search

odelaneau / shapeit5

Segmented HAPlotype Estimation and Imputation Tool
https://odelaneau.github.io/shapeit5/
MIT License
61 stars 9 forks source link

ligater_initialise.cpp typo? #40

Open schnabelr opened 1 year ago

schnabelr commented 1 year ago

When looking at the log for ligate I noticed something that doesn't seem right. It appears that when using a pedigree, it prints the file name from the file listing the chunks to ligate rather than the pedigree file name. It looks like this is in ligater_initialise.cpp lines 43-59. Everything works fine, it just looks like it is printing the wrong file name.

cat TEST051.P.1.25.ligate.log

Files:
  * Input LIST     : [TEST051.P.1.25.common.chunks.txt]
  * Output VCF     : [test.bcf]
  * Index output   : [NO]
  * Output LOG    : [TEST051.P.1.25.ligate.log]

Parameters:
  * Seed           : [15052011]
  * #Threads       : [4]

Read filenames in [TEST051.P.1.25.common.chunks.txt]
  * #files = 2

Read filenames in [TEST051.P.1.25.common.chunks.txt] <-- should be file from --pedigree [FileName]
  * PED file parsing [n=630]
odelaneau commented 1 year ago

Thanks for reporting this! I'll fix this asap.