TMRCA?

[GoogleCodeExporter]

What steps will reproduce the problem?
1. N/A

What is the expected output? What do you see instead?
The times to the most recent common ancestor (TMRCA) for the loci simulated.

What version of the product are you using? On what operating system?
The SVN version downloaded Oct. 2013.

Please provide any additional information below.
I am interested in having the TMRCA for the loci that I simulated. Is there an 
easy way to pull out this from MaCS' output?

Thanks,
Benson

Original issue reported on code.google.com by hsie...@email.arizona.edu on 24 May 2014 at 5:28

[GoogleCodeExporter]

Yes this is easy.

Just check the stderr output. For example:

./macs 10 100 -r 1 -t 1 2>debug

head debug

INPUT: Sample size is now 10
INPUT: Seq length is now 100
INPUT: Scaled recombination rate is now 100
INPUT: Scaled mutation rate is now 100
Debugging: 0

Graph Builder begin
Time for build prior tree: 117 seconds
Tree:0,pos:0,len:2.24993,TMRCA:0.730033,ARG:,len:2.24993,TMRCA:0.730033
iHistoryMax: 0

The first TMRCA is for the local tree and the second is for the ARG.

Original comment by gche...@gmail.com on 26 May 2014 at 1:51

• Changed state: Accepted

[GoogleCodeExporter]

Original comment by gche...@gmail.com on 20 Jun 2014 at 4:48

• Changed state: Done