Code

merge devel into master#143

Code

Merged

Lioscro merged 28 commits intomasterpachterlab/kb_python:masterfrom develpachterlab/kb_python:develCopy head branch name to clipboardJan 19, 2022

+11,841-2,004

Commits

Commits on Jun 10, 2021

• error when no fastqs are found for -x smartseq

  Lioscro

  committed
  b1f2e83

Commits on Jun 22, 2021

• don't remove all variants on collision

  Lioscro

  committed
  d31aa9f

• fix code quality

  Lioscro

  committed
  72e1ad6

Commits on Jul 25, 2021

• bulk and smartseq2

  Lioscro

  committed
  e2ccff3

• smartseq3

  Lioscro

  committed
  57761d8

• Merge branch 'devel' of github.com:pachterlab/kb_python into devel

  Lioscro

  committed
  e0c4b17

Commits on Jul 26, 2021

• add compile command

  Lioscro

  committed
  d8854e5

Commits on Jul 28, 2021

• GTF attribute filtering

  Lioscro

  committed
  de2c198

• bump ngs-tools to 1.5.4

  Lioscro

  committed
  e02216f

Commits on Jul 29, 2021

• use full binary path for --dry-run

  Lioscro

  committed
  cce95d5

Commits on Aug 2, 2021

• disable default for target in compile

  Lioscro

  committed
  9dcadcb

• add --cmake-arguments to compile

  Lioscro

  committed
  724478f

• fix processing hanging due to full buffer

  Lioscro

  committed
  dc9ec90

Commits on Aug 5, 2021

• update smartseq2 and bulk description

  Lioscro

  committed
  2323d3a

Commits on Aug 11, 2021

• don't provide ecmap to bustools inspect

  Lioscro

  committed
  047320f

Commits on Aug 19, 2021

• add --umi-gene and --em options

  Lioscro

  committed
  23e4522

Commits on Aug 20, 2021

• google-style docstrings and typings

  Lioscro

  committed
  df87e26

• update bustools binaries

  Lioscro

  committed
  0ec0861

Commits on Sep 15, 2021

• use semicolon as delimiter instead of comma for transcript_ids columns

  Lioscro

  committed
  f43b02f

Commits on Sep 22, 2021

• fix count directory + better output file validation

  Lioscro

  committed
  2b321b9

• set non-index as categoricals

  Lioscro

  committed
  4cb22fd

• add --gene-names option

  Lioscro

  committed
  0d0d89b

Commits on Oct 21, 2021

• remove --lamanno and --nucleus checks

  Lioscro

  committed
  514e98b

Commits on Oct 25, 2021

• add --ref option to compile

  Lioscro

  committed
  699ca2e

Commits on Jan 19, 2022

• update kallisto binaries and add binary compatibility checks

  Lioscro

  committed
  35e8bb6

• update ci workflow to include python 3.9

  Lioscro

  committed
  8be77e1

• include python 3.9 in setup.py

  Lioscro

  committed
  068c9ef

• Merge branch 'master' into devel

  Lioscro

  authored
  75bd9c9