Ecosyste.ms: Issues

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GitHub / 4dn-dcic/hic2cool issues and pull requests

#71 - Bump setuptools from 68.2.2 to 70.0.0

Pull Request - State: open - Opened by dependabot[bot] 4 months ago
Labels: dependencies

#70 - Bump zipp from 3.17.0 to 3.19.1

Pull Request - State: open - Opened by dependabot[bot] 4 months ago
Labels: dependencies

#69 - Add support for HIC v9 files, weight column and bump version

Pull Request - State: open - Opened by VonAlphaBisZulu 6 months ago - 2 comments

#67 - Restore command line usage and update documentation, bump version

Pull Request - State: closed - Opened by clarabakker about 1 year ago

#66 - Convert to poetry, update versions of all libraries

Pull Request - State: closed - Opened by clarabakker about 1 year ago

#64 - Allow hic2cool_updates.py to write output files

Pull Request - State: closed - Opened by Kelly-ST-HRI over 1 year ago - 11 comments

#63 - No weight column in the converted .mcool file

Issue - State: open - Opened by nikhilp11 over 1 year ago - 1 comment

#62 - HOW to get cool files only with KR normalization

Issue - State: open - Opened by jiangshan529 over 1 year ago

#61 - error: object header message is too large

Issue - State: open - Opened by gabrielluishernandez about 2 years ago - 1 comment

#60 - New .hic format

Issue - State: open - Opened by sa501428 over 2 years ago - 1 comment

#59 - hic2cooler not working with hic v9 formatting from Juicer v2

Issue - State: open - Opened by tonyjhlam over 2 years ago - 1 comment

#58 - h5py 3 requires mode argument

Issue - State: open - Opened by rekado over 2 years ago

#57 - ValueError when converting hic file to cool file

Issue - State: open - Opened by jinkang1234 almost 3 years ago - 1 comment

#56 - Encoding problem while converting a Juicer matrix?

Issue - State: open - Opened by chorzow almost 3 years ago - 6 comments

#55 - Multiprocessing Error

Issue - State: open - Opened by aakashsur almost 3 years ago - 1 comment

#54 - hic2cool command not found on zsh

Issue - State: closed - Opened by rahmas36 over 3 years ago - 3 comments

#53 - Minor typo maybe?

Pull Request - State: open - Opened by pkerpedjiev about 4 years ago

#51 - hic2cool conda version

Issue - State: closed - Opened by joachimwolff over 4 years ago - 6 comments

#50 - partial fix for zlib decompression issue

Pull Request - State: closed - Opened by SooLee over 4 years ago

#49 - zlib.error when converting hic to cool

Issue - State: open - Opened by dejunlin over 4 years ago - 3 comments

#48 - Dep

Pull Request - State: closed - Opened by SooLee over 4 years ago - 1 comment

#47 - Versions

Pull Request - State: closed - Opened by SooLee over 4 years ago

#46 - Update requirements to allow newer versions

Issue - State: closed - Opened by paulmenzel over 4 years ago - 5 comments

#45 - Error -3 while decompressing data

Issue - State: closed - Opened by chenggang108 over 4 years ago - 7 comments

#44 - Drop setup_requires

Pull Request - State: open - Opened by marcelm over 4 years ago - 8 comments

#43 - Dev2

Pull Request - State: closed - Opened by SooLee over 4 years ago - 1 comment

#42 - faster conversion?

