Ecosyste.ms: Issues

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GitHub / brentp/goleft issues and pull requests

#78 - exit zero for "help"

Pull Request - State: closed - Opened by kdm9 2 months ago - 1 comment

#77 - crai resolution in output-indexcov.bed.gz

Issue - State: closed - Opened by corinsexton 4 months ago - 4 comments

#76 - Bump golang.org/x/image from 0.11.0 to 0.18.0

Pull Request - State: open - Opened by dependabot[bot] 5 months ago
Labels: dependencies

#75 - Release Linux aarch64 binary

Issue - State: closed - Opened by martin-g 8 months ago - 4 comments

#74 - indexcov everything is DEL or DUP

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

#73 - covstats: % unmapped calculation seems inaccurate (>3000%, etc)

Issue - State: open - Opened by aofarrel 12 months ago - 5 comments

#72 - Indexcov searching for cram.bai

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

#71 - indexcov: usage with long reads ?

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

#70 - What is the value of the insert size ?

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

#69 - Running Indexcov on cram files with different paths

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

#68 - No longer possible to build from source or include in a Docker image

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

#67 - Negative alnSpan error

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

#66 - error on depth, seems to make temp file it can't find

Issue - State: open - Opened by bioinfowheat about 4 years ago

#65 - Indexcov errors

Issue - State: open - Opened by emmakwiener about 4 years ago - 2 comments

#64 - Feature request: New option --exclude for covstats

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

#63 - indexcov shows stepwise coverage distribution

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

#62 - suggestion: zoomable chromosome depth plots in indexcov

Issue - State: closed - Opened by edg1983 over 4 years ago - 1 comment

#61 - Update README.md

Pull Request - State: closed - Opened by timtribu about 5 years ago

#60 - link to golang typo

Issue - State: open - Opened by przemekl over 5 years ago

#59 - error: bam is required

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

#58 - coverage of the customized genome

Issue - State: open - Opened by weizhu365 over 5 years ago - 2 comments

#57 - goleft_linux64 covstats error: panic: EOF

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

#55 - indexcov support for csi indexes

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

#54 - Feature request: New option --exclude for indexsplit

Issue - State: open - Opened by andreas-wilm almost 6 years ago - 1 comment

#53 - goleft depth sliding window analysis

Issue - State: closed - Opened by lyy005 almost 6 years ago - 1 comment

#52 - Differential header stringency depending on file format

Issue - State: open - Opened by ernfrid about 6 years ago - 4 comments

#51 - Can it be used for NIPT samples?

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

#50 - How to generate the X-Y plots?

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

#49 - indexcov returns "no reference stats found"

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

#48 - Suggestions : paths ; case/control

Issue - State: open - Opened by lindenb about 6 years ago - 3 comments

#47 - indexsplit for 2000 samples fail

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

#46 - Installation & integration with STRetch

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

#45 - covstats supporting cram

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

#44 - indexcov: "panic: sam: malformed header line"

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

#43 - panic in crai.makeSizes

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

#42 - two typos

Pull Request - State: closed - Opened by colindaven over 6 years ago - 2 comments

#41 - indexcov --sex ''

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

#40 - indexcov Unable to run on contigs without a sex chr

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

#38 - indexcov: panic parsing time

Issue - State: open - Opened by CarlosBorroto almost 7 years ago

#36 - indexcov: different coverage scale with cram and bam inputs

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

#35 - call to unintended version of samtools

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

#34 - Support for more than one RG?

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

#33 - indexcov error

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

#32 - indexcov : won't work with multiple crais

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

#31 - crai -- panic: runtime error: index out of range

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

#30 - test

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

#29 - indexcov: producing .html but no other files

Issue - State: closed - Opened by stephenwilliams22 over 7 years ago - 4 comments

#28 - indexcov: incorrect results on chrM / small contig

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

#27 - indexcov: panic: runtime error: index out of range

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

#26 - indexcov: limit to standard chromosomes

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

#25 - indexcov: select or view individual sample tracks

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

#24 - panic: bam: magic number mismatch

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

#23 - new tool: vcfeval

Issue - State: open - Opened by brentp over 7 years ago

#22 - test and correct indexsplit

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

#21 - Error in description of bin plot?

Issue - State: closed - Opened by roblanf almost 8 years ago - 1 comment

#20 - Feature request: option to ignore sex chromosomes?

Issue - State: closed - Opened by roblanf almost 8 years ago - 6 comments

#19 - covmed overestimates coverage?

Issue - State: open - Opened by hdashnow almost 8 years ago - 4 comments

#18 - Update help-sex.md

Pull Request - State: closed - Opened by arq5x almost 8 years ago - 1 comment

#17 - goleft indexcov error parsing header on hg38 BAMs

Issue - State: closed - Opened by chapmanb almost 8 years ago - 3 comments

#16 - indexcov 0.1.11 failing on tiny test bam

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

#15 - Running indexcov on small input BAMs

Issue - State: closed - Opened by chapmanb almost 8 years ago - 5 comments

#14 - index out of range

Issue - State: closed - Opened by nsmackler almost 8 years ago - 3 comments

#13 - 0.1.9 release linux binary is actually 0.1.6?

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

#12 - Incorporate indexcov into MultiQC

Issue - State: closed - Opened by chapmanb almost 8 years ago - 14 comments

#11 - indexcov: Unexpectedly long run time

Issue - State: closed - Opened by sjackman almost 8 years ago - 9 comments

#10 - Please include installation instructions

Issue - State: open - Opened by sjackman almost 8 years ago - 9 comments

#9 - Index depths

Pull Request - State: closed - Opened by brentp almost 8 years ago

#8 - Sambamba Comparison

Issue - State: closed - Opened by dnbaker about 8 years ago - 4 comments

#7 - v1.0.6 bump: Fix help request escaping

Pull Request - State: closed - Opened by chapmanb about 8 years ago - 3 comments

#6 - Update test cases: fix previous and add empty

Pull Request - State: closed - Opened by chapmanb about 8 years ago - 2 comments

#5 - callable: fix issue with entire NO_COVERAGE block

Pull Request - State: closed - Opened by chapmanb about 8 years ago - 1 comment

#4 - Synchronizing depth callable output with bcbio

Issue - State: closed - Opened by chapmanb about 8 years ago - 9 comments

#3 - MaxDepth: add EXCESSIVE_DEPTH to callable regions

Pull Request - State: closed - Opened by chapmanb about 8 years ago

#2 - filter on flag

Issue - State: closed - Opened by brentp about 8 years ago - 3 comments

#1 - depth: prefix should be required.

Issue - State: closed - Opened by brentp about 8 years ago - 14 comments