BUG: default parameters output log_transcription_quotients_vmax.txt instead of log_transcription_quotients.txt

[stanfish06]

Hello! I cloned and compiled the latest code, and after I ran Sanity with default parameters, I got the _vmax.txt matrix, which, according to readme, should only be generated if I explicitly set -max_v.

Here is how to reproduce this behavior

stanfish@StanFishDeb:~/tmp$ git clone https://github.com/jmbreda/Sanity.git
Cloning into 'Sanity'...
remote: Enumerating objects: 634, done.
remote: Counting objects: 100% (114/114), done.
remote: Compressing objects: 100% (19/19), done.
remote: Total 634 (delta 104), reused 97 (delta 95), pack-reused 520 (from 2)
Receiving objects: 100% (634/634), 1.62 MiB | 6.15 MiB/s, done.
Resolving deltas: 100% (311/311), done.
stanfish@StanFishDeb:~/tmp$ cd Sanity/src/
stanfish@StanFishDeb:~/tmp/Sanity/src$ make
g++ -I. -O2 -ffast-math -O3 -fopenmp -std=c++11 -c calc_true_variation_parallel_prior_mu_sigma.cpp
g++ -I. -O2 -ffast-math -O3 -fopenmp -std=c++11 -c ReadInputFiles.cpp
g++ -I. -O2 -ffast-math -O3 -fopenmp -std=c++11 -c FitFrac.cpp
g++ -I. -O2 -ffast-math -O3 -fopenmp -std=c++11 -c FukushimaLambertW.cc
g++ -I. -O2 -ffast-math -O3 -fopenmp -std=c++11 -c Digamma_Trigamma.cpp
g++ -I. -O2 -ffast-math -O3 -fopenmp -std=c++11 -o ../bin/Sanity calc_true_variation_parallel_prior_mu_sigma.o ReadInputFiles.o FitFrac.o FukushimaLambertW.o Digamma_Trigamma.o
stanfish@StanFishDeb:~/tmp/Sanity/src$ cd ../bin/
stanfish@StanFishDeb:~/tmp/Sanity/bin$ ls -l
total 2252
-rwxrwxr-x 1 stanfish stanfish   98608 Feb  3 14:48 Sanity
-rwxrwxr-x 1 stanfish stanfish   45800 Feb  3 14:48 Sanity_distance
-rwxrwxr-x 1 stanfish stanfish   45608 Feb  3 14:48 Sanity_gene_correlation
-rwxrwxr-x 1 stanfish stanfish 2103884 Feb  3 14:48 Sanity_macOS
stanfish@StanFishDeb:~/tmp/Sanity/bin$ cat > matrix.csv <<'EOF'
1,2,3
4,5,6
7,8,9
10,11,12
EOF
stanfish@StanFishDeb:~/tmp/Sanity/bin$ cat matrix.csv
1,2,3
4,5,6
7,8,9
10,11,12
stanfish@StanFishDeb:~/tmp/Sanity/bin$ ./Sanity -f matrix.csv
File type : csv
There were 3 rows
There were 3 genes and 2 cells
Estimated memory usage: 33 KB
Fit gene expression levels
First process now fitting gene 0 out of 0.
Print output
stanfish@StanFishDeb:~/tmp/Sanity/bin$ ls -l
total 2264
-rw-rw-r-- 1 stanfish stanfish      73 Feb  3 14:52 log_transcription_quotients_vmax.txt
-rw-rw-r-- 1 stanfish stanfish      63 Feb  3 14:52 ltq_error_bars_vmax.txt
-rw-rw-r-- 1 stanfish stanfish      27 Feb  3 14:52 matrix.csv
-rwxrwxr-x 1 stanfish stanfish   98608 Feb  3 14:48 Sanity
-rwxrwxr-x 1 stanfish stanfish   45800 Feb  3 14:48 Sanity_distance
-rwxrwxr-x 1 stanfish stanfish   45608 Feb  3 14:48 Sanity_gene_correlation
-rwxrwxr-x 1 stanfish stanfish 2103884 Feb  3 14:48 Sanity_macOS
stanfish@StanFishDeb:~/tmp/Sanity/bin$ rm log_transcription_quotients_vmax.txt ltq_error_bars_vmax.txt
stanfish@StanFishDeb:~/tmp/Sanity/bin$ ls -l
total 2256
-rw-rw-r-- 1 stanfish stanfish      27 Feb  3 14:52 matrix.csv
-rwxrwxr-x 1 stanfish stanfish   98608 Feb  3 14:48 Sanity
-rwxrwxr-x 1 stanfish stanfish   45800 Feb  3 14:48 Sanity_distance
-rwxrwxr-x 1 stanfish stanfish   45608 Feb  3 14:48 Sanity_gene_correlation
-rwxrwxr-x 1 stanfish stanfish 2103884 Feb  3 14:48 Sanity_macOS
stanfish@StanFishDeb:~/tmp/Sanity/bin$ ./Sanity -f matrix.csv -max_v false
File type : csv
There were 3 rows
There were 3 genes and 2 cells
Estimated memory usage: 33 KB
Fit gene expression levels
First process now fitting gene 0 out of 0.
Print output
stanfish@StanFishDeb:~/tmp/Sanity/bin$ ls -l
total 2264
-rw-rw-r-- 1 stanfish stanfish      73 Feb  3 14:53 log_transcription_quotients.txt
-rw-rw-r-- 1 stanfish stanfish      65 Feb  3 14:53 ltq_error_bars.txt
-rw-rw-r-- 1 stanfish stanfish      27 Feb  3 14:52 matrix.csv
-rwxrwxr-x 1 stanfish stanfish   98608 Feb  3 14:48 Sanity
-rwxrwxr-x 1 stanfish stanfish   45800 Feb  3 14:48 Sanity_distance
-rwxrwxr-x 1 stanfish stanfish   45608 Feb  3 14:48 Sanity_gene_correlation
-rwxrwxr-x 1 stanfish stanfish 2103884 Feb  3 14:48 Sanity_macOS
stanfish@StanFishDeb:~/tmp/Sanity/bin$

As you can see, I need to explicitly set -max_v false to get the standard output. Correct me if wrong but I think log_transcription_quotients.txt should be the default output according to the readme.

So I checked the source code, it appears that at line 755 in calc_true_variation_parallel_prior_mu_sigma.cpp, max_v_str is initialized to "true".

int N_param(11);
string extended_output("false");
string no_norm_str("false");
string max_v_str("true");

If an user doesn't specify -max_v, then at line 812, max_v_output will be set to true

if ( max_v_str == "true" || max_v_str == "1" || max_v_str == "only_max_output"){
	max_v_output = true;
	post_v_output = false;
	}

Is this an intended behavior or a bug? Thank you for your time.

[hsuknowledge]

Same observation from me. Please go on to create a pull request fixing that line to init to "false"