Error in my code

Hi all,

I am working on a project that needs to check columns to see if they have duplicate strings, which needs to continue through checking after finding a duplicate but also then to iterate towards other duplicates.

I have a sample matrix:

and this has a number of duplicates along the top. What needs to happen is for each duplicate, it moves the '1' in the column to the first occurance of that string, replaces the duplicate with 0, and replaces the column name. Something like this (but this isnt quite right, its what I have right now, see column 4, 6, 9, 10 are the same but nothing has happened):

As you can see, it is doing a part of what I want, but it is not going through all of them. My code:

matrix=matrix1; //creates duplicate matrix to work in
[no_patients, no_mutations] = size(matrix);
for column_index = 2:no_mutations //first for loop, going through all columns
for column_index2 = 3:no_mutations //second for loop, going through all columns +1 from previous.
    if (strncmp(matrix{1, column_index}, matrix{1,column_index2},28)==1) //check the strings are the same

      for row_index = 2:no_patients //go through rows in that column to find the 1 and clean up
        if matrix{row_index,column_index2} == 1
          matrix{row_index,column_index} = 1;
          matrix{1,column_index2} = duplicate; //sets the string to 'duplicate'
          matrix{row_index,column_index2} = 0;

        end
      end

    end

  end
  break; // Without this break, it doesnt work as expected.

end

As noted there, without that break, it doesnt work as expected at all:

I would really appreciate some advice on what i have wrong with my code. Coding is not my strong point and this does need to work on a very large matrix, so i hope i am not too far off.

Thanks for any help!!