Issues · OBITools / OBITools3

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#56 · opened Sep 19, 2016 by Celine Mercier bug
- CLOSED
- 0
updated Nov 03, 2017
Link quality column to a sequence column

#55 · opened May 30, 2016 by Eric Coissac enhancement
- CLOSED
- 0
updated Nov 03, 2017
Bug when opening an uncompressed file

#54 · opened May 21, 2016 by Eric Coissac bug
- CLOSED
- 1
updated Nov 03, 2017
Column truncating

#53 · opened May 20, 2016 by Celine Mercier discussion
- CLOSED
- 1
updated Nov 03, 2017
Obi import bug: last sequence of fasta files

#52 · opened May 20, 2016 by Celine Mercier bug
- CLOSED
- 1
updated Nov 03, 2017
Quality columns with vectors (multiple elements per line)

#51 · opened May 20, 2016 by Celine Mercier discussion
- CLOSED
- 1
updated Nov 03, 2017
NA value for uint8_t arrays

#50 · opened May 20, 2016 by Celine Mercier discussion
- CLOSED
- 1
updated Nov 03, 2017
Bug during a second import

#49 · opened May 10, 2016 by Eric Coissac bug
- CLOSED
- 1
updated Nov 03, 2017
Global alignment function

#48 · opened May 09, 2016 by Celine Mercier feature
- CLOSED
- 1
updated Nov 03, 2017
Handling of view name uniqueness

#47 · opened May 02, 2016 by Celine Mercier bug discussion
- CLOSED
- 0
updated Nov 03, 2017
Immutable obligatory indexers

#46 · opened May 02, 2016 by Celine Mercier discussion
- CLOSED
- 0
updated Nov 03, 2017
obi commands: dms and view options

#45 · opened May 02, 2016 by Celine Mercier feature
- CLOSED
- 0
updated Nov 03, 2017
obi import: NA values

#44 · opened May 02, 2016 by Celine Mercier discussion enhancement
- CLOSED
- 1
updated Nov 03, 2017
Handling of obligatory columns

#43 · opened May 02, 2016 by Celine Mercier discussion
- CLOSED
- 1
updated Nov 03, 2017
Columns storing sequence quality

#41 · opened May 02, 2016 by Celine Mercier feature
- CLOSED
- 0
updated Nov 03, 2017
Commands to call the different obitools

#39 · opened Feb 24, 2016 by Celine Mercier feature
- CLOSED
- 0
updated Nov 03, 2017
C functions to apply a logical comparison to a column

#36 · opened Feb 24, 2016 by Celine Mercier feature
- CLOSED
- 1
updated Nov 03, 2017
C functions to compare vectors of booleans

#35 · opened Feb 24, 2016 by Celine Mercier feature
- CLOSED
- 1
updated Nov 03, 2017
View comments

#34 · opened Feb 24, 2016 by Celine Mercier feature
- CLOSED
- 1
updated Jul 02, 2022
View-specific names for columns

#33 · opened Feb 24, 2016 by Celine Mercier feature
- CLOSED
- 1
updated Nov 03, 2017
Uniform Resource Identifier

#57 · opened Jul 06, 2017 by Celine Mercier discussion documentation feature
- CLOSED
- 0
updated Apr 10, 2019
obi commands: 'skip on error' option

#42 · opened May 02, 2016 by Celine Mercier feature
- CLOSED
- 1
updated Apr 10, 2019
Installation problems on linux systems

#40 · opened Apr 27, 2016 by Celine Mercier bug
- CLOSED
- 0
updated Apr 10, 2019
Implement taxonomy handling

#38 · opened Feb 24, 2016 by Celine Mercier feature
- CLOSED
- 1
updated Apr 10, 2019
Error handling when operating on a new view

#37 · opened Feb 24, 2016 by Celine Mercier enhancement
- CLOSED
- 1
updated Apr 10, 2019
cbind and rbind equivalents for views

