Ecosyste.ms: Issues

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GitHub / koszullab/hicstuff issues and pull requests

#86 - Segmentation fault core dumped

Issue - State: open - Opened by Axze-rgb 13 days ago

#83 - Small fix stats.py

Pull Request - State: closed - Opened by nmendiboure 5 months ago

#82 - Error : Fetching mapping and pairing stats

Issue - State: closed - Opened by nmendiboure 5 months ago

#81 - Error with rebin function

Issue - State: closed - Opened by aurelepiazza 5 months ago - 1 comment

#80 - 3.2.2

Pull Request - State: closed - Opened by js2264 8 months ago

#79 - rebin does not generate the correct number of bins

Issue - State: open - Opened by js2264 about 1 year ago

#78 - GHA: revamp with micromamba

Pull Request - State: closed - Opened by js2264 about 1 year ago

#77 - 3.2.0 release

Pull Request - State: closed - Opened by js2264 about 1 year ago - 4 comments

#76 - Add `--binning`, `--zoomify` and `--balancing` arguments to pipeline

Pull Request - State: closed - Opened by js2264 about 1 year ago - 3 comments

#75 - issue in bam2pairs

Issue - State: closed - Opened by etiennejourdier over 1 year ago - 6 comments

#74 - installation issue with sklearn dependency

Issue - State: closed - Opened by etiennejourdier over 1 year ago - 2 comments

#73 - multiple bam files

Issue - State: closed - Opened by Jwindler over 1 year ago - 1 comment

#72 - pipeline option to exclude chromosomes

Issue - State: closed - Opened by cmdoret over 1 year ago - 1 comment
Labels: enhancement

#71 - Output binned cool by default

Issue - State: closed - Opened by cmdoret over 1 year ago - 1 comment
Labels: enhancement

#70 - Compatibility with newer versions of python (>= 3.10)

Issue - State: closed - Opened by nmendiboure over 1 year ago - 3 comments

#69 - Typo conda install command

Issue - State: closed - Opened by fstrijth almost 2 years ago - 1 comment

#68 - iterative mode not working on a given dataset whereas normal mode does

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

#67 - log transform in view command causes division by 0

Issue - State: open - Opened by etiennejourdier almost 2 years ago - 5 comments
Labels: enhancement, question

#66 - rebin output format

Issue - State: closed - Opened by etiennejourdier almost 2 years ago - 1 comment

#65 - incompatibility between --trim and --lines in the view command

Issue - State: closed - Opened by etiennejourdier almost 2 years ago - 2 comments
Labels: bug, question

#64 - Is it neccessary to filter hic reads before running hicstuff?

Issue - State: closed - Opened by xiekunwhy over 2 years ago - 1 comment
Labels: question

#63 - hicstuff pipeline Python 3.9 error

Issue - State: closed - Opened by Overcraft90 over 2 years ago - 8 comments
Labels: bug

#62 - Missing File — abs_fragments_contacts_weighted

Issue - State: closed - Opened by Overcraft90 over 2 years ago - 11 comments
Labels: bug

#61 - Error at the end of pipeline execution

Issue - State: closed - Opened by alexvasilikop over 2 years ago - 2 comments
Labels: bug

#60 - add prefix to fig_dir

Pull Request - State: closed - Opened by js2264 over 2 years ago - 1 comment

#59 - Replace travis with github workflow

Pull Request - State: closed - Opened by cmdoret over 2 years ago - 1 comment

#58 - interpret distance law

Issue - State: closed - Opened by gorliver almost 3 years ago - 2 comments

#57 - Better respect for the --threads parameter

Issue - State: closed - Opened by oneillkza almost 3 years ago - 2 comments
Labels: bug

#56 - Add support for gzipped fasta input

Issue - State: closed - Opened by oneillkza almost 3 years ago - 2 comments
Labels: enhancement

#55 - Add functionality to input cut sites when enzymes are unknown

Issue - State: closed - Opened by oneillkza almost 3 years ago - 1 comment
Labels: enhancement

#54 - cutsite mode with dual enzyme

Issue - State: closed - Opened by aurelepiazza almost 3 years ago - 1 comment

#53 - Support for OmniC data

Issue - State: closed - Opened by diriano about 3 years ago - 1 comment
Labels: question

#52 - Issue with the view function

Issue - State: closed - Opened by aurelepiazza about 3 years ago - 2 comments

#51 - Normalization

Issue - State: closed - Opened by sarah872 about 3 years ago - 4 comments

#50 - Cutsite error

Issue - State: closed - Opened by sarah872 about 3 years ago - 2 comments
Labels: bug

#49 - Unable to show plots

Issue - State: closed - Opened by ABignaud about 3 years ago - 1 comment
Labels: bug

#48 - NumExpr detected 40 cores but "NUMEXPR_MAX_THREADS" not set, so enforcing safe limit of 8.

