Ecosyste.ms: Issues

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

GitHub / brentp/mosdepth issues and pull requests

#99 - Error running mosdepth

Issue - State: closed - Opened by kokyriakidis about 5 years ago - 8 comments

#98 - Unsorted positions on sequence error

Issue - State: closed - Opened by tjbencomo about 5 years ago - 10 comments

#97 - --mapq threshold means greater than?

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

#96 - Output mean and median in same run

Issue - State: closed - Opened by shahmj about 5 years ago - 4 comments

#95 - Not able to plot coverage graphs

Issue - State: closed - Opened by Rohit-Satyam about 5 years ago - 11 comments

#94 - MosDepth -F 1804 versus -F 1796

Issue - State: closed - Opened by lemdcock over 5 years ago - 3 comments

#93 - Add mosdepth v0.2.6 to bioconda

Issue - State: closed - Opened by iranmdl over 5 years ago - 3 comments

#92 - Fixed typo in README.md

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

#91 - are secondary hits taken into account?

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

#90 - Evaluated coverage only over non-N bases in the given genome reference

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

#89 - bigwig output

Issue - State: closed - Opened by brentp over 5 years ago - 6 comments

#88 - per-readgroup depth not working in v0.2.5

Issue - State: closed - Opened by chrisamiller over 5 years ago - 3 comments

#86 - Is running on remote BAMs or STDIN possible?

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

#85 - reference fasta file

Issue - State: closed - Opened by kruthikaiyer0990 over 5 years ago - 1 comment

#84 - Compilation (type mismatch) error with v0.2.6

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

#83 - Related to issue #81 Bed file output using the 5th column (score) for counts

Pull Request - State: open - Opened by duartemolha almost 6 years ago - 4 comments

#82 - Question regarding Fast-Mode

Issue - State: closed - Opened by duartemolha almost 6 years ago - 1 comment

#81 - Bed file validation not following bed specifications

Issue - State: open - Opened by duartemolha almost 6 years ago - 2 comments

#80 - Exit status zero upon error

Issue - State: closed - Opened by wdecoster almost 6 years ago - 1 comment

#79 - tmp dir

Issue - State: closed - Opened by nservant almost 6 years ago - 2 comments

#78 - Getting sequencing depth correspond to .vcf file

Issue - State: closed - Opened by beginner984 almost 6 years ago - 3 comments

#77 - add summary file

Pull Request - State: closed - Opened by danielecook almost 6 years ago - 18 comments

#76 - I am not able to install your software

Issue - State: closed - Opened by beginner984 almost 6 years ago - 1 comment

#75 - plot-dist.py output file blank

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

#74 - FR - --reverse-thresholds

Issue - State: closed - Opened by rjsicko almost 6 years ago - 2 comments

#73 - Fully overlapping reads were not correctly detected

Pull Request - State: closed - Opened by jaudoux almost 6 years ago - 1 comment

#72 - Fully overlapping reads not detected (frequent in Amplicon data)

Issue - State: closed - Opened by jaudoux almost 6 years ago - 4 comments

#71 - Memory overconsumption + slowness for coverage over bed defined regions

Issue - State: closed - Opened by Sebastien-Raguideau about 6 years ago - 24 comments

#70 - Docker quay usage

Pull Request - State: closed - Opened by alok123t about 6 years ago

#69 - Running using docker

Issue - State: closed - Opened by alok123t about 6 years ago - 1 comment

#68 - Update README.md

Pull Request - State: closed - Opened by skanwal about 6 years ago

#67 - Normalized coverage

Issue - State: closed - Opened by npatel22526 about 6 years ago - 1 comment

#66 - Bug in coverage calculation with specific quantization settings

Issue - State: closed - Opened by gabeng about 6 years ago - 5 comments

#65 - genome-wide coverage metric for WGS data?

Issue - State: closed - Opened by ggstatgen about 6 years ago - 2 comments

#64 - Median coverage per-window

Issue - State: closed - Opened by shahmj about 6 years ago - 4 comments
Labels: enhancement

#63 - Uneven counts in some regions

Issue - State: closed - Opened by kkapuria3 about 6 years ago - 8 comments

#62 - cannot run mosdepth with only --fast-mode as option

Issue - State: closed - Opened by kkapuria3 about 6 years ago - 2 comments

#61 - output mean depth by chromosome and total

Issue - State: closed - Opened by brentp over 6 years ago - 1 comment

#60 - Feature request: filter by readgroup

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

#59 - updates for travis

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

#58 - Disagreement of results with samtools and bedtools

Issue - State: closed - Opened by apozomt over 6 years ago - 7 comments

#57 - OSX build for bioconda

Issue - State: closed - Opened by virenar over 6 years ago - 11 comments
Labels: help wanted