#32 · opened Feb 24, 2016 by Celine Mercier feature
- 2
updated Jan 18, 2020
Including Doxygen doc in Sphinx doc using Breathe

#28 · opened Nov 16, 2015 by Celine Mercier Updating the documentation documentation
- 0
updated Nov 03, 2017
Multithreading compliance

#24 · opened Nov 16, 2015 by Celine Mercier enhancement
- CLOSED
- 0
updated Apr 10, 2019
Testing on different systems

#23 · opened Nov 16, 2015 by Celine Mercier Testing
- CLOSED
- 0
updated Apr 10, 2019
Cython sphinx documentation

#18 · opened Oct 02, 2015 by Celine Mercier Updating the documentation documentation
- CLOSED
- 0
updated Apr 10, 2019
Update the sphinx documentation

#17 · opened Oct 02, 2015 by Celine Mercier Updating the documentation documentation
- 0
updated Apr 10, 2019
Classes for nucleotide sequences

#31 · opened Feb 24, 2016 by Celine Mercier feature
- CLOSED
- 1
updated Aug 17, 2018
Views for nucleotide sequences

#30 · opened Feb 24, 2016 by Celine Mercier feature
- CLOSED
- 1
updated Aug 17, 2018
Arrays referring to data

#29 · opened Nov 23, 2015 by Celine Mercier discussion
- CLOSED
- 1
updated Aug 17, 2018
Obierrnos

#27 · opened Nov 16, 2015 by Celine Mercier discussion
- CLOSED
- 0
updated Aug 17, 2018
OBIDMS Views

#26 · opened Nov 16, 2015 by Celine Mercier OBIDMS Views feature
- CLOSED
- 1
updated Aug 17, 2018
Handling of DNA sequences

#25 · opened Nov 16, 2015 by Celine Mercier Handling of DNA sequences feature
- CLOSED
- 1
updated Aug 17, 2018
Better unit tests

#22 · opened Nov 16, 2015 by Celine Mercier Testing enhancement
- CLOSED
- 2
updated Aug 17, 2018
Unit testing

#21 · opened Oct 02, 2015 by Celine Mercier feature
- CLOSED
- 1
updated Aug 17, 2018
Enlarging a mmapped region

#20 · opened Oct 02, 2015 by Celine Mercier discussion
- CLOSED
- 1
updated Aug 17, 2018
'Writable' attribute of a column

#19 · opened Oct 02, 2015 by Celine Mercier discussion
- CLOSED
- 3
updated Aug 17, 2018
Checking endianness

#16 · opened Oct 02, 2015 by Celine Mercier discussion
- CLOSED
- 1
updated Aug 17, 2018
Error value for functions returning size_t

#15 · opened Oct 02, 2015 by Celine Mercier discussion
- CLOSED
- 1
updated Aug 17, 2018
Closing OBIDMS, column directories, columns, and arrays

#14 · opened Oct 02, 2015 by Celine Mercier discussion
- CLOSED
- 4
updated Aug 17, 2018
obi_errno initialization

#13 · opened Oct 02, 2015 by Celine Mercier discussion
- CLOSED
- 1
updated Aug 17, 2018
Checking data type when creating a column

#12 · opened Oct 02, 2015 by Celine Mercier discussion
- CLOSED
- 2
updated Aug 17, 2018
distutils

#11 · opened Sep 02, 2015 by Celine Mercier bug
- CLOSED
- 2
updated Aug 17, 2018
Implement column directories

#10 · opened Jun 17, 2015 by Celine Mercier feature
- CLOSED
- 0
updated Aug 17, 2018
openat function problem

#9 · opened Jun 05, 2015 by Celine Mercier bug
- CLOSED
- 4
updated Aug 17, 2018
OBITypes

#8 · opened May 12, 2015 by Eric Coissac Specifications suggestion
- CLOSED
- 0
updated Aug 17, 2018
Python 3 and Sphinx

#7 · opened May 12, 2015 by Celine Mercier enhancement
- CLOSED
- 1
updated Aug 17, 2018
A column is not only stored in a single file.