Issue - State: closed - Opened by Karimi-81 over 3 years ago - 1 comment
Labels: question

#47 - Error with Docker image

Issue - State: closed - Opened by alexcorm over 3 years ago - 2 comments

#46 - Digest map

Pull Request - State: closed - Opened by ABignaud over 3 years ago

#45 - display the limits of the contigs on the matrix

Issue - State: closed - Opened by jflot almost 4 years ago - 2 comments
Labels: enhancement

#44 - Move to BSD 3-Clause License

Pull Request - State: closed - Opened by cmdoret almost 4 years ago

#42 - Throw instead of returning input in normalization

Pull Request - State: closed - Opened by scovit over 4 years ago - 2 comments

#41 - Specify upper and lower bounds for the colorscale in view

Issue - State: closed - Opened by aurelepiazza over 4 years ago - 1 comment
Labels: enhancement

#40 - hicstuff rebin does not update cool metadata

Issue - State: closed - Opened by cmdoret over 4 years ago - 1 comment
Labels: bug

#39 - Can't install latest development

Issue - State: closed - Opened by ghost over 4 years ago - 1 comment

#38 - mapper choice

Issue - State: closed - Opened by ghost over 4 years ago - 4 comments
Labels: enhancement

#37 - Harmless warning?

Issue - State: closed - Opened by ghost over 4 years ago

#36 - pipeline stucks at last step?

Issue - State: closed - Opened by ghost over 4 years ago

#35 - Help wanted on value error in io.py script

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

#34 - Generating Hi-C contact matrix with Hi-C reads from multiple libraries

Issue - State: closed - Opened by Raina-M almost 5 years ago - 2 comments

#33 - Allow subsetting of intra + inter matrices

Issue - State: open - Opened by cmdoret almost 5 years ago
Labels: enhancement

#32 - hicstuff distancelaw legend

Issue - State: closed - Opened by ABignaud about 5 years ago - 2 comments
Labels: bug

#31 - Test cli

Pull Request - State: closed - Opened by cmdoret over 5 years ago - 1 comment

#30 - option -b and -r/-f simultaneously

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

#29 - Distance law CLI with pairs files

Issue - State: closed - Opened by cmdoret over 5 years ago - 1 comment
Labels: enhancement

#28 - Pcr dup

Pull Request - State: closed - Opened by cmdoret over 5 years ago - 1 comment

#27 - Index rework

Pull Request - State: closed - Opened by cmdoret over 5 years ago - 1 comment

#26 - Distance law

Pull Request - State: closed - Opened by cmdoret over 5 years ago - 1 comment

#25 - add option for index

Issue - State: closed - Opened by cmdoret over 5 years ago - 1 comment
Labels: enhancement

#24 - change alignment format

Issue - State: closed - Opened by cmdoret over 5 years ago
Labels: enhancement, suggestion

#23 - Full python

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

#22 - major overhaul

Issue - State: closed - Opened by cmdoret over 5 years ago - 3 comments
Labels: enhancement, suggestion

#21 - pipeline with bowtie2 fails

Issue - State: closed - Opened by psimion over 5 years ago - 1 comment
Labels: bug

#20 - problem with iterative alignment

Issue - State: closed - Opened by rmontagn over 5 years ago - 1 comment
Labels: bug

#19 - unrecognized installment of hicstuff

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

#18 - rebin breaks fragment order

Issue - State: closed - Opened by cmdoret over 5 years ago - 1 comment
Labels: bug

#17 - Implement a resampling function, to perform bootstrap in tool development

Issue - State: closed - Opened by scovit over 5 years ago - 3 comments
Labels: enhancement

#16 - Make a function to load a sparse matrix directly

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

#15 - Add zoom option to view

Issue - State: closed - Opened by cmdoret over 5 years ago - 1 comment
Labels: enhancement

#14 - misc plot

Issue - State: closed - Opened by cmdoret over 5 years ago - 1 comment
Labels: enhancement

#13 - start in the middle of pipeline

Issue - State: closed - Opened by cmdoret over 5 years ago - 1 comment
Labels: enhancement

#12 - binning in physical distance

Issue - State: closed - Opened by aurelepiazza over 5 years ago - 1 comment
Labels: bug

#11 - Kb-binning functions rewrite

Issue - State: closed - Opened by cmdoret over 5 years ago
Labels: help wanted

#10 - preferred kb binning behaviour

Issue - State: closed - Opened by cmdoret over 5 years ago - 2 comments
Labels: help wanted

#9 - Include command line in log

Issue - State: closed - Opened by cmdoret over 5 years ago
Labels: enhancement

#8 - add option to plot fragment threshold

Issue - State: closed - Opened by tfoutelrodier over 5 years ago - 1 comment
Labels: enhancement

#7 - Show size distribution of fragments

Issue - State: closed - Opened by cmdoret almost 6 years ago - 1 comment
Labels: enhancement

#6 - Add "log" option

Issue - State: closed - Opened by cmdoret almost 6 years ago - 1 comment
Labels: enhancement

#5 - Subcommands

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

#4 - single entry point with subcommands

Issue - State: closed - Opened by cmdoret almost 6 years ago - 2 comments
Labels: suggestion

#3 - filter3C causes display-related error on WSL

Issue - State: closed - Opened by cmdoret almost 6 years ago - 3 comments
Labels: bug

#2 - pcr_duplicates and adapter removal

Issue - State: closed - Opened by cmdoret almost 6 years ago - 1 comment
Labels: help wanted

#1 - Add autodetection of the index file for the reference genome

Issue - State: closed - Opened by cmdoret almost 6 years ago - 1 comment
Labels: enhancement