CAST-genomics/haptools

Issues

• snplist support in the `ld` command

  #245 opened 7 months ago by aryarm
  0

• feat: a `dosage` command for storing TR motif counts in PGEN files

  #221 opened a year ago by aryarm
  2

• feat: a `validate` subcommand to check whether a `.hap` file is valid

  #47 opened 3 years ago by aryarm
  3

• github actions and publishing releases

  #117 opened 2 years ago by aryarm
  1

• parallelize reading from a PGEN file

  #253 opened 7 months ago by aryarm
  0

• improvements to the Data module

  #19 opened 3 years ago by aryarm
  2

• Expanding population before simgenotype?

  #242 opened a year ago by KangchengHou
  3

• docs: fix images

  #239 opened a year ago by aryarm
  1

• Provided blocks.det to .hap code produces error

  #235 opened a year ago by RJDan
  7

• Error when using centromeres file for karyogram

  #233 opened a year ago by gymreklab
  0

• speeding up the `transform` command

  #92 opened 2 years ago by aryarm
  6

• support for a TR-based GenotypesPLINK class

  #73 opened a year ago by aryarm
  2

• increase our testing coverage

  #205 opened 2 years ago by aryarm
  0

• support for a TR-based Haplotype class

  #164 opened 2 years ago by aryarm
  2

• feat: add a command or parameter to allow merging of haplotype and genotype VCFs

  #82 opened 2 years ago by aryarm
  4

• pgenlib/numpy binary incompatibility issue

  #138 opened 2 years ago by aryarm
  2

• docs: updates ahead of v0.1.0

  #169 opened 2 years ago by aryarm
  0

• add a `check_sorted()` method for the `data.Genotypes` class

  #161 opened 2 years ago by aryarm
  0

• PGEN support for `simgenotype`

  #99 opened 2 years ago by aryarm
  5

• a flag for `simgenotype` that disables the extra FORMAT fields

  #160 opened 2 years ago by aryarm
  0

• feat: a `--no-normalize` flag for simphenotype

  #147 opened 2 years ago by aryarm
  1

• numpy error when testing `simgenotype`

  #149 opened 2 years ago by armartin
  3

• VCF writing in simgenotype is very slow

  #148 opened 2 years ago by s041629
  3

• genotypes that are all the same can lead to 0s in `simphenotype`

  #95 opened 2 years ago by aryarm
  2

• We need a documentation page about our file formats

  #38 opened 2 years ago by gymreklab
  1

• a new strategy for classes in the data module

  #49 opened 2 years ago by aryarm
  1

• improve docs

  #125 opened 2 years ago by aryarm
  1

• describe logging and `--verbosity` better in the docs

  #118 opened 2 years ago by aryarm
  1

• feat: an `index` subcommand to sort and index a `.hap` file

  #48 opened 2 years ago by aryarm
  2

• exclude haplotypes if they don't fit within a `--region` perfectly

  #93 opened 2 years ago by aryarm
  0

• support for bgzipped and tabix-indexed map files

  #120 opened 2 years ago by aryarm
  1

• loosen requirements for pysam

  #113 opened 2 years ago by aryarm
  0

• handle nan in `Phenotypes.standardize()`

  #11 opened 2 years ago by aryarm
  0

• QoL improvements for the `transform` subcommand

  #75 opened 2 years ago by aryarm
  0

• Simgenotype Test Cases: Parameter Validation

  #54 opened 2 years ago by mlamkin7
  0

• make header lines in a `.hap` file immune to sorting

  #65 opened 2 years ago by aryarm
  2

• stop complaining about additional "extra" fields in the Haplotypes class

  #66 opened 2 years ago by aryarm
  0

• try cases where `.hap` file does not follow format exactly

  #51 opened 2 years ago by aryarm
  5

• documentation for the data module

  #50 opened 2 years ago by aryarm
  1

• test the `data.genotypes.GenotypesRefAlt` class

  #52 opened 2 years ago by aryarm
  0

• support for a haps format spec that extends the VCF format spec

  #33 opened 3 years ago by aryarm
  8

• can we merge the happler and haptools format specs for haplotypes?

  #25 opened 3 years ago by aryarm
  6

• feat: use Hail within the Genotypes class

  #46 opened 3 years ago by aryarm
  1

• allow writing Haplotype objects one by one instead of all at once

  #44 opened 3 years ago by aryarm
  0

• add md files to `docs/`

  #18 opened 3 years ago by aryarm
  1

• Need to deal with centromeres in karyogram plots

  #30 opened 3 years ago by gymreklab
  1

• move py files out of subdirectories?

  #23 opened 3 years ago by aryarm
  0

• need to add matplotlib dependency

  #22 opened 3 years ago by aryarm
  1

• what do we want this tool to be able to do?

  #13 opened 3 years ago by aryarm
  1

• add tests for the data module

  #9 opened 3 years ago by aryarm
  0