#6 · opened May 12, 2015 by Eric Coissac Specifications discussion
- CLOSED
- 1
updated Jan 07, 2019
Doxygen doc generation

#5 · opened May 12, 2015 by Celine Mercier feature
- CLOSED
- 0
updated Jan 07, 2019
OBIDMS Column file names

#4 · opened May 12, 2015 by Eric Coissac Specifications documentation suggestion
- CLOSED
- 3
updated Jan 07, 2019
We are using UML not ULM

#3 · opened May 12, 2015 by Eric Coissac documentation
- CLOSED
- 1
updated Jan 07, 2019
The path in the Doxygen configuration file must be relative

#2 · opened May 12, 2015 by Eric Coissac Specifications bug documentation
- CLOSED
- 1
updated Jan 07, 2019
UML for OBIIntColumn

#1 · opened May 11, 2015 by Celine Mercier A Prototype of an OBIColumn for integers documentation
- CLOSED
- 0
updated Jan 07, 2019
Rebuild the package in a standard way

#58 · opened Mar 22, 2019 by Eric Coissac critical enhancement
- CLOSED
- 1
updated Sep 25, 2019
Basic R API

#59 · opened Apr 10, 2019 by Celine Mercier critical feature
- 1
updated May 30, 2020
Clean reference databases

#60 · opened Apr 10, 2019 by Celine Mercier feature
- 0
updated Apr 10, 2019
Reading merged taxids information when building a reference database

#61 · opened Apr 10, 2019 by Celine Mercier critical enhancement
- CLOSED
- 0
updated Aug 19, 2019
Multithreading

#62 · opened Apr 10, 2019 by Celine Mercier enhancement
- 1
updated Jul 24, 2019
DMS compatibility between OSX and Ubuntu (Linux?)

#63 · opened Apr 10, 2019 by Celine Mercier bug critical
- 1
updated Sep 25, 2019
Taxonomy: add local taxa

#64 · opened Apr 10, 2019 by Celine Mercier critical feature
- CLOSED
- 0
updated Feb 12, 2023
obi clust

#65 · opened Apr 10, 2019 by Celine Mercier feature
- 0
updated Apr 10, 2019
obi uniq re-merge merged informations

#66 · opened Apr 10, 2019 by Celine Mercier bug critical
- CLOSED
- 0
updated Aug 27, 2019
obi clean efficiency

#67 · opened Apr 10, 2019 by Celine Mercier critical enhancement
- CLOSED
- 0
updated May 19, 2019
Make the OBI3 work on the WSL (Windows Subsystem for Linux)

#68 · opened Aug 24, 2019 by Celine Mercier critical feature
- CLOSED
- 3
updated Mar 11, 2021
Running multiple commands on one DMS at the same time

#69 · opened Sep 25, 2019 by Celine Mercier feature
- 0
updated Sep 25, 2019
Extractreads2?

#70 · opened Jan 10, 2020 by Pauline Stud
- CLOSED
- 1
updated Jan 29, 2020
segmentation fault

#71 · opened Feb 20, 2020 by Annelies Haegeman
- CLOSED
- 5
updated Feb 24, 2020
"seq 0 in refs view has no taxid associated" while building custom reference database

#72 · opened Feb 24, 2020 by Annelies Haegeman
- CLOSED
- 6
updated Feb 26, 2020
Complement -h doc and/or wiki

#73 · opened Feb 26, 2020 by Celine Mercier documentation
- 0
updated Feb 26, 2020
alignpairedend score threshold

#74 · opened Feb 26, 2020 by Celine Mercier
- CLOSED
- 1
updated Nov 11, 2021
ngsfilter primer length limit

