ksahlin/BESST issues and pull requests

#86 - Mathstats requirement

Issue - State: closed - Opened by amandaamelo 11 months ago - 3 comments

#85 - TypeError: PosDirCalculatorPE() missing 5 required positional arguments: 'cont2pos', 'matepos', 's2len', 'cont2_len', and 'read_len'

Issue - State: open - Opened by JuniusH about 1 year ago - 1 comment

#84 - AttributeError: 'Graph' object has no attribute 'node'

Issue - State: closed - Opened by NowickiLab over 1 year ago

#83 - Bump scipy from 1.0.0 to 1.10.0

Pull Request - State: open - Opened by dependabot[bot] over 1 year ago
Labels: dependencies

#82 - Multithreading

Issue - State: closed - Opened by ardy20 about 3 years ago - 1 comment

#81 - paired end reads

Issue - State: closed - Opened by ardy20 about 3 years ago - 1 comment

#80 - AttributeError running BESST on test data

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

#79 - Inputfile without mate pair reads

Issue - State: closed - Opened by YuanwenGuo about 4 years ago - 2 comments

#78 - TypeError due to integer division change in python3

Issue - State: open - Opened by nwespe over 4 years ago - 5 comments

#77 - Too many reads filtered out?

Issue - State: open - Opened by melop over 4 years ago - 3 comments

#76 - Contigs could be used multiple times ?

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

#75 - 'Graph' object has no attribute 'edge'

Issue - State: closed - Opened by tk2 almost 5 years ago - 3 comments

#74 - make test failed on command line runBESST

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

#73 - error about BESST/scripts/reads_to_ctg_map.py

Issue - State: closed - Opened by Shirley-Q over 5 years ago - 5 comments

#72 - filter bam for mapq score?

Issue - State: closed - Opened by dcopetti over 5 years ago - 8 comments
Labels: question

#71 - how to set up mutiple threads!

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

#70 - reads_to_ctg_map.py: another error

Issue - State: closed - Opened by bheimbu almost 7 years ago - 4 comments

#69 - Remove backup files

Pull Request - State: closed - Opened by ralic almost 7 years ago

#68 - Incompatibility with networkx 2.0

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

#67 - Py3support

Pull Request - State: closed - Opened by ksahlin almost 7 years ago

#66 - AttributeError: 'Graph' object has no attribute 'edge'

Issue - State: closed - Opened by cistarsa almost 7 years ago - 8 comments

#65 - Update INSTALL.md with requirements in networkx python module

Pull Request - State: closed - Opened by yuragal about 7 years ago

#64 - AttributeError: 'Graph' object has no attribute 'edge'

Issue - State: closed - Opened by yuragal about 7 years ago - 2 comments

#63 - Error running BESST 2.2.7

Issue - State: closed - Opened by anausie about 7 years ago - 2 comments

#62 - Which contigs are joined to produce given scaffold?

Issue - State: closed - Opened by PedroBarbosa about 7 years ago - 5 comments

#61 - TypeError when running BESST

Issue - State: open - Opened by ademcan over 7 years ago - 8 comments

#60 - There are no gaps in my resulting scaffold

Issue - State: closed - Opened by genaev over 7 years ago - 4 comments

#59 - Convert to Python3

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

#58 - Doc incorrect

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

#57 - ZeroDivisionError in get_contamination_metrics

Issue - State: closed - Opened by md5sam over 7 years ago

#56 - Generate output patch

Pull Request - State: open - Opened by sletort over 7 years ago

#55 - AGP/GFF output show no overlap

Issue - State: open - Opened by sletort over 7 years ago - 1 comment

#54 - 454 mate pairs problem: exit with no error msg

Issue - State: closed - Opened by melop over 7 years ago - 13 comments

#53 - MathOverflow warning

Issue - State: open - Opened by melop over 7 years ago - 1 comment
Labels: enhancement

#52 - change the indentation of line 137. => bug in read_to_ctg_map.py

Pull Request - State: closed - Opened by sletort almost 8 years ago - 1 comment

#51 - Output scaffold graph with assembled scaffolds

Issue - State: open - Opened by dbrowneup almost 8 years ago

#50 - Unusual gap and merge numbers

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

#49 - IndexError: list index out of range

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

#48 - validate AGP 2.0 specifications.

