#include <stdio.h>
#include <stdlib.h>
#include <string.h>

#define MAXLEN 4096                            //Line 5, at this moment no string longer than 4096 is allowed.

//strmerg was from: http://effprog.wordpress.com/2010/11/18/concatenation-of-two-strings-omitting-overlapping-string/
char *strmerg(char *dst, char *src)                    //Line 8
{
    size_t dstLen = strlen(dst);
    size_t srcLen = strlen(src);

    char *p = dst + dstLen + srcLen;            /* Line 13, Pointer to the end of the concatenated string */
    char *q = src + srcLen - 1;                    /* Line 14, Pointer to the last character of the src */
    char *r = dst + dstLen - 1;                    /* Line 15, Temp Pointer to the last character of the dst */
    char *end = r;                                /* Line 16, Permanent Pointer to the last character of the dst */
    *p = '\0';                                    /*terminating the concatened string with NULL character */

    while (q >= src) 
{                                                /*Copy src in reverse */
    if (*r == *q) {                                /*Till it matches with the src, decrement r */
        r--;
    } else {
        r = end;
        if (*r == *q) {
        r--;
        }
    }

    *p-- = *q--;
    }

    while (r >= dst)                            /*Copy dst, ending with r */
    *p-- = *r--;

    return p + 1;                                //pointer of string, i.e. the start of string
}

int main(int argc, char **argv)                    //Line 39
{
    const char *str1 = argv[1];                 //Line 41, Original two strings
    const char *str2 = argv[2];                    //Line 42, Original two strings
    char *str3;                                    //Line 43, resulting string

    str1 = malloc(sizeof(char) * MAXLEN);        //Line 45, allocate memory
    str2 = malloc(sizeof(char) * MAXLEN);        //Line 46, allocate memory

    if (argc != 3) {
    printf("Error! \nUsage: ./arg[0]=program argv[1]=string1 argv[2]=string2\n");
    exit(EXIT_FAILURE);
    }

    strcpy(str1, argv[1]);                        //Line 53, 
    strcpy(str2, argv[2]);                        //Line 54, 

    str3=strmerg(str1, str2);                    //Line 56,
    
    printf("Input strings are: \nSeq1=%s\nSeq2=%s\n", str1, str2);
    printf("\nConcatenated string is: Seq_merged=%s\n", str3);
    printf("\nConcatenated string is: Seq_merged=%s\n", strmerg(str1, str2));
    return 0;
}

./prog ACGTGatatat  atatGTGTGTGT  
Input strings are: 
Seq1=ACGTGACGTGatatatGTGTGTGT       //Extra ACGTG
Seq2=atatGTGTGTGT

Concatenated string is: Seq_merged=ACGTGatatatGTGTGTGT
Concatenated string is: Seq_merged=ACGTGACGTGatatatGTGTGTGT           //Extra ACGTG

./prog ACGTGatat   atatatGTGTGTGT  
Input strings are: 
Seq1=ACGTGACGTGatatatGTGTGTGT       //Extra ACGTG
Seq2=atatGTGTGTGT

Concatenated string is: Seq_merged=ACGTGatatatatGTGTGTGT
Concatenated string is: Seq_merged=ACGTGACGTGatatatatGTGTGTGT           //Extra ACGTG