vertgenlab/gonomics issues and pull requests

#839 - style: refactor and improvements eau

Pull Request - State: open - Opened by edotau over 1 year ago - 1 comment

#838 - samAssembler part 8: Summary statistics from base matrices

Pull Request - State: open - Opened by rimangan over 1 year ago - 1 comment

#837 - samAssembler Part 7: Haploid Base Calling from Ancient DNA Reads

Pull Request - State: closed - Opened by rimangan over 1 year ago - 1 comment

#836 - simulateSam: Ancient DNA Damage

Pull Request - State: open - Opened by rimangan over 1 year ago - 1 comment

#835 - interval/query.go

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

#834 - samAssembler Part 6: Diploid Base Calling from Ancient DNA Reads

Pull Request - State: closed - Opened by rimangan over 1 year ago - 1 comment

#833 - Geometric Random Variates

Pull Request - State: closed - Opened by rimangan over 1 year ago - 2 comments

#832 - Craig remove failing test

Pull Request - State: closed - Opened by craiglowe over 1 year ago - 1 comment

#831 - test: axt file to sam test

Pull Request - State: closed - Opened by edotau over 1 year ago - 1 comment

#830 - simulateSam - Error and Coverage

Pull Request - State: closed - Opened by rimangan over 1 year ago - 4 comments

#829 - Gonomics CMD Fix

Pull Request - State: closed - Opened by rimangan over 1 year ago - 1 comment

#828 - Update README.md

Pull Request - State: closed - Opened by rimangan over 1 year ago

#827 - Update golang 1.20.3 eau

Pull Request - State: closed - Opened by edotau over 1 year ago

#826 - Update go1.2 eau

Pull Request - State: closed - Opened by edotau over 1 year ago

#825 - Update go1.2 eau

Pull Request - State: closed - Opened by edotau over 1 year ago

#824 - Update README.md

Pull Request - State: closed - Opened by rimangan over 1 year ago

#823 - Add "keepCellsOption" to fastqFilter

Pull Request - State: closed - Opened by sweavs111 over 1 year ago - 2 comments

#822 - testing on one cmd

Pull Request - State: closed - Opened by rimangan over 1 year ago

#821 - Replace rand.Seed

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

#820 - Update Gonomics for Go 1.2

Pull Request - State: closed - Opened by dasnellings over 1 year ago - 1 comment

#819 - WIP: gunzip io reader eau

Pull Request - State: open - Opened by edotau over 1 year ago - 1 comment

#818 - Upgrade to golang 1.20

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

#817 - style: gonomics spring cleanup refactor edition eau

Pull Request - State: closed - Opened by edotau over 1 year ago - 1 comment

#816 - style: gonomics refactor lint fmt eau

Pull Request - State: closed - Opened by edotau over 1 year ago - 2 comments

#815 - ci: test golint workflow

Pull Request - State: closed - Opened by edotau over 1 year ago - 1 comment

#814 - ci: golint gitactions ci eau

Pull Request - State: closed - Opened by edotau over 1 year ago - 1 comment

#813 - cicd: automate go lint fmt eau

Pull Request - State: closed - Opened by edotau over 1 year ago - 1 comment

#812 - WIP: golint eau

Pull Request - State: closed - Opened by edotau over 1 year ago

#811 - cicd: ubuntu-latest, macos-latest, windows-latest eau

Pull Request - State: closed - Opened by edotau over 1 year ago - 1 comment

#810 - Vcf filter clustered variants

Pull Request - State: closed - Opened by dasnellings over 1 year ago - 1 comment

#809 - WIP: sam assembler part 4 fork from riley eau

Pull Request - State: closed - Opened by edotau over 1 year ago - 1 comment

#808 - wip: cicd coverage eau

Pull Request - State: closed - Opened by edotau over 1 year ago - 1 comment

#807 - Update to fmt workflow to fmt packages inside of packages

Pull Request - State: closed - Opened by dasnellings over 1 year ago - 3 comments

