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

#247 - How to use --d4?

Issue - State: open - Opened by LudvigOlsen 13 days ago - 4 comments

#246 - Full fragment coverage mode for proper pairs

Pull Request - State: closed - Opened by LudvigOlsen 15 days ago - 8 comments

#245 - Mosdepth fails when run with less than 8GB RAM on ~50MB CRAM

Issue - State: open - Opened by dennishendriksen about 2 months ago - 20 comments

#244 - only write requested chroms to d4 file

Pull Request - State: open - Opened by cademirch 2 months ago - 1 comment

#243 - Build sfi index in d4 files?

Issue - State: closed - Opened by cademirch 2 months ago - 10 comments

#242 - Median is Only for Histogram

Issue - State: open - Opened by DarioS 2 months ago

#241 - Range of Per-base Coverage

Issue - State: closed - Opened by DarioS 2 months ago - 2 comments

#240 - v3.9.0 not available via quay.io

Issue - State: open - Opened by bartcharbon 3 months ago - 1 comment

#239 - mosdepth on single bam vs chunks of bam

Issue - State: closed - Opened by reshu23 3 months ago - 1 comment

#238 - plot-dist.py legend

Issue - State: closed - Opened by WWz33 4 months ago - 2 comments

#237 - --d4 Creates d4 files with inf/NaN values

Issue - State: closed - Opened by cademirch 5 months ago - 9 comments

#236 - Fix compilation error by removing 'shallow' for Nim 2.0 compatibility

Pull Request - State: closed - Opened by kojix2 7 months ago - 3 comments

#235 - Update docopt version to 0.7.1

Pull Request - State: closed - Opened by kojix2 7 months ago

#233 - feat: per base in BED regions only?

Issue - State: closed - Opened by cademirch 8 months ago - 3 comments

#232 - D4 support in versions 0.3.7 and 0.3.8

Issue - State: closed - Opened by pdl30 9 months ago - 1 comment

#231 - Unspecific naming of region in summary file

Issue - State: closed - Opened by Krannich479 9 months ago - 2 comments

#230 - `:` in region strings passed to `--chrom`

Issue - State: open - Opened by julibeg 9 months ago

#229 - Long run time with large assembly and many contigs

Issue - State: closed - Opened by ohickl 10 months ago - 9 comments

#228 - Soft and hard clipped bases

Issue - State: closed - Opened by ezherman 10 months ago - 7 comments

#227 - Update Github actions

Pull Request - State: closed - Opened by martin-g 10 months ago - 1 comment

#225 - [question]: mosdepth 0.3.7 via bioconda/docker

Issue - State: open - Opened by tamuanand 11 months ago

#224 - Support for CRAM v3.1

Issue - State: closed - Opened by adthrasher 11 months ago - 5 comments

#223 - Warnings about invalid chromosome intervals .

Issue - State: open - Opened by Heather1999 12 months ago - 1 comment

#222 - Report all chromosomes/regions even though they have zero coverage

Issue - State: open - Opened by xsoleacha 12 months ago - 2 comments

#221 - Write out mean/median mapq

Issue - State: closed - Opened by holtgrewe about 1 year ago - 1 comment

#220 - Summary output with --use-median

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

#219 - Can I get the two result at the same time?

Issue - State: closed - Opened by pickpingk about 1 year ago

#218 - sequencing depth after deduplication

Issue - State: closed - Opened by pickpingk about 1 year ago - 4 comments

#217 - Insert size of 0

Issue - State: closed - Opened by LudvigOlsen about 1 year ago - 3 comments

#216 - Empty per-base output file if all reads in input BAM are unmapped

Issue - State: closed - Opened by julibeg about 1 year ago - 5 comments

#215 - MAPQ 0 reads discarded even if --mapq 0 used

Issue - State: closed - Opened by valeandri about 1 year ago - 2 comments

#214 - Insert size filtering

Pull Request - State: closed - Opened by LudvigOlsen about 1 year ago - 10 comments

#213 - Fragment length filtering

Issue - State: closed - Opened by LudvigOlsen over 1 year ago

#212 - [Question]: mosdepth 0.3.5 in bioconda/docker

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

#211 - Filtering alignments: -F in which format?

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

#210 - funny global depth of coverage plot

Issue - State: closed - Opened by prasundutta87 over 1 year ago - 1 comment

#209 - Build failure with nim 2.0.0

Issue - State: closed - Opened by meanjollies over 1 year ago - 4 comments

#207 - Wrong calculation of minimum coverage?

Issue - State: closed - Opened by xsoleacha over 1 year ago - 8 comments

#206 - --d4 option unavailble in 0.3.4

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

#205 - testrun for region chr1:1000-2000 takes ages

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

#204 - [Question]: mosdepth 0.3.4 via Docker or Conda

Issue - State: open - Opened by tamuanand over 1 year ago - 2 comments

#203 - question about WGS data

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

#202 - Version? 0.3.4?

