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GitHub / bcgsc/tigmint issues and pull requests

#128 - Allow flexible installation location of long-to-linked-pe

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

#127 - Fix path. Never hardcode a path, use long-to-linked-pe from PATH instead

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

#125 - Update README.md

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

#123 - tigmint compilation issue

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

#122 - Prepare for release v1.2.10

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

#121 - Allow fastq.gz and fasta.gz inputs

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

#120 - Understanding tigmint-long outputs

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

#118 - Fix for Dockerfile smell DL3020

Pull Request - State: closed - Opened by grosa1 over 2 years ago - 1 comment

#117 - btllib dependency version update

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

#116 - yet another "make: *** No rule to make target" issue

Issue - State: closed - Opened by salvatierra8 over 2 years ago - 5 comments

#115 - Forward+reverse + long reads

Issue - State: closed - Opened by aabaricalla over 2 years ago - 4 comments
Labels: stale

#114 - Prepare for release v1.2.9

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

#113 - Use sensitive=True for ntLink mappings

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

#112 - If span=auto used with ntLink mappings, throw error

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

#111 - Prepare for release v1.2.8

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

#110 - Add option to use ntLink for mapping step

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

#109 - Fix benchmark for tigmint-long minimap2 stage

Pull Request - State: closed - Opened by lcoombe almost 3 years ago

#108 - Prepare for release v1.2.7

Pull Request - State: closed - Opened by lcoombe almost 3 years ago

#107 - typo fix in tigmint-make

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

#106 - Remove packaged btllib

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

#105 - pre-alignment

Issue - State: closed - Opened by KnudNorNielsen about 3 years ago - 2 comments
Labels: question, stale

#104 - Prepare for release v1.2.6

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

#103 - Update btllib to v1.4.1

Pull Request - State: closed - Opened by lcoombe over 3 years ago - 6 comments

#102 - Accept uncompressed file input for tigmint-long, update btllib

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

#101 - About samtools invalid option in tigmint-make arcs mode

Issue - State: closed - Opened by ClarenceHsiang over 3 years ago - 4 comments
Labels: stale

#100 - Update btllib to 1.2.0

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

#74 - Add sort option

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

#73 - Add sort options

Pull Request - State: closed - Opened by PuneetSS almost 4 years ago - 3 comments

#72 - tigmint-make: minimap2 is being called with -y argument

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

#71 - Preparing for v1.2.5 release

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

#70 - Added tigmint steps to makefile

Pull Request - State: closed - Opened by PuneetSS almost 4 years ago - 1 comment

#68 - tigmint_molecule_paf.py: TypeError: expected string or bytes-like object

Issue - State: closed - Opened by mmokrejs almost 4 years ago - 29 comments
Labels: stale

#66 - Does bin/tigmint_estimate_dist.py really work with FASTA files as well?

Issue - State: closed - Opened by mmokrejs almost 4 years ago - 5 comments

#65 - README does not list all dependencies

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

#64 - Respect PATH and few more parent env variables to speedup sorting

Pull Request - State: closed - Opened by mmokrejs almost 4 years ago - 3 comments
Labels: stale

#62 - pigz may be better replaced by bgzip

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

#61 - samtools sort may be replaced by bamsort which scales better

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

#60 - Respect $TMPDIR as anticipated by sort tool

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

#59 - Add missing dependencies and clarify ONT/PB handling

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

#58 - Tally attempted corrections

Pull Request - State: closed - Opened by janetxinli about 4 years ago

#57 - Check genome size param for span=auto

Pull Request - State: closed - Opened by janetxinli about 4 years ago

#56 - tigmint-long error

Issue - State: closed - Opened by estolle about 4 years ago - 1 comment
Labels: stale

#55 - v1.2.3 release

Pull Request - State: closed - Opened by lcoombe over 4 years ago

#54 - Update stalebot to github actions

Pull Request - State: closed - Opened by lcoombe over 4 years ago

#53 - Remove python long-to-linked code

Pull Request - State: closed - Opened by lcoombe over 4 years ago

#52 - Error : no progress of scaffolding running

Issue - State: closed - Opened by kishore556 over 4 years ago - 5 comments

#51 - Update to streaming reads for tigmint-long

Pull Request - State: closed - Opened by lcoombe over 4 years ago

#50 - Error when attempting tigmint-make arcs

Issue - State: closed - Opened by katherinedougan over 4 years ago - 2 comments
Labels: stale

#49 - clang-tidy fix

Pull Request - State: closed - Opened by MurathanGoktas over 4 years ago - 1 comment

