alimanfoo/vcfnp

Issues

• vcfnp.variants abbreviates strings in CHROM column

  #65 opened 8 years ago by alexhbnr
  3

• number of files doesn't match

  #64 opened 8 years ago by xiekunwhy
  3

• Flatten EFF/ANN annotations?

  #61 opened 8 years ago by alimanfoo
  1

• genotype_ac

  #63 opened 8 years ago by alimanfoo
  0

• Compress files created by vcf2npy

  #59 opened 8 years ago by alimanfoo
  0

• Remove numpy build dependency

  #46 opened 8 years ago by alimanfoo
  0

• Convert C++ exceptions into Python exceptions

  #48 opened 8 years ago by kyleabeauchamp
  11

• vcfnpy2blz

  #37 opened 8 years ago by alimanfoo
  1

• EFF Amino_Acid_Change field being truncated

  #62 opened 8 years ago by travc
  2

• full vcf to hdf5...

  #50 opened 9 years ago by travc
  3

• bug generating hdf5 from vcf

  #54 opened 9 years ago by travc
  1

• vcfnpy2hdf5 increase default chunk size to 1Mb

  #57 opened 9 years ago by alimanfoo
  1

• Local parallelisation for vcf2npy

  #40 opened 9 years ago by alimanfoo
  1

• git clone error

  #49 opened 9 years ago by travc
  3

• vcfnp2hdf5 less verbose logging on load

  #38 opened 9 years ago by alimanfoo
  0

• Remove version logging from scripts

  #47 opened 9 years ago by alimanfoo
  0

• Genotype packed

  #41 opened 9 years ago by alimanfoo
  1

• Support PY3

  #43 opened 10 years ago by alimanfoo
  0

• vcfnp2hdf5 add vcf header definitions as attributes on datasets

  #39 opened 10 years ago by alimanfoo
  0

• vcfnpy2hdf5 add chunk width option

  #36 opened 10 years ago by alimanfoo
  0

• Reorganise variants as group with child dataset per field

  #33 opened 10 years ago by alimanfoo
  0

• Fix calldata fields such that all dimensions are included in shape

  #34 opened 10 years ago by alimanfoo
  0

• Change samples to dataset

  #35 opened 10 years ago by alimanfoo
  0

• titv function

  #9 opened 11 years ago by alimanfoo
  1

• Missing genotype but non-missing calldata

  #32 opened 11 years ago by alimanfoo
  0

• qsub_vcf2npy breaks for -tc or any similar qsub option

  #31 opened 11 years ago by alimanfoo
  0

• flatten EFF field in vcf2csv

  #30 opened 11 years ago by alimanfoo
  0

• EFF defaults

  #29 opened 11 years ago by alimanfoo
  0

• Use (optionally) pandas instead of view2d

  #7 opened 11 years ago by lbeltrame
  2

• script for converting VCF to CSV

  #26 opened 11 years ago by alimanfoo
  2

• fix command line script incorrect use of nargs

  #28 opened 11 years ago by alimanfoo
  0

• fix bug for string fields with multiple values

  #27 opened 11 years ago by alimanfoo
  1

• script for loading hdf5

  #25 opened 11 years ago by alimanfoo
  0

• scripts for parallelizing conversion to npy

  #24 opened 11 years ago by alimanfoo
  0

• log last variant position with progress

  #23 opened 11 years ago by alimanfoo
  0

• add more default INFO dtypes

  #22 opened 11 years ago by alimanfoo
  0

• user-specified cachedir

  #21 opened 11 years ago by alimanfoo
  0

• if no variants match region, defaults to all variants?

  #15 opened 11 years ago by alimanfoo
  0

• variants() throws ValueError reporting two fields with the same name?

  #16 opened 11 years ago by alimanfoo
  1

• combine info() and variants()

  #18 opened 11 years ago by alimanfoo
  1

• flatten FILTER

  #17 opened 11 years ago by alimanfoo
  1

• calldata_2d

  #19 opened 11 years ago by alimanfoo
  0

• auto cache

  #20 opened 11 years ago by alimanfoo
  0

• handle missing INFO declarations in header

  #14 opened 11 years ago by alimanfoo
  1

• Gracefully handle VCFs with duplicate field definitions in header

  #10 opened 11 years ago by lbeltrame
  6

• support for custom parsers/transformers of INFO field values

  #12 opened 11 years ago by alimanfoo
  1

• add allele lengths custom field to variants array

  #13 opened 11 years ago by alimanfoo
  1

• Rtfd

  #8 opened 12 years ago by alimanfoo
  0

• Move parameters from comments to docstrings

  #5 opened 12 years ago by lbeltrame
  4

• workaround badly declared info types

  #4 opened 12 years ago by alimanfoo
  0