#806 - fix: go docs + fmt eau

Pull Request - State: closed - Opened by edotau over 1 year ago - 1 comment

#805 - Explicitly zero out any unused fields in bam

Pull Request - State: closed - Opened by dasnellings over 1 year ago - 1 comment

#804 - samAssembler Part 5: Scoring output alignments

Pull Request - State: closed - Opened by rimangan over 1 year ago - 2 comments

#803 - Update scCount.go Usage

Pull Request - State: closed - Opened by RavenYL over 1 year ago - 1 comment

#802 - simulateEvol qName Option

Pull Request - State: closed - Opened by rimangan over 1 year ago - 1 comment

#801 - samAssembler Part 4: The Complete Program

Pull Request - State: closed - Opened by rimangan over 1 year ago - 4 comments

#800 - feat: auto generate pr template eau

Pull Request - State: closed - Opened by edotau over 1 year ago - 5 comments

#799 - samAssembler Part 3: Haploid Call From Pileup

Pull Request - State: closed - Opened by rimangan over 1 year ago - 3 comments

#798 - WIP: gonomic cmd embed fork eau

Pull Request - State: closed - Opened by edotau over 1 year ago - 1 comment

#797 - build: Dockerfile container size optimization eau

Pull Request - State: closed - Opened by edotau over 1 year ago - 1 comment

#796 - build: Dockerfile container optimize eau

Pull Request - State: closed - Opened by edotau over 1 year ago

#795 - Sam assembly part1

Pull Request - State: closed - Opened by rimangan over 1 year ago

#794 - fix: change bedpeOverlap name eau

Pull Request - State: closed - Opened by edotau over 1 year ago - 1 comment

#793 - test: compare gene and other struct tests

Pull Request - State: closed - Opened by edotau over 1 year ago - 1 comment

#792 - changed comment line

Pull Request - State: closed - Opened by sweavs111 over 1 year ago - 3 comments

#791 - First version of geneIdToName

Pull Request - State: closed - Opened by sweavs111 over 1 year ago - 4 comments

#790 - dna: faster BasesToString

Pull Request - State: closed - Opened by dolmen over 1 year ago - 7 comments

#789 - /!\ Fix incorrect counting of 'n' in dna.Count, dna.CountMask

Pull Request - State: closed - Opened by dolmen over 1 year ago

#788 - dna: simplify Dist implementation

Pull Request - State: closed - Opened by dolmen over 1 year ago - 1 comment

#787 - dna: simplify IsLower, DefineBase

Pull Request - State: closed - Opened by dolmen over 1 year ago - 1 comment

#786 - dna: safer Extract

Pull Request - State: closed - Opened by dolmen over 1 year ago - 1 comment

#785 - geneIdToName

Pull Request - State: closed - Opened by sweavs111 over 1 year ago - 1 comment

#784 - Bedpe overlap

Pull Request - State: closed - Opened by sweavs111 over 1 year ago - 5 comments

#783 - Run gonomics cmd without source code

Pull Request - State: closed - Opened by dasnellings over 1 year ago - 3 comments

#782 - Add .bam functionality to samToWig

Pull Request - State: closed - Opened by sweavs111 over 1 year ago - 2 comments

#781 - fixing gonomics cmd

Pull Request - State: closed - Opened by dasnellings over 1 year ago - 1 comment

#778 - samAssembler Part 2: Diploid INDEL calling from Pileup

Pull Request - State: closed - Opened by rimangan over 1 year ago

#777 - SamAssembler Part 1: Diploid Variant Calling from Pileup

Pull Request - State: closed - Opened by rimangan over 1 year ago - 1 comment

#776 - Vcf context

Pull Request - State: closed - Opened by dasnellings over 1 year ago - 3 comments

#775 - mergeMultiFa

Pull Request - State: closed - Opened by rimangan over 1 year ago - 1 comment

#770 - simulateEvol with transition bias

Pull Request - State: closed - Opened by rimangan over 1 year ago - 1 comment

#765 - Modernize simulateSam

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

#764 - multiFaToVcf double counting bug

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

#763 - simulateEvol BranchLength with Indels

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

#760 - samConsensus Indel support

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

#758 - quickOrthologs

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

#757 - updates to liftCoordinates

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

#756 - bedToWig useRange

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

#753 - dnaTwoBit Rearrangement

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

#752 - BedFormat Asymmetric Padding

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

#751 - tfMatchComp

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

#750 - Motif Package

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

#749 - jaspar pfm parser

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

#747 - small changes to lastZWriter

Pull Request - State: closed - Opened by cfauci almost 2 years ago - 3 comments

#745 - wigPeaks Minima

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

#744 - wigFilter

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

#743 - Update README.md

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

#742 - multiFaToChain

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

#741 - multiFaToAxt

Pull Request - State: closed - Opened by rimangan about 2 years ago - 3 comments

#740 - FaPredictSet - lots of new tools

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

#738 - 3dGREAT Part 2: Filling the space

Pull Request - State: open - Opened by rimangan about 2 years ago - 1 comment

#737 - wigMath

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

#735 - Raven alignAnchor gorgor5

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

#734 - bedGraphToWig and wigToTrainingSet

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

#733 - bedGraph Package

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

#732 - idea for realign in Dunn

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

#731 - 3dGREAT Part 1: Laying the foundation

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

#729 - bedPeOverlap bedSelect

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

#728 - catMultiFa Ignore Names

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

#721 - first draft of hiCarOverlap. Which sorts hiCarContact data based on a…

Pull Request - State: closed - Opened by sweavs111 about 2 years ago - 1 comment
Labels: do not merge

#715 - Create bins

Pull Request - State: closed - Opened by cfauci about 2 years ago - 2 comments
Labels: do not merge

#713 - faUniq

Pull Request - State: closed - Opened by shaesimpson over 2 years ago

#704 - faFormat Rev

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

#686 - value of sam cigar for unmapped read

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

#673 - intervalOverlap does not work with bam files

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

#409 - benchmark gtf EffectPrediction vs gene EffectPrediction

Issue - State: closed - Opened by dasnellings over 3 years ago

#406 - testing coverage for interval/interval.go

Issue - State: closed - Opened by dasnellings over 3 years ago

GitHub / vertgenlab/gonomics issues and pull requests