#48 - Change azure-pipelines.yml to use conda environment

Pull Request - State: closed - Opened by lcoombe over 4 years ago

#46 - Long to linked pe cpp port

Pull Request - State: closed - Opened by jwcodee over 4 years ago

#45 - Paf tigmint molecule

Pull Request - State: closed - Opened by lcoombe over 4 years ago

#44 - tigmint-make tigmint error

Issue - State: closed - Opened by wjj666 over 4 years ago - 2 comments
Labels: question, stale

#43 - Prepare for Release Version 1.2.2

Pull Request - State: closed - Opened by janetxinli almost 5 years ago - 3 comments

#42 - Speed up and calculate dist parameter for tigmint-long

Pull Request - State: closed - Opened by janetxinli almost 5 years ago - 3 comments

#41 - Fix barcode naming bug

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

#40 - Release version 1.2.0

Pull Request - State: closed - Opened by janetxinli about 5 years ago - 2 comments

#39 - Tigmint not making cuts

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

#38 - Add tigmint-long functionality

Pull Request - State: closed - Opened by janetxinli about 5 years ago - 4 comments
Labels: enhancement

#37 - Implement azure pipeline for CI and user tests

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

#36 - Stalebot

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

#35 - tigmint parameters with multiple linked reads

Issue - State: closed - Opened by hidvegin about 5 years ago - 17 comments
Labels: question, stale

#34 - Changing /tmp location

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

#33 - Tigmint performance on large genome

Issue - State: closed - Opened by andreaswallberg almost 6 years ago - 3 comments
Labels: question

#32 - tigmint-molecule silent

Issue - State: closed - Opened by francicco almost 6 years ago - 3 comments
Labels: question

#31 - Tigmint-cut not working correctly

Issue - State: closed - Opened by majogomezhughes about 6 years ago - 1 comment
Labels: question

#30 - tigmint molecule Error 1

Issue - State: closed - Opened by darencard about 6 years ago - 4 comments
Labels: stale

#29 - tigmint-molecule

Issue - State: closed - Opened by francicco about 6 years ago - 11 comments
Labels: question

#28 - Tigmint liftover

Pull Request - State: closed - Opened by jesszha over 6 years ago - 1 comment
Labels: stale

#26 - pip installation corrupt

Issue - State: closed - Opened by schellt over 6 years ago - 5 comments
Labels: stale

#25 - support pysam 0.15.1

Pull Request - State: closed - Opened by lhui2010 over 6 years ago - 1 comment
Labels: stale

#24 - Unknown error preventing tigmint-make across multiple installation methods

Issue - State: closed - Opened by DrPintoThe2nd over 6 years ago - 2 comments

#23 - multiple intervals with the same barcode

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

#22 - Can I get the breakpoint information?

Issue - State: closed - Opened by luyang93 almost 7 years ago - 2 comments

#21 - gsed: command not found

Issue - State: closed - Opened by mossishahi almost 7 years ago - 16 comments
Labels: question

#20 - Add parameter for min reads per molec (for tigmint-molecule), fix missing molecule bug

Pull Request - State: closed - Opened by lcoombe about 7 years ago - 2 comments
Labels: stale

#19 - Liftover compatible version

Pull Request - State: closed - Opened by jesszha about 7 years ago - 1 comment
Labels: stale

#18 - Tigmint span

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

#17 - Tigmint only works when files are in working directory

Issue - State: closed - Opened by lculibrk about 7 years ago - 2 comments
Labels: stale

#16 - Tigment not found by Linuxbrew

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

#15 - Scaffolds output tigmint-arcs error

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

#14 - Runtime on finding breakpoints

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

#13 - myassembly.myreads.as0.65.nm5.molecule.tsv in null

Issue - State: closed - Opened by shameem356 over 7 years ago - 7 comments

#12 - tigmint-make errors

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

#11 - Using MinION reads

Issue - State: closed - Opened by asdcid over 7 years ago - 6 comments
Labels: stale

#10 - Provide 'make install' procedure

Issue - State: closed - Opened by mmokrejs over 7 years ago - 1 comment
Labels: enhancement

#9 - Tigmint's principle to break sequences

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

#8 - write temporary bam files

Issue - State: closed - Opened by dcopetti over 7 years ago - 16 comments
Labels: question

#7 - brew install arcs failed

Issue - State: closed - Opened by QiushiLi over 7 years ago - 2 comments
Labels: question

#6 - ImportError: /lib64/libc.so.6: version `GLIBC_2.18' not found

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

#5 - samtools sort error (sort: invalid option -- 't')

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

#3 - "No rule to make target"

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

#2 - Filter alignments in a single step

Issue - State: closed - Opened by abmudd about 8 years ago - 7 comments
Labels: enhancement