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Develop #122

Merged
merged 34 commits into from
Dec 16, 2024
Merged

Develop #122

merged 34 commits into from
Dec 16, 2024

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jamesli124
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More fixes, mostly dealing with cleavage-profile

jamesli124 and others added 30 commits December 10, 2024 19:35
@jamesli124
update quickstart
e80fe00
@jamesli124
add wiki link to index
1063c74
@jamesli124
update docs
fcd8da2
@jamesli124
add wiki to pyproject
249b2c5
@jamesli124
rename fraction_low and fraction_high to min_length and max_length fo…
fa54cdf 
…r wps
@jamesli124
renamed size arguments for cleavage_profile
eb666e7
@jamesli124
update arg names
38db4d6
@jamesli124
fix aliases for min and max
2b8dd4b
@jamesli124
make parallelized implementation of cleavage profile available in API
d84c16d
@jamesli124
only take frag files instead of BED6 format fragmentation files
bc434da
@jamesli124
frag_generator handles files of the wrong format
9efa1d3
@jamesli124
frag_generator checks format of tabix-indexed files, and issues a war…
d718ac4 
…ning if the file does not conform to the fragment file specification
@jamesli124
made chrom-sizes optional for cleavage-profile and added it as option…
5175318 
… for wps
@jamesli124
rename genome_file to chrom_sizes
f2d2fe0
@jamesli124
rename autosomes to chrom-sizes for delfi
48b7c69
@jamesli124
deprecated cli_delfi_gc_correct
94dd682
@jamesli124
update help for cleavage-profile
68d8ece
@jamesli124
missing import
d5dc0b8
@jamesli124
skip a test in github
fa5a1ff
@jamesli124
fix some options when normalizing
688a09b
@jamesli124
fixed issue where first fragment is not read in a tabix file
e5897a6
@jamesli124
fixed issue with multiple fetch statements in frag_generator.
c82b8a6 
    - fixed one incorrect test in test_frag_io
@jamesli124
update changelog
ce03523
@jamesli124
fixed issues with cleavage-profile
7c1760b 
    - also fixed some docstrings
    - updated changelog
@jamesli124
cleavage profile and wps have no return in the API. This is because t…
2f2deda 
…he previous implementation was incorrect and used too much memory. Future versions might return a file handle or path
@jamesli124
cleavage_profile and wps return output file
5a2e422
@jamesli124
fix writing to bw
c62d1b5
@jamesli124
update docs
af82c4b
@jamesli124
update descriptions
e4ef1d1
@jamesli124
regenerate docs
8ec7715
@jamesli124 jamesli124 linked an issue Dec 13, 2024 that may be closed by this pull request
Getting a ValueError, start is greater than end in cleavage-profile. #115
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ravibandaru-lab
ravibandaru-lab approved these changes Dec 16, 2024
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👍

@ravibandaru-lab ravibandaru-lab merged commit 701c142 into main Dec 16, 2024
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@ravibandaru-lab ravibandaru-lab ravibandaru-lab approved these changes

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Getting a ValueError, start is greater than end in cleavage-profile.
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@jamesli124 @ravibandaru-lab