This program analyzes large genotyping data. In particular it checks for mismatches in the data between child and mother. The program is coded in Java, using the Apache POI for treating Excel (as well as Calc) files. Consider the input size to be n times m, with n the number of individuals, and m the number of locus'. The algorithm proceeds in a linear fashion, comparing siblings' genomes to the mother's genomes. It thus runs in optimal time O(nm). Small improvements may be made to improve practical running time, but are not needed currently. Memory usage is bounded by O(m).

This README contains two parts:

• the context in which this program was developed;
• how to execute the program and read the results.

To be determined.

A specific file format is mandatory for the correctness of the results. This format is presented in format.xlsx, and two example data sets respecting this format are given in the input folder.

If this is the first time using this program, we recommend going through the first time installations below.

Once everything is installed, the program may be executed as follows:

1. Put the Excel data file (respecting the format) in input folder.

2. Open terminal in mismatchfinder folder.

3. Enter:

   sh mismatchfinder.sh
   

(This will execute the program on all files in input folder.)

4. Wait until terminal prints:

   ------------------    
   All files treated.    
   ------------------
   

5. Find results in the output folder.

The results include:

• Sheet results: for each mother, the number of mismatches is given.
• Sheet results_details: for each mismatch, the mother and descendant with corresponding genotypes are given, as well as the locus and their position in the dataset.
• Sheet locus_mismatches: for each mother and locus, the number of mismatches is given.
• Sheet heterozygous_children: for each mother and locus, the number of heterozygous siblings is given.
• Sheet mismatches_vs_heterozygous: For each mother and locus, the number of mismatches is compared to the number of heterozygous descendants.

Start by downloading mismatchfinder.zip on https://github.com/jschoete/mismatchfinder and unzip it in the desired location. A copy of this README can be found inside.

Java

1. Open terminal. (For Windows users, press windows button and enter cmd.)

2. Check if Java is installed, by entering:

   java -version
   

3. If Java is not installed, the terminal will print:

   Java command not found
   

4. In this case, install Java's latest version: https://docs.oracle.com/en/java/javase/index.html

Cygwin (for Windows users)

1. Install Cygwin: http://www.cygwin.com/

2. During setup, when prompted to select packages, search for chere package and replace skip with latest version.

3. Open Cygwin terminal (press Windows button and enter Cygwin64 Terminal) and enter:

   chere -i -t mintty -s bash
   

4. Users can now open terminals in folders through the right click menu, with Bash Prompt Here.