arq5x/poretools issues and pull requests

#100 - python3 support?

Issue - State: open - Opened by pfaucon about 8 years ago - 9 comments

#99 - select different basecall_1D_00X sets for fastq/fasta export

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

#98 - Trying to get times of reads in fail file

Issue - State: open - Opened by EpiBlake about 8 years ago - 1 comment

#97 - [documentation question] what are facets?

Issue - State: open - Opened by cjprybol about 8 years ago

#96 - v0.6.0 for windows not released

Issue - State: open - Opened by pancheto about 8 years ago - 2 comments

#95 - poretools hist - indexError: list index out of range

Issue - State: closed - Opened by falkomathes about 8 years ago

#94 - Use the full GPG key ID.

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

#93 - poretools: command not found

Issue - State: open - Opened by ShaoyuanTan about 8 years ago - 1 comment

#92 - R9 fix

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

#91 - unable to use events function with new R9 data

Issue - State: closed - Opened by EpiBlake about 8 years ago

#90 - potential fix for #78

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

#89 - readstats module is broken?

Issue - State: open - Opened by dbtara over 8 years ago

#88 - Added notification that fastq and fasta files are send to standard ou…

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

#87 - Tarfile based fastq extraction

Issue - State: open - Opened by timp0 over 8 years ago - 2 comments

#86 - New type: best

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

#85 - Dockerfile fixes for matplotlib and cython modules

Pull Request - State: open - Opened by omsai over 8 years ago - 1 comment

#84 - docker build fails

Issue - State: open - Opened by Jeltje over 8 years ago - 5 comments

#83 - no .jpg nor .png allowed for qualpos

Issue - State: open - Opened by pancheto over 8 years ago - 2 comments

#82 - Interpretation of the qualpos

Issue - State: open - Opened by athulmenon over 8 years ago - 3 comments

#81 - poretools times only measures template read times

Issue - State: open - Opened by timp0 over 8 years ago

#80 - 0.5.1 retagged?

Issue - State: open - Opened by tdsmith over 8 years ago - 1 comment

#79 - --theme-bw not working

Issue - State: open - Opened by igordot over 8 years ago

#78 - couldn't connect to display error

Issue - State: open - Opened by igordot over 8 years ago - 4 comments

#77 - KeyError in yield_plot and occupancy

Issue - State: open - Opened by sshs21 over 8 years ago - 4 comments

#76 - TODO before next 0.5.1 release

Issue - State: closed - Opened by arq5x over 8 years ago

#75 - add appveyor

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

#74 - Conversion to Fasta generates same read names

Issue - State: open - Opened by athulmenon over 8 years ago - 2 comments

#73 - index function and file I/O exception handling

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

#72 - Getting Could not extract template events Warning when trying to squiggle

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

#71 - Issue with "Fast5File.py"

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

#70 - poretools yield_plot fails with newer 'ggplot2 2.0.0' R pacakge

Issue - State: open - Opened by agordon almost 9 years ago - 1 comment

#69 - Watchdog deps for OSX (no XCode)

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

#68 - Seg fault with latest R

Issue - State: closed - Opened by noncodo almost 9 years ago

#67 - Add support for WIMP

Issue - State: open - Opened by nickloman almost 9 years ago - 3 comments

#66 - Occupancy, yield and hist error

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

#65 - fastq_path 1D change

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

#64 - Standardizing read names

Issue - State: closed - Opened by mw55309 about 9 years ago - 5 comments

#63 - Standardising FASTA/Q headers

Issue - State: closed - Opened by mw55309 about 9 years ago - 6 comments

#62 - R Minimum Version Mismatch

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

#61 - Metrichor can write new basecalls with alternative serial numbers

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

#60 - explanation of result of events output

Issue - State: open - Opened by km1500 over 9 years ago

#59 - Added functionality to extract read metadata from the fast5 files

Pull Request - State: closed - Opened by Phelimb over 9 years ago - 1 comment

#58 - Added support for extracting pre-basecalled events

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

#57 - get rid of rpy2 deps

Pull Request - State: closed - Opened by brentp over 9 years ago - 7 comments

#56 - max read length

Pull Request - State: closed - Opened by ml4wc over 9 years ago - 3 comments

#55 - Fast5File destructor doesn't close files

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

#54 - Full 2D (2d_hq) reads incorrectly calculated by is_high_quality function

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

#53 - Remove R dependencies

Issue - State: closed - Opened by gawbul over 9 years ago - 20 comments

#52 - Error in find_read_number_block

Issue - State: open - Opened by kdurbrow over 9 years ago - 3 comments

#51 - Add support for new read UUID field in FAST5 files

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

#50 - Barcode sensitive FASTQ extract

Issue - State: open - Opened by timp0 over 9 years ago - 2 comments

#49 - More intelligent tmpdirs.

