Ecosyste.ms: Issues

An open API service for providing issue and pull request metadata for open source projects.

GitHub / 38/d4-format issues and pull requests

#85 - Fix Dockerfile

Pull Request - State: open - Opened by northwestwitch 4 days ago

#84 - Fix issue with wrong values for overlapping bed-ranges

Pull Request - State: closed - Opened by Jakob37 about 1 month ago - 1 comment

#83 - feat: Add percent coverage option to stat

Pull Request - State: closed - Opened by cademirch 2 months ago - 30 comments

#82 - Efficiently summing coverage tracks from multiple d4 files

Issue - State: open - Opened by percyfal 3 months ago - 3 comments

#81 - New stat function: % of positions in intervals with coverage >X

Issue - State: open - Opened by Jakob37 4 months ago - 11 comments

#81 - New stat function: % of positions in intervals with coverage >X

Issue - State: open - Opened by Jakob37 4 months ago - 2 comments

#80 - Wrong mean coverage values from indexed d4 file

Issue - State: open - Opened by Jakob37 4 months ago

#80 - Wrong mean coverage values from indexed d4 file

Issue - State: open - Opened by Jakob37 4 months ago

#80 - Wrong mean coverage values from indexed d4 file

Issue - State: open - Opened by Jakob37 4 months ago

#79 - Fix coverage spillover bug

Pull Request - State: closed - Opened by Jakob37 4 months ago - 6 comments

#78 - Occasionally large differences in coverage for same gene region in same sample

Issue - State: closed - Opened by Jakob37 5 months ago - 10 comments

#77 - add -L to curl in build_htslib

Pull Request - State: closed - Opened by cademirch 6 months ago - 16 comments

#76 - hack ref_len -1

Pull Request - State: open - Opened by andypexai 7 months ago

#75 - Bug: off-by-one bug on bam reads

Issue - State: open - Opened by andypexai 7 months ago - 1 comment

#74 - Can't install latest pyd4 release

Issue - State: closed - Opened by cademirch 12 months ago - 1 comment

#73 - Cut a new release please

Issue - State: open - Opened by mrvollger about 1 year ago - 5 comments

#72 - [ENH] convert BED to d4 file.

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

#71 - misaligned pointer dereference in `read_next_value`

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

#70 - Bug: OSError: memory map must have a non-zero length in load_to_np_impl

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

#68 - d4tools view - Flag `--region-file` not working.

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

#67 - Part size limit causing odd results every 10M bases?

Issue - State: open - Opened by onordesjo almost 2 years ago

#66 - Infer type in bamfile

Pull Request - State: open - Opened by dotinspace almost 2 years ago - 1 comment

#65 - fix bug with "~" option exclusive bam mask

Pull Request - State: closed - Opened by petersudmant almost 2 years ago - 2 comments

#64 - no apparent size reduction of multi-track files as function of no of samples

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

#63 - WIP: solidify start

Pull Request - State: open - Opened by brentp about 2 years ago - 5 comments

#62 - Missing columns when merging multicolumn files depending on order

Issue - State: closed - Opened by mrvollger about 2 years ago - 4 comments

#61 - fixed a typo and clarified help message in d4tools view

Pull Request - State: closed - Opened by mrvollger about 2 years ago - 1 comment

#60 - Enable `create` to take input from stdin

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

#59 - Bug in view? different values when including the first position in a chromosome

Issue - State: closed - Opened by mrvollger about 2 years ago - 4 comments

#58 - Does not compile on M1 mac

Issue - State: closed - Opened by jdidion about 2 years ago - 4 comments

#57 - Mapping quality filter not functioning

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

#56 - create fails on some cram/bams

Issue - State: closed - Opened by petersudmant about 2 years ago - 13 comments

#55 - [enhancement] stat for a region/list of regions

Issue - State: closed - Opened by darked89 about 2 years ago - 5 comments

#54 - Bug in encoding data with pyd4 when using sparse

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

#53 - Multitrack D4 from python API without writing multiple intermediate d4 files

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

#51 - `d4tools create` builds empty d4 file for small input files

Issue - State: closed - Opened by pamelarussell over 2 years ago - 6 comments

#50 - Maintainance of plotters

Issue - State: closed - Opened by AaronErhardt over 2 years ago

#49 - pyd4 manylinux wheel

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

#48 - pip install fails

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

#47 - Update README

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

#46 - change tracking

Issue - State: closed - Opened by brentp over 2 years ago - 7 comments

#45 - Dockerfile no longer works with edition = "2021"

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

#44 - Add some basic stat options: count / sum

Issue - State: closed - Opened by af8 over 2 years ago - 1 comment

#43 - exclude bam flag rather than include ?

