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

char* extractUID(char *header) {
    char *uid = strdup(header + 1); // Skip '>'
    char *end = strchr(uid, ' ');
    if (end != NULL) {
        *end = '\0'; // Terminate at the first space
    }
    return uid;
}

void printStats(char *uid, long long length, long long A_count, long long T_count, long long G_count, long long C_count, FILE *output) {
    long long total_count = A_count + T_count + G_count + C_count;
    fprintf(output, "Chromosome UID: %s\n", uid);
    fprintf(output, "Length: %lld\n", length);
    fprintf(output, "Nucleotide frequencies:\n");
    fprintf(output, "A: % 10lld % 5.2f%%\n", A_count, ((double)A_count / total_count) * 100);
    fprintf(output, "T: % 10lld % 5.2f%%\n", T_count, ((double)T_count / total_count) * 100);
    fprintf(output, "G: % 10lld % 5.2f%%\n", G_count, ((double)G_count / total_count) * 100);
    fprintf(output, "C: % 10lld % 5.2f%%\n", C_count, ((double)C_count / total_count) * 100);
    fprintf(output, "GC content:    %.2f%%\n\n", ((double)(G_count + C_count) / total_count) * 100);
}


void printFileContent(FILE *file) {
    int c;
    rewind(file);
    while ((c = fgetc(file)) != EOF) {
        putchar(c);
    }
    printf("\n");
}

void processFasta(FILE *fasta, FILE *output) {
    char *line = NULL;
    size_t len = 0;
    ssize_t read;
    char *currentUID = NULL;
    int in_sequence = 0;
    long long A_count = 0, T_count = 0, G_count = 0, C_count = 0, length = 0;
    long long A_global_count = 0, T_global_count = 0, G_global_count = 0, C_global_count = 0, length_global = 0;

    while ((read = getline(&line, &len, fasta)) != -1) {
        if (line[0] == '>') {
            if (in_sequence) {
                length_global += length;
                A_global_count += A_count;
                T_global_count += T_count;
                G_global_count += G_count;
                C_global_count += C_count;
                printf("Processing chromosome: %s\n", currentUID);
                printStats(currentUID, length, A_count, T_count, G_count, C_count, output);
                free(currentUID);
                A_count = T_count = G_count = C_count = length = 0;
            }
            currentUID = extractUID(line);
            in_sequence = 1;
        } else {
            for (int i = 0; line[i] != '\0' && line[i] != '\n'; i++) {
                char c = toupper(line[i]);
                if (isalpha(c)) {
                    length++;
                    if (c == 'A') {
                        A_count++;
                    } else if (c == 'T') {
                        T_count++;
                    } else if (c == 'G') {
                        G_count++;
                    } else if (c == 'C') {
                        C_count++;
                    }
                }
            }
        }
    }

    if (in_sequence) {
        length_global += length;
        A_global_count += A_count;
        T_global_count += T_count;
        G_global_count += G_count;
        C_global_count += C_count;
        printf("Processing chromosome: %s\n", currentUID);
        printf("A=%lld, G=%lld, C=%lld, T=%lld\n\n", A_count, G_count, C_count, T_count);
        printStats(currentUID, length, A_count, T_count, G_count, C_count, output);
        free(currentUID);
    }

    fprintf(output, "=============================================\nSummary statistics for the whole human genome.\n");
    printStats("WholeGenome", length_global, A_global_count, T_global_count, G_global_count, C_global_count, output);

    free(line);
}

int main() {
    FILE *fasta = fopen("/home/lukaskoz/tmp/lab7_wdi/chm13v2.0.fa", "r");
    //FILE *fasta = fopen("/home/lukaskoz/tmp/lab7_wdi/chm13v2.0.fa_5M", "r"); //%M contains 2 chromosomes only
    FILE *output = fopen("/home/lukaskoz/tmp/lab7_wdi/genome_stats_full.txt", "w");

    if (fasta == NULL || output == NULL) {
        perror("Error opening files");
        return 1;
    }

    processFasta(fasta, output);

    fclose(fasta);
    fclose(output);

    // Display output file content
    FILE *outputFile = fopen("/home/lukaskoz/tmp/lab7_wdi/genome_stats_full.txt", "r");
    if (outputFile == NULL) {
        perror("Error opening output file");
        return 1;
    }

    printf("\n\n=============================================\n\nContent of output file:\n\n");
    printFileContent(outputFile);

    fclose(outputFile);

    return 0;
}