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
#85 - nanopolish: src/alignment/nanopolish_anchor.cpp:141: HMMRealignmentInput build_input_for_region(const string&, const string&, const Fast5Map&, const string&, int, int, int, const string&): Assertion `template_idx != -1 && (!sr.has_events_for_strand(C_IDX) || complement_idx != -1)' failed.
Issue -
State: closed - Opened by JohnUrban almost 8 years ago
- 10 comments
#84 - SegFault for 'nanopolish variants --consensus' without window parameter
Issue -
State: closed - Opened by ChristianBrossette almost 8 years ago
- 4 comments
#83 - Alphabet error: ./src/common/nanopolish_alphabet.h:173... Assertion `IUPAC::isValid(out[i])' failed
Issue -
State: closed - Opened by gringer 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
#69 - Assertion `read->read_type != SRT_2D' failed. nanopolish_train_poremodel_from_basecalls
Issue -
State: closed - Opened by gkutish 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
#32 - Enable recalibration of var, which actually scales SDs, by taking sqrt(var)
Pull Request -
State: closed - Opened by ljdursi over 8 years ago
#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
#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