Code

Yaml input#114

Code

Merged

andrewprzh merged 17 commits intomasterablab/IsoQuant:masterfrom yaml_inputablab/IsoQuant:yaml_inputCopy head branch name to clipboardNov 6, 2023

+537-186

Commits

Commits on Oct 26, 2023

• added option for yaml file, check that not both yaml and illumina bam are given

  

  rkpfeil

  authored and

  andrewprzh

  committed
  db8e31c

• First version of extracting long read files and names from yaml. Illumina bam not yet extracted

  

  rkpfeil

  authored and

  andrewprzh

  committed
  61ae35d

Commits on Nov 6, 2023

• Added illumina file to yaml input.

  

  rkpfeil

  authored and

  andrewprzh

  committed
  9a2e3b8

• added multiple illumina bam files

  

  rkpfeil

  authored and

  andrewprzh

  committed
  c8ae10b

• do not aggregate counts in annotation-free mode

  andrewprzh

  committed
  d482b29

• added multiple illumina bams, changed readme to include yaml and illumina

  

  rkpfeil

  authored and

  andrewprzh

  committed
  9c4d723

• changed no files to critical, changed file name

  

  rkpfeil

  authored and

  andrewprzh

  committed
  ad5bd73

• changed file check to accomodate for multiple illumina bams

  

  rkpfeil

  authored and

  andrewprzh

  committed
  2579bdb

• adapting for multiple illumina bams with one sample

  

  rkpfeil

  authored and

  andrewprzh

  committed
  48aaa8f

• udate requirements

  andrewprzh

  committed
  cfb5c85

• Correcting test for single illumina file input, adding tests for multiple illumina file input

  

  rkpfeil

  authored and

  andrewprzh

  committed
  228c198

• renamed function

  

  rkpfeil

  authored and

  andrewprzh

  committed
  5f0dd18

• added illumina bam for bam file input

  

  rkpfeil

  authored and

  andrewprzh

  committed
  5dc0b2f

• switch to join

  andrewprzh

  committed
  c0427e7

• restructure input data in the readme

  andrewprzh

  committed
  385bc96

• added tests for Illumina and yaml input

  

  rkpfeil

  authored and

  andrewprzh

  committed
  b505709

• allow relative paths in yaml config

  andrewprzh

  committed
  041de73