#56 - Exclude BED regions even with thresholds enabled

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

#55 - per-base coverage, break out into per-base for each position

Issue - State: closed - Opened by stephenturner over 6 years ago - 3 comments

#54 - Out of memory error

Issue - State: closed - Opened by johnomics over 6 years ago - 12 comments

#53 - Base Quality Thresholding

Issue - State: closed - Opened by crutching over 6 years ago - 1 comment

#52 - Add output file with # of alignment records used and ignored

Issue - State: open - Opened by af8 over 6 years ago - 5 comments

#51 - Fill insert size between mates

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

#50 - per-base.bed.gz with --by

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

#49 - could not load: libhts.so

Issue - State: closed - Opened by indapa over 6 years ago - 14 comments

#48 - understanding regions.bed file

Issue - State: closed - Opened by ghost over 6 years ago

#47 - mosdepth now in linuxbrew

Issue - State: closed - Opened by tseemann over 6 years ago - 1 comment

#46 - calculating mean per chromosome

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

#45 - ./mosdepth: ��f)�: ELF: x: Error 1195033751

Issue - State: closed - Opened by tseemann over 6 years ago - 7 comments

#44 - [hts-nim] error in bam.queri

Issue - State: closed - Opened by hdashnow over 6 years ago - 10 comments

#43 - Update BioConda Version with latest release

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

#42 - lower coverage observed than actual

Issue - State: closed - Opened by kkapuria3 over 6 years ago - 4 comments

#41 - Fails for long chromosomes

Issue - State: closed - Opened by kaspernie almost 7 years ago - 3 comments

#40 - Weird results in `.region.dist.txt`

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

#39 - mosdepth pronunciation

Issue - State: closed - Opened by pdiakumis almost 7 years ago - 1 comment

#38 - number of decimals in .global.list.txt

Issue - State: closed - Opened by avilella almost 7 years ago - 3 comments

#37 - adapting plot-dist.py

Pull Request - State: closed - Opened by wdecoster almost 7 years ago

#36 - BAPQ filtering

Issue - State: closed - Opened by EgirardBioinfo almost 7 years ago - 1 comment

#34 - change print to be python3 compatible

Pull Request - State: closed - Opened by wdecoster almost 7 years ago - 1 comment

#33 - Warnings about invalid chromosome intervals for very short contigs?

Issue - State: closed - Opened by philippbayer almost 7 years ago - 3 comments

#32 - Output only to two decimal places in $prefix.mosdepth.dist.txt

Issue - State: closed - Opened by alizraksi almost 7 years ago - 2 comments

#31 - Empty "mosdepth.dist.txt" file

Issue - State: closed - Opened by gwaybio about 7 years ago - 2 comments

#30 - [E::cram_read_container] Container header CRC32 failure

Issue - State: closed - Opened by silvewheat about 7 years ago - 6 comments

#29 - Add instruction to fix pcre issue

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

#28 - typo tresholds -> thresholds

Pull Request - State: closed - Opened by hyphaltip about 7 years ago - 1 comment

#27 - SIGSEGV: Illegal storage access. (Attempt to read from nil?)

Issue - State: closed - Opened by wresch about 7 years ago - 13 comments

#26 - Increase precision of mean depth in output

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

#25 - $BRANCH undefined in install.sh script

Issue - State: closed - Opened by monkollek about 7 years ago

#24 - Mosdepth on Windows OS

Issue - State: closed - Opened by unikzforce about 7 years ago - 6 comments

#23 - ENH: output per-region counts (not means) for --by

Issue - State: closed - Opened by brentp about 7 years ago - 8 comments

#22 - Sort error

Issue - State: closed - Opened by kellogg76 about 7 years ago - 1 comment

#21 - Filter by alignment score (AS) and number of mismatches (NM) [feature request]

Issue - State: closed - Opened by sjackman about 7 years ago - 6 comments

#20 - Package on Arch platforms

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

#18 - Full per base output despite 'by' region definition

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

#17 - Region-level distribution

Issue - State: closed - Opened by vladsavelyev over 7 years ago - 8 comments

#16 - Feature Request - base quality filter

Issue - State: closed - Opened by jasper1918 over 7 years ago - 3 comments

#15 - Quantize

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

#14 - Update README.md

Pull Request - State: closed - Opened by arq5x over 7 years ago

#13 - feature request: per base depth in regions

Issue - State: closed - Opened by matthdsm over 7 years ago - 5 comments

#12 - Fix my own typo :-/

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

#11 - Add version requirement for hstlib to README.md

Pull Request - State: closed - Opened by dwinter over 7 years ago - 1 comment

#10 - /lib64/libc.so.6: version `GLIBC_2.14' not found

Issue - State: closed - Opened by drramki-chop over 7 years ago - 9 comments

#9 - plot-dist.py scripts not working

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

#8 - "Out of memory" if the BED file has track lines

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

#7 - Docker for mosdepth

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

#6 - unhandled exception: pair_depth == 0

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

#5 - travis-ci

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

#4 - Build binaries with older glibc Centos 6

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

#3 - Replacing usage of sambamba depth with mosdepth

Issue - State: closed - Opened by chapmanb over 7 years ago - 10 comments

#2 - Potential speed up

Issue - State: closed - Opened by jkbonfield over 7 years ago - 6 comments

#1 - images

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