apriha/snps

Issues

• ValueError: invalid literal for int() with base 10: '48169282.0': Error while type casting for column 'pos'

  #177 opened 6 months ago by IMingGarson
  0

• GenomePrep databases are offline

  #173 opened 8 months ago by ElSaico
  1

• Identify SNP array cluster

  #145 opened 2 years ago by apriha
  1

• Identify and filter low quality SNPs

  #146 opened 2 years ago by apriha
  1

• parse only a specific region (or chromosome)

  #159 opened 2 years ago by IsmailM
  0

• VCF parsing issue with ezancestry

  #158 opened 2 years ago by apriha
  0

• Support latest version of black

  #144 opened 3 years ago by apriha
  0

• mapmygenome filter on GC.Score

  #95 opened 4 years ago by satishmp
  2

• Drop support for Python 3.6

  #140 opened 3 years ago by apriha
  0

• Getting "404: Not Found" when trying to use get_opensnp_datadump_filenames()

  #130 opened 4 years ago by mkbond777
  2

• Use temp dir for output files during tests

  #99 opened 4 years ago by apriha
  0

• Detect build 38 Exome files

  #47 opened 4 years ago by willgdjones
  4

• Change "generic" source to "unknown"

  #122 opened 4 years ago by apriha
  0

• AttributeError: 'str' object has no attribute '_output_dir'

  #120 opened 4 years ago by lakishadavid
  9

• Class based source readers?

  #119 opened 4 years ago by afaulconbridge
  1

• openSNPs downloads

  #117 opened 4 years ago by afaulconbridge
  3

• Optimize normalized snps dataframe dtypes

  #108 opened 4 years ago by apriha
  4

• Consolidate issues into one dataframe

  #112 opened 4 years ago by apriha
  0

• Deduplicate loci

  #107 opened 4 years ago by apriha
  0

• Use Pandas nullable integer for position in for normalized snps dataframe

  #109 opened 4 years ago by afaulconbridge
  1

• Merge SNPs for a chromosome

  #102 opened 4 years ago by apriha
  0

• Multisample VCF

  #105 opened 4 years ago by kkarbasi
  1

• Use f-strings for string formatting

  #100 opened 4 years ago by apriha
  0

• mapmygenome DTC file format has changed.

  #94 opened 4 years ago by satishmp
  0

• Add `SNPs.merge` method

  #88 opened 4 years ago by apriha
  0

• Rename `SNPs` methods and properties

  #92 opened 4 years ago by apriha
  0

• Usage of `check_exact` raises `AssertionError`

  #89 opened 4 years ago by apriha
  0

• Tabular output for use in GEDmatch and other tools

  #66 opened 4 years ago by GerardManning
  1

• Inconsistent output of mitochondrial SNPs in Ancestry/23andme merge

  #65 opened 4 years ago by GerardManning
  1

• Drop support for Python 3.5

  #64 opened 4 years ago by apriha
  0

• Errors running tests on MacOSX

  #77 opened 5 years ago by willgdjones
  2

• Indel SNPs rejected due to mismapping issue

  #68 opened 5 years ago by GerardManning
  0

• VCF / GVCF parsing issue

  #67 opened 5 years ago by deniseho-98
  5

• Handle error message when saving invalid genotype files to VCF?

  #57 opened 5 years ago by PhilPalmer
  2

• Truncated position values in output files

  #59 opened 5 years ago by apriha
  0

• Output 23andMe from snps cannot be read by snps

  #54 opened 5 years ago by PhilPalmer
  1

• Can't save snps object generated from VCF

  #53 opened 5 years ago by PhilPalmer
  3

• Consolidate code to resolve SNP issues

  #42 opened 5 years ago by apriha
  6

• Remove duplication of X chromosome alleles

  #43 opened 5 years ago by apriha
  7

• Add `phased` property

  #44 opened 5 years ago by apriha
  2

• Investigate updating thresholds and methods for `determine_sex`

  #49 opened 5 years ago by apriha
  0

• Assign SNPs on chromosome 0

  #13 opened 6 years ago by apriha
  2

• Populate missing RSIDs

  #19 opened 5 years ago by apriha
  0

• Consider refactoring `genotype` column

  #45 opened 5 years ago by apriha
  6

• Exception catching

  #38 opened 5 years ago by willgdjones
  1

• Help to set output directory

  #36 opened 5 years ago by apedreira
  4

• documentation for reading VCF missing

  #18 opened 5 years ago by DSLituiev
  1

• Use logging instead of print statements

  #22 opened 5 years ago by apriha
  2

• Questions: regarding using VCF & PLINK input files

  #34 opened 5 years ago by PhilPalmer
  3

• Read/Write to memory buffer

  #16 opened 5 years ago by willgdjones
  1