Issue - State: closed - Opened by af8 over 2 years ago - 3 comments

#42 - Build fails on CentOS7 : asks for -fPIC option

Issue - State: closed - Opened by af8 over 2 years ago - 7 comments

#41 - Bug in build_htslib.sh?

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

#40 - d4toh5.py used for manuscript?

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

#39 - Typo in page title - Quantatative

Issue - State: closed - Opened by bossiep1 over 2 years ago

#38 - cargo build. => feature `edition2021` is required

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

#37 - Expired SSL certificate causes d4-hts installation to fail

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

#36 - d4tools is not on cargo, version numbers/releases?

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

#35 - Which d4utils version to use?

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

#34 - D4 file format magic number

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

#33 - Update README.md

Pull Request - State: closed - Opened by arq5x about 3 years ago

#32 - README.md refers to nonexistent d4tools crate

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

#31 - Adds Dockerfile

Pull Request - State: closed - Opened by moonso about 3 years ago - 1 comment

#30 - Dockerfile

Issue - State: closed - Opened by moonso about 3 years ago

#29 - Dockerfile

Pull Request - State: closed - Opened by Mropat about 3 years ago

#28 - Update README.md

Pull Request - State: closed - Opened by arq5x about 3 years ago

#27 - [ENH] Is there utility for single-cell genomics?

Issue - State: open - Opened by arq5x about 3 years ago - 18 comments

#26 - [ENH] Multiple file/track support

Issue - State: closed - Opened by arq5x about 3 years ago - 1 comment

#25 - [ENH] Add HTTP range support

Issue - State: closed - Opened by arq5x about 3 years ago

#24 - Update main.rs

Pull Request - State: closed - Opened by arq5x about 3 years ago

#23 - Odd results from stat command

Issue - State: closed - Opened by arq5x about 3 years ago

#22 - Version numbers for util subcommands are 0.1.0

Issue - State: closed - Opened by snystrom about 3 years ago

#21 - Allow view to accept a BED file of regions as input

Issue - State: closed - Opened by arq5x about 3 years ago - 3 comments

#20 - Auto-detect sparse (k=0) format.

Issue - State: closed - Opened by arq5x about 3 years ago

#19 - Update README.md

Pull Request - State: closed - Opened by arq5x over 3 years ago

#18 - change max bin for stat histogram

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

#17 - d4tools create randomly fails

Issue - State: closed - Opened by af8 over 3 years ago - 1 comment

#16 - BAM records filtering based on flag ?

Issue - State: closed - Opened by af8 over 3 years ago - 4 comments

#15 - Specification for D4 Format?

Issue - State: closed - Opened by ssadedin over 3 years ago - 1 comment

#14 - Add links and examples for the C and Python API to the main README.

Issue - State: closed - Opened by arq5x almost 4 years ago

#13 - Update README.md

Pull Request - State: closed - Opened by arq5x almost 4 years ago

#12 - stat produces incorrect results when using secondary table

Issue - State: closed - Opened by snystrom almost 4 years ago - 8 comments

#11 - Suggestion: automate binary deployment w/ github releases

Issue - State: open - Opened by snystrom almost 4 years ago

#10 - rename binary d4tools to be consistent with manuscript and convention

Issue - State: closed - Opened by arq5x almost 4 years ago - 1 comment

#9 - depth is 0 for samtools/examples/toy.sam

Issue - State: closed - Opened by lindenb almost 4 years ago - 3 comments

#8 - stats from repeated regions behave strangely

Issue - State: closed - Opened by snystrom almost 4 years ago - 8 comments

#7 - stat breaks pipes

Issue - State: closed - Opened by snystrom almost 4 years ago - 2 comments

#6 - Update cli.yml

Pull Request - State: closed - Opened by arq5x almost 4 years ago

#5 - d4 view and d4 stat should accept a BED file of regions to report on.

Issue - State: closed - Opened by arq5x almost 4 years ago - 1 comment

#4 - Update README.md

Pull Request - State: closed - Opened by arq5x almost 4 years ago

#3 - c-api doesn't allow setting parameters when writing a new d4 file

Issue - State: open - Opened by brentp almost 4 years ago - 2 comments

#2 - d4utils stat: show available stats

Issue - State: closed - Opened by brentp almost 4 years ago

#1 - LICENSE

Issue - State: closed - Opened by brentp about 4 years ago