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dereneaton
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ipyrad
Interactive assembly and analysis of RAD-seq data sets
http://ipyrad.readthedocs.io
GNU General Public License v3.0
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Changed astral annotation to default
#417
camayal
closed
3 years ago
0
missing depencies in the documentation
#416
oliviermattelaer
closed
3 years ago
3
Merge exists with 1
#415
miguelpmachado
closed
3 years ago
1
analysis.pca: Impute missing as random value
#414
isaacovercast
opened
4 years ago
0
Merged assembly project_dir collision
#413
isaacovercast
closed
3 years ago
1
Make later versions available in PyPI
#412
davidlougheed
closed
4 years ago
1
Stats output truncates long sample names
#411
isaacovercast
closed
4 years ago
1
trim_loci not working for 3' R1 and 5' R2
#410
isaacovercast
opened
4 years ago
3
Changes in Drawing class
#409
camayal
closed
3 years ago
0
Can't build targets without any engines
#408
djlduckett
closed
4 years ago
2
reference method not adding indels
#407
isaacovercast
opened
4 years ago
1
reads not clustering/mapping to reference genome
#406
joshuahallas
closed
4 years ago
1
off by 1 error in step 6
#405
isaacovercast
closed
4 years ago
3
step3: cannot copy sequence with size 142 to array axis with dimension 0 when build clusters with clustmap.py
#404
Liut035
closed
4 years ago
6
1-based/0-based rabbit hole in 'reference' assemblies
#403
isaacovercast
closed
4 years ago
1
Step 7: ambiguities in reference sequence cause KeyError: ##
#402
laninsky
closed
4 years ago
2
docs aren't building <eom>
#401
isaacovercast
closed
4 years ago
1
STRUCTURE k=1?
#400
pabuveery
closed
4 years ago
3
can't run ABBA-BABA test in ipyrad
#399
Bean061
closed
4 years ago
2
Problem with [min_samples_locus] in reference analysis
#398
edgardomortiz
closed
4 years ago
5
Step#7 vcf file ValueError: invalid literal for int() with base 10: '43;*9'
#397
jqrichmond
closed
4 years ago
2
Remove write_outputs backward compatibility
#396
isaacovercast
opened
4 years ago
0
Encounter an Error while sorting reads
#395
wpearman1996
closed
4 years ago
21
ipa.vcf_to_hdf5 ValueError: invalid literal for long() with base 10: 'T'
#394
TomaszSuchan
closed
3 years ago
5
Bring back debug logging.
#393
isaacovercast
opened
4 years ago
1
Step 6 KeyError: 'reference'
#392
isaacovercast
closed
4 years ago
1
Handle massively clustered paralogs in step 6
#391
isaacovercast
closed
4 years ago
3
Step 2: Any samples failing kill this entire step
#390
isaacovercast
closed
4 years ago
2
Step 3 Fatal error: Files compressed with gzip are not supported
#389
lz41
closed
4 years ago
4
Step 7 doesn't automatically skip samples without data
#388
edgardomortiz
closed
4 years ago
1
Cosmetic issue in .alleles file
#387
edgardomortiz
closed
4 years ago
3
Print stack trace on error (disable -d necessity)
#386
isaacovercast
closed
4 years ago
1
Problems wwith ipyrad.bpp
#385
k-sanchez
closed
4 years ago
2
mrbayes install UnsatisfiableError
#384
isaacovercast
closed
3 years ago
5
Checkpointing for steps 3 & 6
#383
isaacovercast
opened
4 years ago
0
write_outputs: 3s output format
#382
isaacovercast
opened
4 years ago
0
Unbound local error
#381
MarnusStoltz
closed
4 years ago
4
Step 6 - Fixing threading optimization
#380
isaacovercast
opened
4 years ago
0
min_sample_locus and popfile
#379
giorgio-92
closed
4 years ago
2
Merging after step 2 creates `concatedit` file in cwd, which is not ideal.
#378
isaacovercast
closed
4 years ago
1
Debugging bioconda
#377
isaacovercast
closed
1 year ago
4
denovo+reference/denovo-reference not supported in v0.9 (yet)
#376
leonardslog
opened
4 years ago
25
Step 6 KeyError with pops file if sample name not in assembly
#375
isaacovercast
closed
4 years ago
5
v0.9 - Step 6 "AssertionError: no consensus files found"
#374
isaacovercast
closed
4 years ago
2
i5 demux PCR duplicates
#373
eaton-lab
opened
4 years ago
0
insert size hackersonly override
#372
eaton-lab
closed
3 years ago
1
baba module not updated to 0.9 version
#371
isaacovercast
opened
4 years ago
5
Update documentation
#370
brpark29
closed
4 years ago
2
Exception in step 5: ValueError(All chunk dimensions must be positive (all chunk dimensions must be positive))'
#369
isaacovercast
closed
4 years ago
3
Step 3 fails for FASTQ+64 formatted data
#368
isaacovercast
closed
3 years ago
5
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