Ecosyste.ms: Issues

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GitHub / jts/nanopolish issues and pull requests

#100 - nanopolish variants --consensus fails with assertion error

Issue - State: closed - Opened by joshualoving almost 8 years ago - 12 comments

#99 - make test fails in new Docker container

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

#98 - Extract polished reads

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

#97 - core dumped

Issue - State: closed - Opened by igordot almost 8 years ago - 15 comments
Labels: bug

#96 - Unable to extract sequences

Issue - State: closed - Opened by matiasirazoqui almost 8 years ago - 24 comments

#95 - nanopolish variants threads

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

#94 - nanopolish variants --consensus argument

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

#93 - alba-core basecalling causes assertion to faill

Issue - State: closed - Opened by bernhard314 almost 8 years ago - 3 comments

#92 - added option to extract fastq

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

#91 - Support region strings like "41,000,000"

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

#90 - nanopolish extract fast5 into fastq

Issue - State: closed - Opened by yuhongning almost 8 years ago - 7 comments

#89 - Raw data

Issue - State: closed - Opened by gegberts almost 8 years ago - 7 comments

#88 - --models unrecognised option

Issue - State: closed - Opened by PDSc0tt almost 8 years ago - 19 comments

#87 - Nanopolish eventalign Error: unknown model:

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

#86 - R7.3

Issue - State: closed - Opened by JohnUrban almost 8 years ago - 26 comments

#84 - SegFault for 'nanopolish variants --consensus' without window parameter

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

#82 - No extract on reads with no events

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

#81 - consensus fails to go to completion

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

#80 - unable to make

Issue - State: closed - Opened by proukakis almost 8 years ago - 29 comments

#79 - nanopolish extract

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

#78 - R7 and R9 samples

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

#77 - python3 failed to run the program

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

#76 - problem with bam generated with nanopolish

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

#75 - HDF5 issue

Issue - State: closed - Opened by flauro almost 8 years ago - 10 comments

#74 - Consensus/variant caller hang up

Issue - State: closed - Opened by zascavage about 8 years ago - 10 comments

#73 - Corrupt read, but which one?

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

#72 - Error: dereferencing pointer to incomplete type 'struct passwd'

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

#71 - Enable calling methylation from 1D reads

Issue - State: closed - Opened by jts about 8 years ago - 1 comment

#70 - HDF5 error

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

#68 - Previous versions of nanopolish not compiling

Issue - State: closed - Opened by shao4 about 8 years ago - 7 comments

#67 - software aborts when lowercase letters are in the reference sequences

Issue - State: closed - Opened by rachelglover about 8 years ago - 2 comments
Labels: bug

#66 - `read_var` should be scaled down by `read_scale`

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

#65 - compile failure on 0.5.0

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

#64 - Option to use locally installed EIGEN package

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

#63 - eventalign silently does not work when the input bam file is not indexed

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

#62 - Error: nanopolish_profile_hmm.cpp

Issue - State: closed - Opened by jaesvi about 8 years ago - 2 comments

#61 - Update to latest fast5 release (0.5.6)

Pull Request - State: closed - Opened by 0xaf1f about 8 years ago

#60 - error: could not find fast5 path

Issue - State: closed - Opened by johnsolk about 8 years ago - 13 comments

#59 - Nanopolish consensus won't run to completion or on subsequence

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

#58 - Using Nanopolish with R9 reads

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

#57 - Build issues with GCC6

Issue - State: closed - Opened by 0xaf1f about 8 years ago - 4 comments

#56 - Calculate L1 residual when recalibrating model, return it as a parameter

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

#55 - Calculate L1 residual when recalibrating model, return it as a parameter

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

#54 - [fai_fetch_seq] The sequence "" not found

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

#53 - Add capability to recalibrate holding drift=0

Pull Request - State: closed - Opened by ljdursi over 8 years ago - 1 comment

#52 - HDF5-DIAG: Error detected in HDF5

Issue - State: closed - Opened by Ecogpr over 8 years ago - 3 comments

#51 - /bin/bash: nanopolish: command not found

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

#50 - no @SQ lines in the header. Missing header?

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

#49 - Unitig split into multiple contigs after nanopolish

Issue - State: closed - Opened by ml12220 over 8 years ago - 3 comments

#48 - Update Dockerfile make invocation

Pull Request - State: closed - Opened by ljdursi over 8 years ago

#47 - make: *** No rule to make target `libhdf5.install'. Stop.

Issue - State: closed - Opened by proukakis over 8 years ago - 21 comments

#46 - Create full VCF header with "nanopolish variants" module?

Issue - State: closed - Opened by tomsasani over 8 years ago - 3 comments

#45 - Can SQK-MAP005 and SQK-MAP006 data be used at the same time?

