chrome_funcs.c

#include "chrome_funcs.h"

// Add chrome name to hash table
void init_chrome_hash(HashNode** hashTable, int* hash_table_size, char** chrName, int chrCnt)
{
    int i;
    for(i = 0; i < chrCnt; i++) {
        hash_table_insert(hashTable, hash_table_size, chrName[i], i);
    }
	fprintf(stderr, "%d chromes loaded.\n", i);
}

// Init chrome name array and length array
void init_chrome_name_len(char* refSeqFile, int* chrCnt, char** chrName, int* chrLen)
{
    char* readBuffer = (char*)malloc(sizeof(char) * BUFSIZE);
	int len = 0;
	int lines = 0;
	int chrNum = 0;

	FILE* iFPtr;
    char* token;
	char seps[] = " \t\n\r";
	char chrNameCur[200];

    if(!(iFPtr = fopen(refSeqFile, "r"))) {
		printf("File %s open error.\n", refSeqFile);
		exit(1);
	}

    while(fgets(readBuffer, BUFSIZE, iFPtr)) {
		if(strlen(readBuffer) >= BUFSIZE - 1) {
            fprintf(stderr, "Too many characters in one row! Try to split the long row into several short rows (fewer than %d characters per row).\n", BUFSIZE);
            exit(1);
        }

		if(readBuffer[0] == '>') {
            if(lines > 0) {
                // Save name and length
                strcpy(chrName[chrNum], chrNameCur);
                chrLen[chrNum] = len;
                chrNum++;
                // Check
                if(chrNum == INITIAL_CHR_NUM - 1) {
                    fprintf(stderr, "Too many chromesomes!\n");
                    exit(1);
                }
            }
			token = strtok(readBuffer + 1, seps);
			strcpy(chrNameCur, token);
			len = 0;
		}
		else {
			// Substract \n
			len += strlen(readBuffer) - 1;
		}

		lines++;
	}

	if(lines > 0) {
		strcpy(chrName[chrNum], chrNameCur);
        chrLen[chrNum] = len;
        chrNum++;
	}

    *chrCnt = chrNum;

    fclose(iFPtr);
    free(readBuffer);
}

// Load seq content array
void init_chrome_seq(HashNode** hashTable, char* refSeqFile, char** chrSeqArray, int* chrLen)
{

	FILE* fPtr = fopen(refSeqFile, "r");
	if(!fPtr) {
		// Check file existance
		printf("File %s open error.\n", refSeqFile);
		exit(1);
	}
	fclose(fPtr);

	char* readBuffer = chrSeqArray[0];
	int readBufferPtr = 0;
	int readSeqPtr = 0;
	int lines = 0;

	char* token;
	char seps[] = " \t\n\r";
	char chrName[50];

	fPtr = fopen(refSeqFile, "r");
	while(fgets(readBuffer + readBufferPtr, BUFSIZE, fPtr)) {
		if(*(readBuffer + readBufferPtr) == '>') {
			if(lines > 0) {
				// Check old buffer
				if(readBufferPtr != chrLen[readSeqPtr] ) {
					printf("Length of seq %s error! %d vs %d!\n", chrName, readBufferPtr, chrLen[readSeqPtr]);
					exit(1);
				}
			}
			// Set new buffer
			token = strtok(readBuffer + readBufferPtr + 1, seps);
			strcpy(chrName, token);
			readSeqPtr = hash_table_lookup(hashTable, chrName);
			if(readSeqPtr == -1) {
				printf("Error find sequence with name %s!\n", chrName);
				exit(1);
			}
			readBuffer = chrSeqArray[readSeqPtr];
			readBufferPtr = 0;
		}
		else {
			// Substract \n
			readBufferPtr += strlen(readBuffer + readBufferPtr) - 1;
			// Check buffer boundary
			if(readBufferPtr > chrLen[readSeqPtr]) {
				printf("Length of seq %s error at line %d! %d vs %d!\n", chrName, lines, readBufferPtr, chrLen[readSeqPtr]);
				exit(1);
			}
		}

		lines++;
	}
	// Check old buffer
	if(readBufferPtr != chrLen[readSeqPtr] ) {
		printf("Length of seq %s error! %d vs %d!\n", chrName, readBufferPtr, chrLen[readSeqPtr]);
		exit(1);
	}
	fclose(fPtr);
}