Issue - State: closed - Opened by fanc-WU almost 5 years ago - 3 comments

#41 - Hic2cool convert error

Issue - State: open - Opened by Captaincapture almost 5 years ago - 2 comments

#40 - juicer hic (fragment level matrix) convert into cooler

Issue - State: closed - Opened by Linhua-Sun almost 5 years ago - 2 comments

#39 - Error in converting .hic to .cool

Issue - State: closed - Opened by rahmas36 about 5 years ago - 1 comment

#38 - hic2cool convert error with Juicer hic file

Issue - State: closed - Opened by wyim-pgl about 5 years ago - 3 comments

#37 - ability to convert selected chromosomes

Issue - State: open - Opened by rikrdo89 about 5 years ago - 1 comment

#36 - Pin pandas version for py2 and add some readme stuff

Pull Request - State: closed - Opened by carlvitzthum over 5 years ago

#35 - Installation problem

Issue - State: closed - Opened by francicco over 5 years ago - 5 comments

#34 - Preserve chromosome names from hic

Issue - State: closed - Opened by carlvitzthum over 5 years ago - 2 comments

#33 - 0.7.2

Pull Request - State: closed - Opened by carlvitzthum over 5 years ago

#32 - wrong chromosome names appear in warning messages

Issue - State: closed - Opened by balwierz over 5 years ago - 1 comment

#31 - 0.7.1

Pull Request - State: closed - Opened by carlvitzthum over 5 years ago

#30 - 0.6.1 fix for hic2cool update

Pull Request - State: closed - Opened by carlvitzthum over 5 years ago

#29 - hic2cool update

Issue - State: closed - Opened by imerelli over 5 years ago - 4 comments

#28 - Schema version

Pull Request - State: closed - Opened by carlvitzthum over 5 years ago

#27 - cool required attributes not found in hic files converted to cool files

Issue - State: closed - Opened by koustav-pal over 5 years ago - 11 comments

#26 - Balancing weight inversion, or not

Issue - State: closed - Opened by Phlya over 5 years ago - 1 comment

#25 - 0.5.1

Pull Request - State: closed - Opened by carlvitzthum over 5 years ago

#24 - pip version broken

Issue - State: closed - Opened by joachimwolff almost 6 years ago - 7 comments

#23 - 0.5.0

Pull Request - State: closed - Opened by carlvitzthum almost 6 years ago

#22 - how to output normalization counts?

Issue - State: closed - Opened by zhixuqiu almost 6 years ago - 5 comments

#21 - Pip install error with os/lzma_stub.h

Issue - State: closed - Opened by pkerpedjiev about 6 years ago - 1 comment

#20 - Type of start/end columns in cooler bins is int32

Issue - State: closed - Opened by sergpolly over 6 years ago - 4 comments

#19 - Fix allowing for missing normalizations in hic files

Pull Request - State: closed - Opened by carlvitzthum over 6 years ago

#18 - Slight travis tweak

Pull Request - State: closed - Opened by carlvitzthum about 7 years ago

#17 - 0.4.1

Pull Request - State: closed - Opened by carlvitzthum about 7 years ago

#16 - 0.4.0

Pull Request - State: closed - Opened by carlvitzthum about 7 years ago

#15 - key error

Issue - State: closed - Opened by lidaof about 7 years ago - 1 comment

#14 - IndexError: list index out of range

Issue - State: closed - Opened by lidaof about 7 years ago - 7 comments

#13 - unicode error

Issue - State: closed - Opened by lidaof about 7 years ago - 3 comments

#12 - Meta updates for 0.3.7

Pull Request - State: closed - Opened by carlvitzthum about 7 years ago

#11 - Record the final bin1_offset

Pull Request - State: closed - Opened by nvictus about 7 years ago

#10 - 0.3.6 setup

Pull Request - State: closed - Opened by carlvitzthum about 7 years ago

#9 - FF-843

Pull Request - State: closed - Opened by carlvitzthum over 7 years ago

#8 - Error converting hic file

Issue - State: closed - Opened by pkerpedjiev over 7 years ago - 1 comment

#7 - Installing hic2cool doesn't install executable

Issue - State: closed - Opened by pkerpedjiev over 7 years ago - 1 comment

#6 - Make formatting more pep8 compliant

Pull Request - State: closed - Opened by nvictus over 7 years ago

#5 - memory issue

Issue - State: open - Opened by SooLee over 7 years ago - 5 comments

#4 - fixed hic2coo_utils.py countsnot->counts

Pull Request - State: closed - Opened by SooLee over 7 years ago

#3 - Both FF-735 and FF-715

Pull Request - State: closed - Opened by carlvitzthum over 7 years ago

#2 - Adds 'chr' to chromosome names already containing 'chr'

Issue - State: closed - Opened by golobor almost 8 years ago - 2 comments

#1 - Add signature string to `info` attributes

Issue - State: closed - Opened by nvictus almost 8 years ago - 2 comments