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]
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.