Ecosyste.ms: Issues

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GitHub / bcgsc/nanosim issues and pull requests

#99 - need more information on the Input files

Issue - State: closed - Opened by yhg926 about 4 years ago - 1 comment
Labels: question

#98 - Bug: fastq sequence and quality length different

Issue - State: closed - Opened by myhsi over 4 years ago - 7 comments
Labels: bug

#97 - keyError: 0 Simulate.py

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

#96 - Merge meta

Pull Request - State: closed - Opened by cheny19 over 4 years ago - 2 comments

#95 - Error rate of cDNA model in NanoSim

Issue - State: closed - Opened by gy-chop over 4 years ago - 3 comments

#94 - bug

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

#93 - DNA adapter in DRS

Issue - State: closed - Opened by Huanle over 4 years ago - 2 comments

#92 - memory error

Issue - State: closed - Opened by arunvv90 over 4 years ago - 5 comments

#91 - Fastq bug fix

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

#90 - Fixed README and argument documentation regarding "strand" option

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

#89 - Incorrect "strand" simulator documentation

Issue - State: closed - Opened by fairliereese over 4 years ago - 1 comment

#88 - Suggested HTSeq v0.12.4 compatibility changes

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

#87 - Whether NanoSim could generate Nanopore reads by simulation

Issue - State: open - Opened by Jingquan-Li over 4 years ago - 12 comments
Labels: enhancement, help wanted

#85 - cannot import name 'joblib' from 'sklearn.externals'

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

#84 - Polya basequal sim update

Pull Request - State: closed - Opened by cheny19 over 4 years ago

#83 - Better descriptions of input file formats

Issue - State: closed - Opened by fairliereese over 4 years ago - 3 comments

#82 - Missing file in NA12878 dRNA pre-trained model

Issue - State: closed - Opened by fairliereese over 4 years ago - 2 comments

#81 - Simulator script crashes when loading KDF pickle file

Issue - State: closed - Opened by jeizenga over 4 years ago - 11 comments

#80 - Simulate polyA tails and base qualities

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

#79 - processing

Issue - State: closed - Opened by chenyonx over 4 years ago - 6 comments

#78 - It hard to get how to use pretrained models

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

#77 - missing files in pre-trained e. coli models?

Issue - State: closed - Opened by clb21565 almost 5 years ago - 9 comments

#76 - simulator.py taking very long to run and RAM usage above 768 GB

Issue - State: closed - Opened by andrese52 almost 5 years ago - 8 comments

#75 - Does NanoSim work with PacBio?

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

#74 - Dev

Pull Request - State: closed - Opened by cheny19 almost 5 years ago

#73 - Overflow Warning

Issue - State: closed - Opened by stopalopa about 5 years ago - 1 comment

#72 - Multiprocessing using process instead of pool

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

#71 - How can I specify the Minimap2 location as it does not work?

Issue - State: closed - Opened by Kumereng about 5 years ago - 2 comments

#70 - Multiprocessing simulation stage

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

#69 - Index error fix

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

#68 - Fixed IR Bug

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

#67 - Interpreting starting- and insertion-positions

Issue - State: closed - Opened by BenjaminAlbrecht84 about 5 years ago - 3 comments

#66 - Know mean read length from training outputs

Issue - State: closed - Opened by sdjebali over 5 years ago - 1 comment

#65 - MD flag not requested

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

#64 - RAM overload

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

#63 - 'dict_ref_structure' is not defined

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

#62 - What does "WARNING! Deletion parameters may not be optimal!" mean?

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

#61 - sklearn not found

Issue - State: closed - Opened by splaisan over 5 years ago - 1 comment

#60 - example files absent

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

#59 - problem with dna_type

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

#57 - Division by zero and other edge case errors

Issue - State: closed - Opened by baraaorabi over 5 years ago - 9 comments

#56 - Merge NanoSim and Trans-NanoSim

Pull Request - State: closed - Opened by SaberHQ over 5 years ago - 2 comments

#55 - Define read length parameters

Issue - State: closed - Opened by Raymi1 over 5 years ago - 1 comment

#54 - Feature request: reporting SAM file for simulated reads

Issue - State: closed - Opened by seryrzu over 5 years ago - 3 comments
Labels: enhancement

#53 - Index out of range

Issue - State: closed - Opened by Raymi1 over 5 years ago - 6 comments

#52 - NanoSim Simulation and reference use

Issue - State: closed - Opened by ghost almost 6 years ago - 4 comments

#51 - problem ftp adress with example data

Issue - State: closed - Opened by bmx-mt almost 6 years ago - 3 comments

#50 - all reads aligned bug?

