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#include <stdlib.h>
#include <stdio.h>
#include <string.h>
#include "bitread.h"
#include "sequence.h"
#include "error.h"
void genRandomSequence(char * str, int len) {
for (int i = 0; i < len; i++) {
switch (rand() % 4) {
case 0:
str[i] = 'A';
break;
case 1:
str[i] = 'C';
break;
case 2:
str[i] = 'G';
break;
case 3:
str[i] = 'T';
break;
}
}
}
bool testExtract() {
int len, offset;
int i, j;
char str[1024], str1[256];
char * fname[1];
int64 space[16];
int64 * key = &space[8];
int ret;
fname[1] = new char[128];
strcpy(fname[1], "./tmp_test.fa");
genRandomSequence(str, 1000);
FILE * file = fopen(fname[1], "w");
for (i = 0; i < 20; i++) {
for (j = 0; j < 50; j++) {
fprintf(file, "%c", str[i * 50 + j]);
}
fprintf(file, "\n");
}
fclose(file);
CompactSequence * sequence = new CompactSequence(true);
sequence->build(fname, 1, 36, 2);
if (ret != SUCCESS)
{
printf("Failed to load reference sequences.\n");
return false;
}
int64 * seq = sequence->getSequence();
printf("Testing extract... ");
for (len = 36; len <= 36; len++) {
offset = rand() % 500;
BitRead::extract(seq, key, offset * BITS_PER_BASE, len * BITS_PER_BASE);
CompactSequence::decompose(str1, len, key);
for (i = 0; i < len; i++) {
if (str[i + offset] != str1[i]) {
printf("Failed at %d bps\n", len);
return false;
}
}
}
printf("Passed\n");
return true;
}
bool testRemoveHead() {
int len;
int head, i;
char str1[256], str2[256];
int64 space1[16], space2[16];
int64 mask[WORDS_PER_READ];
int64 * key1, *key2;
key1 = &space1[8];
key2 = &space2[8];
printf("Testing remove head... ");
for (len = 36; len <= 128; len++) {
genRandomSequence(str1, len);
CompactSequence::compose(str1, len, key1);
for (head = len - 10; head < len; head++) {
BitRead::genHeadMask(mask, head * BITS_PER_BASE);
BitRead::removeHead(key1, key2, mask);
CompactSequence::decompose(str2, head, key2);
/*
printf("\n");
for (i = 0; i < len; i++)
printf("%c", str1[i]);
printf("\n");
for (i = 0; i < len - head; i++)
printf(" ");
for (i = 0; i < head; i++)
printf("%c", str2[i]);
printf("\n");
*/
//check
for (i = 0; i < head; i++) {
if (str1[i + len - head] != str2[i]) {
printf("Failed at %d bps, %d head\n", len, head);
return false;
}
}
}
}
printf("Passed\n");
return true;
}
bool testRemoveInterval() {
int len;
int p, offset, i;
char str1[256], str2[256];
int64 space1[16], space2[16];
int64 * key1, *key2;
key1 = &space1[8];
key2 = &space2[8];
printf("Testing remove interval... ");
for (len = 36; len <= 128; len++) {
genRandomSequence(str1, len);
CompactSequence::compose(str1, len, key1);
for (p = 2; p <= 8; p++) {
for (offset = 0; offset < len / p * p; offset += len / p) {
BitRead::removeInterval(key1, key2, offset * BITS_PER_BASE
, len / p * BITS_PER_BASE);
CompactSequence::decompose(str2, len - len / p, key2);
/*
for (i = 0; i < len; i++)
printf("%c", str1[i]);
printf("\n");
for (i = 0; i < len - offset - len/p; i++)
printf("%c", str2[i]);
for (i = 0; i < len/p; i++)
printf(" ");
for (i = len - offset - len/p; i < len - len/p; i++)
printf("%c", str2[i]);
printf("\n\n");
*/
//check
for (i = 0; i < len - offset - len / p; i++) {
if (str1[i] != str2[i]) {
printf("Failed at %d bps, %d partition, %d offset\n", len, p,
offset);
return false;
}
}
for (i = len - offset - len / p; i < len - len / p; i++) {
if (str1[i + len / p] != str2[i]) {
printf("Failed at %d bps, %d partition, %d offset\n", len, p,
offset);
return false;
}
}
}
}
}
printf("Passed\n");
return true;
}
int main() {
int i = 1;
int j = 2;
// testExtract();
testRemoveHead();
testRemoveInterval();
return 0;
}
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