#75 · opened Mar 12, 2020 by Celine Mercier critical
- CLOSED
- 0
updated Apr 09, 2020
ecopcr fails unexpectedly

#76 · opened Apr 08, 2020 by Fabian Roger
- CLOSED
- 6
updated Apr 13, 2020
Memory bug

#77 · opened Apr 12, 2020 by Celine Mercier bug critical
- CLOSED
- 1
updated May 30, 2020
obi uniq fails with "Error enlarging a column file"

#78 · opened Apr 13, 2020 by Fabian Roger
- CLOSED
- 25
updated May 30, 2020
Dictionary efficiency issue

#79 · opened Apr 23, 2020 by Celine Mercier critical enhancement
- 0
updated Apr 23, 2020
ecotag output

#80 · opened Apr 23, 2020 by Celine Mercier enhancement
- CLOSED
- 0
updated Jun 09, 2020
ecotag fails with DMS does not exist

#81 · opened Apr 28, 2020 by Fabian Roger
- CLOSED
- 4
updated Apr 29, 2020
ecotoag assigns only very small proportion of reads

#82 · opened Apr 29, 2020 by Fabian Roger
- CLOSED
- 8
updated May 30, 2020
get full taxonomic annotation of reads

#83 · opened Apr 29, 2020 by Fabian Roger
- CLOSED
- 4
updated Apr 30, 2020
Deleting/overwrithing a view (ecopcr)

#84 · opened May 08, 2020 by joran vanhollebeke
- CLOSED
- 2
updated May 08, 2020
Obi concatenate issue

#85 · opened Aug 14, 2020 by Lotte Skovmand
- CLOSED
- 9
updated Sep 09, 2020
import Error

#86 · opened Jan 22, 2021 by Mitica Ciorpac
- CLOSED
- 4
updated Jan 30, 2021
obi import error

#87 · opened Feb 02, 2021 by Mitica Ciorpac
- CLOSED
- 6
updated Apr 15, 2021
Crash in obi less

#88 · opened Feb 08, 2021 by Eric Coissac bug critical
- CLOSED
- 0
updated Feb 10, 2021
Crash when path includes non-ascii letters...

#89 · opened Feb 09, 2021 by Eric Coissac bug
- CLOSED
- 1
updated Dec 07, 2021
obi annotate

#90 · opened Feb 10, 2021 by Gabriele Cananzi
- CLOSED
- 2
updated Mar 14, 2021
Problem of quoting quotes when reporting obi commands including quotes in the history

#91 · opened Feb 11, 2021 by Eric Coissac bug
- 0
updated Feb 11, 2021
add a rm subcommand

#92 · opened Feb 11, 2021 by Eric Coissac feature
- CLOSED
- 1
updated Mar 21, 2021
Add a findtaxon sub command

#93 · opened Feb 11, 2021 by Eric Coissac feature
- 0
updated Feb 11, 2021
Read the PR2 database

#94 · opened Feb 21, 2021 by Celine Mercier feature
- 0
updated Feb 21, 2021
ecopcr problem

#95 · opened Feb 23, 2021 by Mingfei Chen
- CLOSED
- 2
updated Feb 24, 2021
ecotag: sequences not assigned

#96 · opened Feb 24, 2021 by Mingfei Chen
- CLOSED
- 1
updated Mar 02, 2021
Fail to assign sequences in ecotag (AttributeError: 'bytes' object has no attribute 'name')

#98 · opened Mar 16, 2021 by Sichao Huang
- CLOSED
- 1
updated Sep 07, 2021
ngsfilter: identify primer dimers

#99 · opened Mar 21, 2021 by Celine Mercier enhancement
- 0
updated Mar 21, 2021
import: no progress bar option

#100 · opened Mar 21, 2021 by Celine Mercier enhancement
- CLOSED
- 1
updated Jul 21, 2021
escape character in option value

#101 · opened Mar 28, 2021 by Celine Mercier bug
- CLOSED
- 1
updated Apr 06, 2021