Ecosyste.ms: Issues

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GitHub / ksamuk/pixy issues and pull requests

#84 - pixy (apparently) not using all requested cores

Issue - State: closed - Opened by rafmarcondes over 1 year ago
Labels: help wanted

#83 - Why are the results so different when using pixy and vcftools

Issue - State: open - Opened by Wennie-s over 1 year ago - 5 comments
Labels: help wanted

#82 - Version of numpy and htslib doesn't work

Issue - State: closed - Opened by conJUSTover over 1 year ago - 2 comments
Labels: help wanted

#81 - No variable sites

Issue - State: open - Opened by avanwallendael over 1 year ago - 2 comments

#80 - Attribute Error During Help Menu Call

Issue - State: open - Opened by cizydorczyk over 1 year ago - 1 comment
Labels: help wanted

#79 - ability to handle sex chromosomes

Issue - State: open - Opened by jtweir almost 2 years ago - 1 comment
Labels: enhancement, todo, high priority

#78 - Support for New Missing Data Formatting from GATK

Issue - State: open - Opened by ksamuk almost 2 years ago
Labels: enhancement, todo, high priority

#77 - attribute error

Issue - State: closed - Opened by glaudelrio almost 2 years ago - 4 comments
Labels: help wanted

#75 - Pixy does not detect variable sites

Issue - State: closed - Opened by sPuechmailleGitHub almost 2 years ago - 2 comments
Labels: help wanted

#74 - Problem running pi on pixy

Issue - State: closed - Opened by bvaditi almost 2 years ago - 5 comments
Labels: help wanted

#73 - IndexError: list index out of range

Issue - State: closed - Opened by edgarwly almost 2 years ago
Labels: help wanted

#72 - csi index

Issue - State: open - Opened by giuliafrascarelli about 2 years ago - 1 comment
Labels: enhancement, todo

#71 - Pixy estimations are wrong

Issue - State: closed - Opened by lisagrigoreva about 2 years ago - 2 comments
Labels: bug

#70 - Pandas error: too many columns specified

Issue - State: closed - Opened by sabrinamostoufi about 2 years ago - 2 comments
Labels: bug

#69 - IndexError: list index out of range

Issue - State: closed - Opened by Pcariman about 2 years ago - 2 comments
Labels: help wanted

#68 - Error message - TypeError: stat: path should be string, bytes, os.PathLike or integer, not NoneType

Issue - State: closed - Opened by aliceatikesse about 2 years ago - 1 comment
Labels: help wanted

#67 - IndexError: list index out of range

Issue - State: closed - Opened by jiangqiuqiuu about 2 years ago - 4 comments
Labels: help wanted

#66 - What has been calculated in the pi output if there is only one individual?

Issue - State: closed - Opened by Jolleboll over 2 years ago - 4 comments
Labels: help wanted

#65 - can pixy be used in haploid species

Issue - State: closed - Opened by wushyer over 2 years ago - 3 comments
Labels: help wanted

#64 - VCF from fast file?

Issue - State: closed - Opened by olgakozhar over 2 years ago - 2 comments
Labels: help wanted

#63 - Better Error Message for .tbi Files in Place of VCFs

Issue - State: open - Opened by ksamuk over 2 years ago
Labels: enhancement, todo

#62 - UnicodeDecodeError when running pixy for the first time

Issue - State: closed - Opened by olgakozhar over 2 years ago - 4 comments
Labels: bug

#61 - heterozygous sites increase nucleotide diversity?

Issue - State: closed - Opened by caixu0518 over 2 years ago - 1 comment
Labels: enhancement

#60 - [pixy] ERROR: the provided VCF appears to contain no variable sites.

Issue - State: closed - Opened by StefanoLonardi over 2 years ago - 2 comments
Labels: bug

#59 - Understanding how missing data are taken into account in avg_pi

Issue - State: closed - Opened by gsgarlata almost 3 years ago - 4 comments
Labels: help wanted

#58 - Hard or soft filtering input VCF?

Issue - State: closed - Opened by mwersebe almost 3 years ago - 2 comments
Labels: help wanted

#57 - Per marker stats

Issue - State: closed - Opened by ricebrian almost 3 years ago - 2 comments
Labels: help wanted

#56 - window_size 1

Issue - State: closed - Opened by fxfish almost 3 years ago - 1 comment
Labels: help wanted

#55 - --sites_file argument ouputs only NAs in avg_pi column

Issue - State: closed - Opened by tshalev about 3 years ago - 10 comments

#54 - Output Fst variance components

Issue - State: open - Opened by SethMusker about 3 years ago
Labels: enhancement, todo

#53 - permutation test

Issue - State: closed - Opened by biozzq about 3 years ago - 1 comment
Labels: enhancement, wontfix

#52 - Make Pixy into a library for importing into Python scripts

Issue - State: closed - Opened by vlrieg over 3 years ago - 2 comments
Labels: enhancement

#51 - average fst across windows

Issue - State: closed - Opened by danielwood1992 over 3 years ago - 4 comments
Labels: help wanted

#50 - window and step options

Issue - State: closed - Opened by amsamani over 3 years ago - 1 comment
Labels: help wanted

#49 - LD pruning before calculating Fst/dxy?