Issue - State: closed - Opened by serge2016 over 1 year ago - 1 comment

#201 - issue with bed file

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

#200 - High memory usage for very small BAM files

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

#199 - specific chromosome list for mosdepth running

Issue - State: closed - Opened by zhangjy859 almost 2 years ago - 2 comments

#198 - misleading output in `summary.txt` file

Issue - State: open - Opened by nservant almost 2 years ago - 3 comments

#197 - "SIGSEGV: Illegal storage access. (Attempt to read from nil?)" when using bed file

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

#196 - Update Docker installation in README from v0.2.4 -> v0.3.3

Pull Request - State: closed - Opened by jethror1 almost 2 years ago - 1 comment

#195 - [hts-nim] error adding to csi index

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

#194 - Exclusion of reads with -F flag

Issue - State: closed - Opened by aklein-705 about 2 years ago - 2 comments

#193 - question: `--by` and quantized output

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

#192 - depth per strand

Issue - State: closed - Opened by onordesjo about 2 years ago - 1 comment

#191 - `REF_PATH` differs from samtools behaviour

Issue - State: closed - Opened by multimeric about 2 years ago - 1 comment

#190 - .mosdepth.region.dist.txt missing values?

Issue - State: open - Opened by adamrtalbot about 2 years ago

#189 - Support for streaming

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

#187 - equivalent to genomeCoverageBed

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

#186 - Percentage of Coverage for Exome Bed file

Issue - State: open - Opened by kiranpatil222 over 2 years ago - 1 comment

#185 - compute best sliding window coverage per chromosome

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

#184 - Coverage by region vs. Global dist

Issue - State: open - Opened by hlfreund over 2 years ago - 8 comments

#183 - how coverage in region is calculated

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

#182 - --by capture.bed still give out region not in bed

Issue - State: closed - Opened by worker000000 over 2 years ago - 6 comments

#181 - Error building 0.3.3

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

#180 - Optionally report uncovered contigs in summary file

Issue - State: open - Opened by dpryan79 over 2 years ago

#179 - difference in X-Coverage calculated by Mosdepth and Samtools Coverage

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

#178 - plot.dist.py output to screen only

Issue - State: open - Opened by space-beaver over 2 years ago - 4 comments

#177 - sorting issue

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

#175 - Support streaming from cloud storage buckets

Issue - State: open - Opened by SHuang-Broad almost 3 years ago - 5 comments

#174 - error: unhandled exception: invalid integer: 0.065 [ValueError]

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

#173 - Exact sorting of the output bed file?

Issue - State: open - Opened by Dario-Galanti almost 3 years ago - 2 comments

#172 - mosdepth.summary.txt region differs much with bed region

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

#171 - Version 0.3.3 "zsh: exec format error: mosdepth" error on Mac

Issue - State: open - Opened by Calvinblue almost 3 years ago - 2 comments

#170 - coverage per base

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

#169 - How to use flag option?

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

#168 - Custom index pointer

Issue - State: closed - Opened by philip-scorpiontx about 3 years ago - 11 comments

#167 - SIGSEGV issues reported when running mosdepth

Issue - State: closed - Opened by JiaweiShen1116 about 3 years ago - 1 comment

#166 - How to calculate % ( what % is 10X, 30X, 50%) along with 1,10,20,30X

Issue - State: closed - Opened by Kiran936 about 3 years ago - 5 comments

#165 - Avg depth for multiple BAMs with BED input

Issue - State: open - Opened by Kiran936 about 3 years ago - 1 comment

#164 - Discrepancy between mosdepth coverage and bam profiles on IGV

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

#163 - Retrieve Index File

Issue - State: closed - Opened by priyambial123 about 3 years ago - 3 comments

#162 - mosdepth binary provided under releases is Linux only

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

#161 - Out of memory Issue

Issue - State: open - Opened by yangyxt about 3 years ago - 5 comments

#160 - Quantized output does not correspond to --by .bed file

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

#159 - Metrics in output thresholds.bed reports less coverage than BAM file

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

#158 - mosdepth.global.dist.txt third column

Issue - State: closed - Opened by asmlgkj over 3 years ago - 11 comments

#156 - Coverage 0 for entire chr when using --by

Issue - State: open - Opened by elleira over 3 years ago - 7 comments

#154 - mosDepth vs plotCoverage

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

#140 - 0.3.1 version from bioconda missing --d4 option

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

#131 - Index Error

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

#122 - Add in min read length threshold?

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

#115 - Dash in Chromsome Name

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

#114 - N region?

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

#112 - legend alignment

Issue - State: closed - Opened by mike-molnar almost 5 years ago - 1 comment

#100 - Fragment coverage for pair-end data?

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