all considered a single segment.
and the first few are correct too. So I'm pretty sure it's working without any padding now.

test-data/bedouthi_qlo_notset_sample
::::::::::::::
chr1    0       10      fake.bigwig_1   1
chr1    20      30      fake.bigwig_1   1
chr1    40      50      fake.bigwig_1   1
chr1    60      70      fake.bigwig_1   1
chr1    200     1000    fake.bigwig_1   1

@fubar2 fubar2 changed the title Bug fix: pad bed segment end by 1nt for bigwig_outlier_bed Bug fix: fix bed start and end in bigwig_outlier_bed Sep 10, 2024
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fubar2 commented Sep 10, 2024

ok, restored some of the old histograms and long beds @bernt-matthias.
Is this better?
Now I see that the Merlin bigwig I use for testing JBrowse2 is peculiar....

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fubar2 commented Sep 15, 2024

@bernt-matthias: is this ok now?

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Thanks @fubar2!

Will wait for @bernt-matthias as well before merging.

@bernt-matthias bernt-matthias merged commit 06c54e8 into galaxyproject:main Sep 15, 2024
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Thanks a lot.

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fubar2 commented Sep 16, 2024

@bernt-matthias - thank you! Thoughtful and constructive suggestions much appreciated...

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3 participants