awk '/SVTYPE=Fusion/{                                                                                                 #### Searching the string SVTYPE=Fusion on each line. If it is found then perform following actions.
                        match($5,/].*]/);                                                                             #### Using match functionality by providing the regex where it will match from ] to till ] in 5th field.
                        sub(/.COS.*/,"",$3);                                                                          #### Substituting the .COS.* means from .COS to everything to NULL in 3rd field.
                        sub(/-/,"",$3);                                                                               #### Substituting -(dash) with NULL in 3rd field.
                        sub(/\./,"-",$3);                                                                             #### Substituting DOT with - in 3rd field.
                        VAL=substr($5,RSTART+1,RLENGTH-2);                                                            #### Putting the values of subtring whose value starts from RSTART+1 to RLENGTH-2, here point to be noted RSTART and RLENGTH are the OOTB awk's keywords which will be SET when a match is found, we have done this match for 5th field above.
                        num=split($8, array,";");                                                                     #### Splitting field 8th whose delimiter is ";" and storing it's length(array's length) to variable named num. 
                        for(i=1;i<=num;i++){                                                                          #### Starting a loop which will start from value 1 of variable i to till value of variable num.
                                                if(array[i] ~  /SVTYPE/){                                             #### Checking here condition if any array's value is equal to /SVTYPE/ then do following.
                                                sub(/.*=/,"",array[i]);                                               #### If above condition is TRUE then substituting the .*= everything till = to NULL in array[i]'s value.
                                                svtype=array[i];                                                      #### Keeping array[i]'s value in variable named svtype.
                                                                        };
                                                if(array[i] ~ /READ_COUNT/){                                          #### Checking another condition where checking if array a's value is equal to /READ_COUNT/ then perform following actions.
                                                sub(/.*=/,"",array[i]);                                               #### substituting everything till = to NULL in array[i]'s value.
                                                read_count=array[i]                                                   #### Storing value of array[i]'s in read_count.
                                                                           }
                                           };
                        match($0,/oncomineGeneClass.*,/);                                                             #### Using match function of awk to perform a match from  /oncomineGeneClass.*/ here.
                        print $1":"$2 "-" VAL OFS svtype OFS substr($0,RSTART+20,RLENGTH-22) OFS $3 OFS read_count;   #### printing the values of $1, $2, VAL(which is having the values of 1st match which we performed above for $5), svtype, subtring of above used match for /oncomineGeneClass.* then read_count values.
                    }
    '   Input_file                                                                                                    #### Mentioning the Input_file.