karel-brinda/rnftools issues and pull requests

#77 - Wrong read name - more than 2 reads in tuple?

Issue - State: open - Opened by rsuchecki over 5 years ago

#76 - RNF spec inaccessible

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

#75 - No output from rnftools.mishmash.DwgSim

Issue - State: open - Opened by zihhuafang almost 6 years ago - 2 comments

#74 - gnuplot error

Issue - State: open - Opened by alperyilmaz almost 6 years ago - 1 comment
Labels: bug

#73 - Don't use absolute paths in input: / output:

Issue - State: open - Opened by karel-brinda over 6 years ago

#72 - Error Producing LAVEnder Report

Issue - State: open - Opened by RSherman15 over 6 years ago - 6 comments

#71 - Add support for VCF output of DWGsim

Pull Request - State: closed - Opened by karel-brinda over 6 years ago

#70 - DWGSim hangs, then deletes files when job is killed

Issue - State: closed - Opened by RSherman15 over 6 years ago - 3 comments

#69 - Pickling Error

Issue - State: open - Opened by RSherman15 over 6 years ago - 5 comments

#68 - ArtIllumina's number_of_read_tuples does not work

Issue - State: open - Opened by simonepignotti over 6 years ago - 1 comment

#67 - max ( read_nb, (coverage * genome_size / read_len) )

Pull Request - State: open - Opened by simonepignotti over 6 years ago

#66 - Devel linux build fails on Travis

Issue - State: open - Opened by simonepignotti over 6 years ago

#65 - Use number_of_read_tuples param when greater than coverage's

Issue - State: open - Opened by simonepignotti over 6 years ago

#64 - [dwgsim] 0 reads error for low coverage and short genomes

Issue - State: closed - Opened by simonepignotti over 6 years ago - 1 comment

#63 - Add support for curesim random reads

Pull Request - State: closed - Opened by karel-brinda over 7 years ago

#62 - Mark random reads that are mixed in by simulator in LRN (genome ID)

Issue - State: closed - Opened by sibyllewohlgemuth over 7 years ago - 5 comments

#61 - CIGAR extension in suffix of LRN

Issue - State: open - Opened by sibyllewohlgemuth over 7 years ago

#60 - Subseq

Pull Request - State: closed - Opened by karel-brinda over 7 years ago

#59 - Update

Pull Request - State: closed - Opened by karel-brinda over 7 years ago

#58 - Minor update

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

#57 - RNFtools resurrection

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

#56 - rnftools liftover - AssertionError - assert (last_right1 is None) or (last_right1==left1)

Issue - State: open - Opened by karel-brinda about 8 years ago - 1 comment
Labels: bug

#55 - Fix subparser bug in cli variant of rnftools

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

#54 - program rnftools: argparse does not work

Issue - State: closed - Opened by karel-brinda over 8 years ago - 1 comment
Labels: bug

#53 - Dwgsim - error when 0 simulated reads

Issue - State: open - Opened by karel-brinda over 8 years ago
Labels: bug

#52 - Local variable 'single_reads_statistics' referenced before assignment

Issue - State: open - Opened by karel-brinda over 8 years ago - 1 comment
Labels: bug

#51 - question: how to override mapper parameters?

Issue - State: closed - Opened by astewart-twist almost 9 years ago - 2 comments
Labels: question

#50 - Dockerization

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

#49 - Any idea what this error

Issue - State: closed - Opened by astewart-twist almost 9 years ago - 15 comments

#48 - Problem with mapper evaluation example?

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

#47 - Pdf

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

#46 - RNFtools 0.2.7

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

#45 - RNFtools 0.2.6

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

#44 - RNFtools 0.2.5

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

#43 - LAVEnder: text log

Issue - State: closed - Opened by karel-brinda about 9 years ago
Labels: wontfix, feature-request

#42 - RNFtools 0.3

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

#41 - Errors when Snakefile changed and old experiment directory kept

Issue - State: open - Opened by karel-brinda about 9 years ago - 1 comment
Labels: bug

#40 - Wrong RNF names in simulations using DwgSim

Issue - State: open - Opened by karel-brinda about 9 years ago
Labels: bug

#39 - _open() takes at least 1 positional argument (0 given)

Issue - State: closed - Opened by karel-brinda about 9 years ago - 1 comment
Labels: bug

#38 - 0.2.3.1

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

#37 - Prevent number_of_read_tuples being equal to 0

Issue - State: closed - Opened by karel-brinda over 9 years ago - 1 comment
Labels: bug

#36 - MIShmash: support for naming samples and additional RNF comments

Issue - State: open - Opened by karel-brinda over 9 years ago
Labels: feature-request

#35 - RNFtools 0.2.3

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

#34 - FAQ - git behind proxy

Issue - State: closed - Opened by karel-brinda over 9 years ago
Labels: enhancement

#33 - Art - error when coverage is too low

Issue - State: closed - Opened by karel-brinda over 9 years ago
Labels: bug

#32 - FqMerger - too many open files

Issue - State: open - Opened by karel-brinda over 9 years ago - 2 comments
Labels: bug

#31 - MIShmash option: remove auxiliary directory

Issue - State: open - Opened by karel-brinda over 9 years ago
Labels: enhancement

#30 - Position of key for overall graphs

Issue - State: closed - Opened by karel-brinda over 9 years ago
Labels: enhancement

#29 - Correct example in RNF spec (take it from the RNF paper)

Issue - State: open - Opened by karel-brinda over 9 years ago
Labels: bug

#28 - Minor update

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

#27 - MIShmas: text log

Issue - State: open - Opened by karel-brinda over 9 years ago
Labels: feature-request

#26 - Add a unit test for rnftools sam2roc

Issue - State: open - Opened by karel-brinda over 9 years ago
Labels: enhancement

#25 - Add unit tests for rnftools liftover

Issue - State: open - Opened by karel-brinda over 9 years ago
Labels: enhancement

#24 - "rnftools liftover" - id of genome should be required

Issue - State: closed - Opened by karel-brinda over 9 years ago
Labels: bug

#23 - Support for curve style functions for LAVEnder graphs

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

#22 - rnftools liftover

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

#21 - Range autoadjustment

Issue - State: closed - Opened by karel-brinda over 9 years ago - 1 comment
Labels: enhancement

#20 - Improvements for HTML reports produced by LAVEnder

Issue - State: closed - Opened by karel-brinda over 9 years ago
Labels: enhancement

#19 - Several improvements, refactoring

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

#18 - Support for Flux

Issue - State: open - Opened by karel-brinda over 9 years ago
Labels: feature-request

#17 - Tests of correctness of produced RNF names

Issue - State: closed - Opened by karel-brinda over 9 years ago
Labels: enhancement

#16 - More definitions of correctly mapped reads

Issue - State: open - Opened by karel-brinda over 9 years ago
Labels: enhancement

#15 - GnuPlot without PDF terminal

Issue - State: closed - Opened by karel-brinda over 9 years ago - 2 comments
Labels: bug

#14 - Version 0.2.0b0

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

#13 - Add a Gitter chat badge to README.rst

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