Issue - State: closed - Opened by nitinra over 3 years ago - 2 comments
Labels: help wanted

#48 - sites_file argument not working

Issue - State: closed - Opened by JesseGarcia562 over 3 years ago - 5 comments
Labels: bug

#47 - Haploid VCF

Issue - State: closed - Opened by Jolvii85 over 3 years ago - 2 comments
Labels: help wanted

#46 - Duplicated sites in pixy output using bed intervals?

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

#45 - pi output gives NA values when there is viable data

Issue - State: closed - Opened by anitato over 3 years ago - 5 comments
Labels: bug

#44 - error says my vcf has no invariant

Issue - State: closed - Opened by amsamani over 3 years ago - 9 comments
Labels: bug

#43 - Best practice for estimating πN/πS in pixy

Issue - State: closed - Opened by tshalev over 3 years ago - 2 comments
Labels: help wanted

#42 - Fst estimation error

Issue - State: closed - Opened by Gandasegui over 3 years ago - 10 comments
Labels: bug

#41 - How should I compare my pi results from pixy with studies that use other approaches?

Issue - State: closed - Opened by tshalev over 3 years ago - 2 comments
Labels: help wanted

#40 - Single site calculation of dxy

Issue - State: closed - Opened by BaHole over 3 years ago - 3 comments
Labels: help wanted

#39 - CHROMOSOMES

Issue - State: closed - Opened by BaHole over 3 years ago - 1 comment
Labels: enhancement

#38 - Tajima's D

Issue - State: open - Opened by vlrieg over 3 years ago - 1 comment
Labels: enhancement, todo

#37 - Filtering on site quality removes many invariant sites in a VCF from GATK

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

#36 - Persite Fst - 'float' object is not iterable

Issue - State: closed - Opened by erikenbody over 3 years ago - 7 comments
Labels: bug

#35 - Fix setup.py for pip install

Pull Request - State: closed - Opened by niemasd over 3 years ago

#34 - Installing pixy using "pip install pixy" doesn't yield "pixy" executable

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

#33 - chromosome and zarr_path

Issue - State: closed - Opened by BaHole almost 4 years ago - 4 comments
Labels: bug

#32 - bed file regions (with chromosomes just as numbers)

Issue - State: closed - Opened by danielwood1992 almost 4 years ago - 2 comments

#31 - KeyError: nan

Issue - State: closed - Opened by djeffares almost 4 years ago - 11 comments
Labels: help wanted

#30 - Hudson FST

Issue - State: closed - Opened by biozzq almost 4 years ago - 1 comment
Labels: enhancement

#29 - --output_folder prepends working directory path onto paths from root

Issue - State: closed - Opened by tintori almost 4 years ago - 1 comment
Labels: bug

#28 - No invariant sites found in simulated VCF file

Issue - State: closed - Opened by vlrieg almost 4 years ago - 5 comments
Labels: bug

#27 - vcf file indexing error

Issue - State: closed - Opened by sandipmkale almost 4 years ago - 3 comments

#26 - Pi calculation error - ValueError: Cannot convert non-finite values (NA or inf) to integer

Issue - State: closed - Opened by mishaploid almost 4 years ago - 4 comments
Labels: bug

#25 - TypeError: zip argument #3

Issue - State: closed - Opened by ClaudimarceO almost 4 years ago - 2 comments
Labels: bug

#24 - Missing comma in requirements for setup.py

Issue - State: closed - Opened by mishaploid almost 4 years ago - 1 comment
Labels: bug

#23 - Issue in D xy calculation

Issue - State: closed - Opened by Doniol-Valcroze almost 4 years ago - 3 comments
Labels: bug

#22 - bed file as input

Issue - State: closed - Opened by stsmall almost 4 years ago - 2 comments

#21 - IndexError during Fst calc when chrom has no variants passing filter

Issue - State: closed - Opened by mscharmann almost 4 years ago - 2 comments

#20 - import pixy

Issue - State: closed - Opened by MAl-Ajaji about 4 years ago - 1 comment

#19 - add option to always have intervals spanning entire chromosomes

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

#18 - Error in NUMEXPR dependency

Issue - State: closed - Opened by mscharmann about 4 years ago - 3 comments

#17 - ERROR: the following samples are listed in the population file but not in the VCF

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

#15 - File not found error

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

#14 - Discrepency in pi estimates between vcftools and pixy

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

#13 - max () arg is an empty sequence

Issue - State: closed - Opened by nitinra about 4 years ago - 1 comment

#12 - No such file

Issue - State: closed - Opened by konopinski about 4 years ago - 3 comments

#11 - Installation problem

Issue - State: closed - Opened by willright28 over 4 years ago - 3 comments

#10 - The --reuse_zarr flag and memory use

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

#9 - Finishing time same as starting time

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

#8 - Runtimes

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

#7 - ANGSD/peñalba calc.dxy post-processing script

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

#6 - Error message for missing FORMAT fields

Issue - State: closed - Opened by ksamuk almost 5 years ago - 1 comment

#5 - Multi-Chromosome VCF Support

Issue - State: closed - Opened by ksamuk almost 5 years ago - 1 comment

#4 - Improvements in general

Pull Request - State: closed - Opened by marcelotrevisani over 5 years ago

#3 - Fix `scripts` option

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

#2 - filtration and parsing sections updated

Pull Request - State: closed - Opened by ksamuk over 5 years ago

#1 - New filtration functionality and output formatting

Pull Request - State: closed - Opened by ksamuk over 5 years ago