v0.1.0-rc.1

Capabilities

This is the first release candidate of yamet v0.1.0 after refactoring and rewriting in C++.

• Offers a sample entropy within cells, Shannon's entropy across cells, average methylation by/across cells in C++
• Includes simplistic tests on simulated data and valgrind and cppcheck profiling

Known issues

Requires GCC > 13.

Installation

cd method
bash build.sh

Usage

• CLI takes a reference file listing cytosine coordinates, as many (covered) cytosine reports as cells, and a bedfile to filter in regions to calculate the metrics from. Metrics are calculated per bedfile interval.
• CLI help:

input:
  -t [ --tsv ] arg                      tab separated files for different cells
                                        in the following format
                                        
                                         1    5    0    2    0
                                         1    9    1    1    1
                                         2    2    3    4    1
                                        
                                        where the columns are the chromosome, 
                                        position, number of methylated reads, 
                                        total number of reads and the rate 
                                        respectively
  -r [ --ref ] arg                      tab separated file for reference sites 
                                        in the following format
                                        
                                         1    5     7
                                         1    7     9
                                         1    9     11
                                         1    11    13
                                         2    2     4
                                         2    4     6
                                        
                                        where the columns are the chromosome, 
                                        start position and the end position 
                                        respectively
  -b [ --bed ] arg                      path to bed file for regions of 
                                        interest in the following format
                                        
                                         1    5     7
                                         1    10    30
                                         2    1     6
                                        
                                        where the columns are the chromosome, 
                                        start position and the end position 
                                        respectively

output:
  -d [ --det-out ] arg                  (optional) path to detailed output file
  -o [ --out ] arg                      (optional) path to simple output file

resource utilisation:
  --n-cores arg (=0)                    number of cores used for simultaneously
                                        parsing methylation files
  --n-threads-per-core arg (=1)         number of threads per core used for 
                                        simultaneously parsing methylation 
                                        files

verbose:
  --print-bed                           print parsed regions file
  --print-ref                           print parsed reference file
  --print-sampens [=arg(=true)] (=true) print computed sample entropies

misc:
  -h [ --help ]                         produce help message
  --version                             current version information