1.5.9

Merge pull request #27 from oicr-gsi/fix-low-count

Fix low count

1.5.8

• Changed call-hrdetect such that now tumours with low mutation counts are counted as HRD- rather than as failing QC
• Added R tests and accompanying simulated test data

v1.3.4

avoids crash on zero signatures fit

v1.3.3

More catches for low numbers of variants

v1.3.2

Do not extend LOH segments

v1.3.1

fixed bug in indel cutoff

v1.3

Merge pull request #8 from oicr-gsi/update-Rprocess

Update R processes

v1.2

Updated sigTools_runthrough.R to function with update to sigtools (from 2.0 to 2.1.2)
Added optparse to sigTools_runthrough.R

v1.1

Updates incl.

• Changed name of workflow to HRDetect
• Changed plotting from .pdf to .png, and changes intake format
• Annotated HRDetect R results script, added loop for low indel results and added genomeVersion argument
• merged SNV and INDEL filtering using alias in wdl
• added filtering option parameters (instead of hardcoded)

v1.0

Merge pull request #4 from oicr-gsi/first_script

First script