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

#47 - Conflicting scaffold name in output

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

#46 - Mate pair processing

Issue - State: closed - Opened by ptranvan about 8 years ago - 3 comments
Labels: question

#45 - Metagenomics

Issue - State: open - Opened by davidvilanova about 8 years ago - 1 comment
Labels: question

#44 - BESST freezes after step 1

Issue - State: closed - Opened by KamilSJaron about 8 years ago - 2 comments

#43 - a few things

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

#42 - division by zero on very long insert libraries

Issue - State: closed - Opened by rchikhi about 8 years ago - 6 comments

#41 - IndexError wite mate paire library

Issue - State: closed - Opened by albodrug about 8 years ago - 6 comments

#40 - Statistics interpretation and values

Issue - State: closed - Opened by mebbert over 8 years ago - 9 comments
Labels: question

#39 - skip orientation ... as there are not enough pairs

Issue - State: closed - Opened by mebbert over 8 years ago - 7 comments
Labels: question

#38 - Another ZeroDivisionError: float division by zero

Issue - State: closed - Opened by dbrowneup over 8 years ago - 10 comments

#37 - "too few data" detection

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

#36 - Is the final scaffolds in BESST_output/pass1/Scaffolds_pass1.fa?

Issue - State: closed - Opened by sjackman over 8 years ago - 2 comments
Labels: question

#35 - Please tag a stable release of 2.2.4

Issue - State: closed - Opened by sjackman over 8 years ago - 3 comments
Labels: enhancement

#34 - RE: reads_to_ctg_map.py

Issue - State: open - Opened by Malabady over 8 years ago - 10 comments
Labels: bug

#33 - ZeroDivisionError: float division by zero

Issue - State: closed - Opened by vishnubob over 8 years ago - 18 comments
Labels: bug

#32 - does repeats fasta contain all detected repeats?

Issue - State: closed - Opened by albodrug over 8 years ago - 3 comments
Labels: question

#31 - mathstats

Issue - State: closed - Opened by phpeters over 8 years ago - 2 comments

#30 - 2nd round of scaffolding error

Issue - State: closed - Opened by PedroBarbosa over 8 years ago - 17 comments

#29 - run error

Issue - State: closed - Opened by peterdfields over 8 years ago - 10 comments
Labels: bug

#28 - Coverage based filtering of repeats fails to converge for some instances

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

#27 - No improvement after scaffolding

Issue - State: closed - Opened by vasanth87 over 8 years ago - 9 comments

#26 - Develop

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

#25 - Enhanced usability of reads_to_cfg_map.py

Pull Request - State: closed - Opened by sidorov-si about 9 years ago - 2 comments

#24 - Usage of -q argument

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

#23 - --orientation argument

Issue - State: closed - Opened by sidorov-si about 9 years ago - 1 comment
Labels: enhancement

#22 - Install error

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

#21 - no improvement with BESST

Issue - State: closed - Opened by macmanes about 9 years ago - 3 comments

#20 - custom number of threads in sampe alignment + small fix

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

#19 - KeyError: 11012

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

#18 - RuntimeError

Issue - State: closed - Opened by leo-dagata over 9 years ago - 3 comments

#17 - Small fix

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

#16 - Fixed issue #15, by always removing the created temporary directory.

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

#15 - reads_to_ctg_map.py: temp files are not deleted

Issue - State: closed - Opened by AskPascal over 9 years ago - 2 comments

#14 - Added shebang line in reads_to_ctg_map.py

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

#13 - Catching division by zero error during mean cov computation if there onl...

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

#12 - Contigs singeled out due to length constraints

Issue - State: closed - Opened by sarasumic almost 10 years ago - 1 comment

#11 - Different size of MP library

Issue - State: closed - Opened by wyim-pgl almost 10 years ago - 2 comments

#10 - Bugfixes for libmetrics.py

Pull Request - State: closed - Opened by olest almost 10 years ago - 3 comments

#9 - Bugfixes for libmetrics

Pull Request - State: closed - Opened by olest almost 10 years ago - 1 comment

#8 - pulp.solvers.PulpSolverError: Pulp:

Issue - State: closed - Opened by stby about 10 years ago - 2 comments

#7 - Develop

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

#6 - Update errorhandle.py

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

#5 - Moved INSTALL.txt and MANUAL.txt to MarkDown versions

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

#4 - ZeroDivisionError

Issue - State: closed - Opened by ctSkennerton almost 11 years ago - 3 comments

GitHub / ksahlin/BESST issues and pull requests