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Peak calling fixing the merging bug #50

Merged
merged 10 commits into from
Jan 12, 2019
Merged

Peak calling fixing the merging bug #50

merged 10 commits into from
Jan 12, 2019
+126 −32

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anastasiia
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fixing the bug with merging of footprints, the code will soon be edited to look nice

@anastasiia anastasiia closed this Jan 9, 2019
@renewiegandt renewiegandt reopened this Jan 9, 2019
@renewiegandt
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Thank you! The script is working. Please clean it up a little bit. Then it's ready to be merged.

@renewiegandt
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I noticed that your max pos column shows weird values:

#chr	start	end	name	score	strand	len	max_pos	bonus_info	contains_maxpos	sequence
chr1	3062850	3062913	f_265557.0	0.646041	.	63	-3062842	mDuxNeg_1,mDuxPos_1;NA;NA;NA;NA;NA;NA;NA;NA;NA	0	TCTTGGTGCCTGTTGCCAGCCTGTAGGTGATTTGCTGGATACTGTCTCCTGAATATCTCAAGG
chr1	3062931	3062945	f_265557.1	0.646041	.	14	-3062923	mDuxNeg_1,mDuxPos_1;NA;NA;NA;NA;NA;NA;NA;NA;NA	0	GTGTCTTGGAGAAC
chr1	3063012	3063058	f_265559.0	0.643709	.	46	-3062988	mDuxNeg_1,mDuxPos_1;NA;NA;NA;NA;NA;NA;NA;NA;NA	0	AGTGGCACCAAGGACTAAGCCAGCCTACTCAAGGCTGGGGGAGGCT
chr1	3063102	3063122	f_265559.1	0.643709	.	20	-3063078	mDuxNeg_1,mDuxPos_1;NA;NA;NA;NA;NA;NA;NA;NA;NA	0	CTTATTTCACATACTGAATA

@anastasiia
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the shown output is not from my script, as I don't write the column with the sequence

@renewiegandt
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Yeah i noticed it. Sorry, it was late at night :D

renewiegandt
renewiegandt requested changes Jan 10, 2019
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My suggestion is to merge it to dev even if it may contain a bug. We need to get everything together to do a proper check.
But please remove the comments that contain code.

@anastasiia
adding a validation while printing to the output file. If there are p…
2fe66fd 
…roblems with start/end positions or max_pos, the footprint will not be written to the output file
@anastasiia
deleting the print statements, adding some comments
1523096
@renewiegandt
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I would rename the parameter max_bp_between to max_gapor max_bp_gap

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ok, I have changed the name of parameter from max_bp_between to min_gap

@anastasiia anastasiia merged commit c398ce3 into dev Jan 12, 2019
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@renewiegandt renewiegandt renewiegandt approved these changes

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@anastasiia @renewiegandt