Issue - State: closed - Opened by hjjansen over 8 years ago - 2 comments

#44 - samtools -f option is removed

Issue - State: closed - Opened by hjjansen over 8 years ago - 6 comments

#43 - [fai_fetch_seq] The sequence "tig00000000" not found : Error while polishing

Issue - State: closed - Opened by athulmenon over 8 years ago - 5 comments

#42 - Fix cut-and-paste error in usage documentation

Pull Request - State: closed - Opened by druvus over 8 years ago - 1 comment

#41 - clean up warnings

Pull Request - State: closed - Opened by mateidavid over 8 years ago

#40 - Errors while running nanopolish. Polished result of 0 bytes!

Issue - State: closed - Opened by athulmenon over 8 years ago - 5 comments

#39 - seg fault/no-output with consensus

Issue - State: closed - Opened by kpalin over 8 years ago - 3 comments

#38 - Release

Issue - State: closed - Opened by druvus over 8 years ago - 4 comments

#37 - Multiple Rounds of polishing

Issue - State: closed - Opened by jarrodscott over 8 years ago - 6 comments

#36 - Suggested Pipeline Help

Issue - State: closed - Opened by jarrodscott over 8 years ago - 3 comments

#35 - Bring master up to date with alternative models, fix some bugs

Pull Request - State: closed - Opened by nickloman over 8 years ago

#34 - Assertion `!alignments.empty()' failed.

Issue - State: closed - Opened by jts over 8 years ago - 1 comment

#33 - Use angle-bracket includes to allow flexibile placement of dependencies

Pull Request - State: closed - Opened by 0xaf1f over 8 years ago - 5 comments

#31 - Second round of nanopolishing

Issue - State: closed - Opened by rmcolq almost 9 years ago - 6 comments

#30 - nanopolish consensus asserts on short contigs

Issue - State: closed - Opened by jts almost 9 years ago - 1 comment

#29 - C++11 threads

Pull Request - State: closed - Opened by mateidavid almost 9 years ago

#28 - test training

Pull Request - State: closed - Opened by mateidavid almost 9 years ago

#27 - enable use of multisets for logsums via compile define

Pull Request - State: closed - Opened by mateidavid almost 9 years ago

#26 - gaussian training in logspace

Pull Request - State: closed - Opened by mateidavid almost 9 years ago - 1 comment

#25 - train sd_mean

Pull Request - State: closed - Opened by mateidavid almost 9 years ago - 1 comment

#24 - Error running nanopolish on MAP006 dataset

Issue - State: closed - Opened by kkrizanovic almost 9 years ago - 5 comments

#23 - Error running (newest) nanopolish

Issue - State: closed - Opened by rmcolq almost 9 years ago - 5 comments

#22 - Barcoding compatibility?

Issue - State: closed - Opened by tantrev almost 9 years ago - 2 comments

#21 - Scorereads

Pull Request - State: closed - Opened by ljdursi almost 9 years ago

#20 - Model stdv

Pull Request - State: closed - Opened by mateidavid about 9 years ago

#19 - fixed CXX/CPP flags; rm -f

Pull Request - State: closed - Opened by mateidavid about 9 years ago

#18 - Fix Makefile compilation flags

Issue - State: closed - Opened by jts about 9 years ago - 1 comment

#17 - Usage instructions clarification

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

#16 - Missing omp.h on mac

Issue - State: closed - Opened by PeteHaitch about 9 years ago - 2 comments

#15 - added option to print read names instead of indexes

Pull Request - State: closed - Opened by mateidavid about 9 years ago

#14 - Osx

Pull Request - State: closed - Opened by jts about 9 years ago

#13 - refactoring alignment

Pull Request - State: closed - Opened by jts about 9 years ago

#12 - Refactor

Pull Request - State: closed - Opened by jts about 9 years ago

#11 - Consensus vcf

Pull Request - State: closed - Opened by jts about 9 years ago

#10 - consensus-preprocess.pl: Use #!/usr/bin/env perl

Pull Request - State: closed - Opened by sjackman over 9 years ago - 2 comments

#9 - problem opening h5Fopen

Issue - State: closed - Opened by lfaino over 9 years ago - 4 comments

#8 - level of parallelism in eventalign

Issue - State: closed - Opened by vadimzalunin over 9 years ago - 2 comments

#7 - default log level is verbose

Issue - State: closed - Opened by vadimzalunin over 9 years ago - 2 comments

#6 - Added dockerfile for easy requirements install

Pull Request - State: closed - Opened by Phelimb over 9 years ago - 3 comments

#5 - Fix make consensus

Pull Request - State: closed - Opened by robegan21 over 9 years ago - 2 comments

#4 - missing build.sh

Issue - State: closed - Opened by davebiffuk over 9 years ago - 2 comments

#3 - Does not list C++11 compiler as a dependency

Issue - State: closed - Opened by adamnovak over 9 years ago - 1 comment

#2 - Please tag a stable release of version 0.2.0

Issue - State: closed - Opened by sjackman over 9 years ago - 3 comments

#1 - Data availability

Issue - State: closed - Opened by alexbw over 9 years ago - 4 comments