Issue - State: open - Opened by arq5x over 9 years ago - 1 comment

#48 - Add support for determining translocation speed to poretools

Issue - State: open - Opened by nickloman over 9 years ago

#47 - Depends checking

Issue - State: open - Opened by mcnelsonphd over 9 years ago - 2 comments

#46 - ImportError: No module named 'scripts'

Issue - State: closed - Opened by burkesquires almost 10 years ago

#45 - Added two more necessary packages for Mac OS X install instructions

Pull Request - State: closed - Opened by neurons almost 10 years ago - 4 comments

#44 - Add a Bitdeli Badge to README

Pull Request - State: closed - Opened by bitdeli-chef almost 10 years ago

#43 - Problem with pip install on Mac

Issue - State: closed - Opened by nickloman about 10 years ago - 4 comments

#42 - recurse into dirs same as into tarball

Pull Request - State: open - Opened by misha-at-genestack about 10 years ago - 1 comment

#41 - Consider moving to ggvis

Issue - State: open - Opened by nickloman about 10 years ago - 2 comments

#40 - Recurse into directories

Issue - State: open - Opened by nickloman about 10 years ago - 1 comment

#39 - API example for documentation.

Issue - State: closed - Opened by arq5x about 10 years ago

#38 - Qual v pos

Pull Request - State: closed - Opened by JohnUrban about 10 years ago - 1 comment

#37 - Events table format has changed

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

#36 - Data concentration plot

Pull Request - State: open - Opened by JohnUrban about 10 years ago - 5 comments

#35 - Feature n50

Pull Request - State: closed - Opened by JohnUrban about 10 years ago - 1 comment

#34 - squiggle to create plots in current dir

Pull Request - State: closed - Opened by misha-at-genestack about 10 years ago

#33 - Tarball iterator

Pull Request - State: closed - Opened by misha-at-genestack about 10 years ago - 1 comment

#32 - Support multiple directories on command line

Issue - State: open - Opened by nickloman about 10 years ago

#31 - Bash completion file.

Pull Request - State: closed - Opened by charles-plessy about 10 years ago

#30 - Galaxy wrappers.

Issue - State: open - Opened by arq5x about 10 years ago

#29 - hist plot like in MinKNOW

Issue - State: open - Opened by nickloman about 10 years ago

#28 - Identity v. Length plot

Issue - State: open - Opened by arq5x about 10 years ago

#27 - Read stats break down by fwd, rev, 2D

Issue - State: closed - Opened by nickloman about 10 years ago - 1 comment

#26 - Occupancy plot

Issue - State: open - Opened by nickloman about 10 years ago - 17 comments

#25 - added Dockerfile for docker build; documented docker build

Pull Request - State: closed - Opened by stephenturner about 10 years ago - 1 comment

#24 - Put poretools on PyPi

Issue - State: open - Opened by arq5x about 10 years ago

#23 - added docker container

Pull Request - State: closed - Opened by stephenturner over 10 years ago - 1 comment

#22 - Problem loading libhdf5

Issue - State: closed - Opened by flashton2003 over 10 years ago - 2 comments

#21 - Problem with HDF5 dependency

Issue - State: closed - Opened by flashton2003 over 10 years ago - 2 comments

#20 - Squiggle/Output

Issue - State: open - Opened by timp0 over 10 years ago - 1 comment

#19 - --saveas doesn't work on squiggle

Issue - State: closed - Opened by stephenturner over 10 years ago - 2 comments

#18 - added link to AMI

Pull Request - State: closed - Opened by stephenturner over 10 years ago

#17 - set default cran mirror for package installations

Pull Request - State: closed - Opened by stephenturner over 10 years ago

#16 - fix emdash with --

Pull Request - State: closed - Opened by stephenturner over 10 years ago

#15 - Add fwd/rev/2D stats to poretools stats

Issue - State: closed - Opened by nickloman over 10 years ago - 1 comment

#14 - Extract 'high quality' reads

Issue - State: closed - Opened by nickloman over 10 years ago - 1 comment

#13 - Add support for cDNA workflow

Issue - State: open - Opened by nickloman over 10 years ago

#12 - Swap pytables for h5py

Issue - State: closed - Opened by nickloman over 10 years ago

#11 - Remove leading '@' in fasta headers

Issue - State: closed - Opened by druvus over 10 years ago - 1 comment

#10 - No module named common

Issue - State: closed - Opened by gibiansky over 10 years ago - 1 comment

#9 - Make an IPython notebook demonstrating functionality.

Issue - State: closed - Opened by arq5x over 10 years ago

#8 - Consider h5py over pytables

Issue - State: closed - Opened by arq5x over 10 years ago - 1 comment

#7 - Allow the events tool to create a wiggle plot of a single FAST5

Issue - State: closed - Opened by arq5x over 10 years ago - 1 comment

#6 - combine FAST5 files from a single run

Issue - State: closed - Opened by arq5x over 10 years ago - 9 comments

#5 - Need a proper unit testing suite.

Issue - State: open - Opened by arq5x over 10 years ago

#4 - Use R for plots via rpy2.

Issue - State: closed - Opened by arq5x over 10 years ago - 1 comment

#3 - How do to deal with corrupt HDF5 files?

Issue - State: closed - Opened by nickloman over 10 years ago - 4 comments

#2 - How best to handle runs with _many_ fast5 files?

Issue - State: closed - Opened by arq5x over 10 years ago - 3 comments

#1 - Missing test data

Issue - State: open - Opened by mdshw5 over 10 years ago - 14 comments

GitHub / arq5x/poretools issues and pull requests