Issue - State: closed - Opened by machand almost 6 years ago - 3 comments

#49 - simulator.py gets stuck (training done on NGMLR bam file)

Issue - State: closed - Opened by sdjebali almost 6 years ago - 1 comment

#48 - Error encountered in the KernelDensity function

Issue - State: closed - Opened by lfaller-zymergen almost 6 years ago - 2 comments

#46 - model fitting

Issue - State: closed - Opened by jannaf almost 6 years ago - 3 comments

#45 - simulator.py: UnicodeDecodeError

Issue - State: closed - Opened by wdecoster almost 6 years ago - 1 comment

#44 - Make easy installable package using pip or bioconda

Issue - State: closed - Opened by wdecoster almost 6 years ago - 5 comments
Labels: enhancement

#43 - 1D simulation reads

Issue - State: closed - Opened by zhangjuncsu almost 6 years ago - 1 comment

#42 - indexerror: string index out of range

Issue - State: closed - Opened by harisankarsadasivan about 6 years ago - 4 comments

#40 - Covering the entire genome

Issue - State: closed - Opened by harisankar991 about 6 years ago - 1 comment

#39 - Change read length distribution simulated reads

Issue - State: closed - Opened by FiniDG about 6 years ago - 21 comments

#38 - Will NanoSim adapt to revisions in nanopore chemistry?

Issue - State: closed - Opened by harisankar991 about 6 years ago - 1 comment

#37 - Requirement of latest nanopore MinION reads

Issue - State: closed - Opened by harisankar991 about 6 years ago - 1 comment

#36 - Identifying if bacteria is circular or linear

Issue - State: closed - Opened by harisankar991 about 6 years ago - 1 comment

#35 - Unavailability of long Read MinION template

Issue - State: closed - Opened by harisankarsadasivan about 6 years ago - 3 comments

#34 - .log file for read_analysis.py? (Killed error)

Issue - State: closed - Opened by FiniDG about 6 years ago - 5 comments

#33 - Excuse me. You program can take consider the coverage information?

Issue - State: closed - Opened by xiangni128182 over 6 years ago - 3 comments

#32 - power overflow

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

#31 - Read length distribution unexpected peaks

Issue - State: closed - Opened by GeorgiaBreckell over 6 years ago - 9 comments

#30 - Read Simulation: reference length limitation?

Issue - State: closed - Opened by ampodu over 6 years ago - 4 comments

#29 - "Index out of range" Error in read_analysis.py

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

#28 - Minimap2 vs Last running time

Issue - State: closed - Opened by npavlovikj over 6 years ago - 5 comments

#27 - NanoSim v2.0

Pull Request - State: closed - Opened by SaberHQ over 6 years ago
Labels: enhancement

#26 - using nanosim to generate fastq files?

Issue - State: closed - Opened by nick-youngblut over 6 years ago - 2 comments
Labels: enhancement

#25 - not python>=2.6 compatible

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

#24 - Enable user-specified seed for PRNG

Pull Request - State: closed - Opened by abremges almost 7 years ago - 1 comment

#23 - What will NanoSim do when it encounters NNNN region?

Issue - State: closed - Opened by cytham almost 7 years ago - 1 comment

#22 - Calculate length of simulated reads

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

#21 - nanopore data

Issue - State: closed - Opened by rojinsafavi about 7 years ago - 1 comment

#20 - Using "sam" alignments with "read_analysis.py"

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

#19 - Changes to handle large reference files

Pull Request - State: closed - Opened by haghshenas over 7 years ago - 1 comment

#18 - Does NanoSim works for large genomes?

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

#17 - Progress bar

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

#16 - Maybe a bug in the error_list function

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

#15 - Creata a PyPI package

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

#14 - Let LAST use all available CPU cores

Pull Request - State: closed - Opened by karel-brinda almost 8 years ago - 2 comments

#13 - Improve the example

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

#12 - Python 3

Pull Request - State: closed - Opened by karel-brinda almost 8 years ago - 4 comments

#11 - Training model failure

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

#10 - Options min_len and max_len throw an error or do not work

Issue - State: closed - Opened by mw55309 almost 8 years ago - 1 comment

#9 - Readnaming consistency when simulating perfect reads.

Pull Request - State: closed - Opened by jasperlinthorst about 8 years ago - 1 comment

#7 - Add option to control error percentage

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

#6 - Simulator fails using different reads

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

#5 - ecdf files are incorrectly written in head_align_tail_dist.py if max_length <25000

Issue - State: closed - Opened by psarkozy over 8 years ago - 4 comments
Labels: bug

#4 - Perfect option gives error

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

#3 - Read Output ID

Issue - State: closed - Opened by JustinChu almost 9 years ago - 1 comment
Labels: question

#2 - Unaligned read fraction is sampled from only a single strand of refernce

Issue - State: closed - Opened by JustinChu almost 9 years ago - 1 comment
Labels: bug

#1 - Be able to specify threads with when using LAST

Issue - State: closed - Opened by JustinChu almost 9 years ago - 2 comments
Labels: enhancement