static stList *getRandomPairwiseAlignments() {
stList *pairwiseAlignments = stList_construct3(0, (void(*)(void *)) destructPairwiseAlignment);
int64_t randomAlignmentNumber = st_randomInt(0, 10);
for (int64_t i = 0; i < randomAlignmentNumber; i++) {
char *contig1 = stString_print("%" PRIi64 "", i);
char *contig2 = stString_print("%" PRIi64 "", i * 10);
int64_t start1 = st_randomInt(100000, 1000000);
int64_t start2 = st_randomInt(100000, 1000000);
int64_t strand1 = st_random() > 0.5;
int64_t strand2 = st_random() > 0.5;
int64_t end1 = start1;
int64_t end2 = start2;
struct List *operationList = constructEmptyList(0, NULL);
while (st_random() > 0.1) {
int64_t length = st_randomInt(0, 10);
int64_t type = st_randomInt(0, 3);
assert(type < 3);
listAppend(operationList, constructAlignmentOperation(type, length, 0));
if (type != PAIRWISE_INDEL_Y) {
end1 += strand1 ? length : -length;
}
if (type != PAIRWISE_INDEL_X) {
end2 += strand2 ? length : -length;
}
}
stList_append(pairwiseAlignments,
constructPairwiseAlignment(contig1, start1, end1, strand1, contig2, start2, end2, strand2, 0.0, operationList));
free(contig1);
free(contig2);
}
return pairwiseAlignments;
}
// copied from cPecanRealign
struct PairwiseAlignment *convertAlignedPairsToPairwiseAlignment(char *seqName1, char *seqName2, double score,
int64_t length1, int64_t length2, stList *alignedPairs) {
//Make pairwise alignment
int64_t pX = -1, pY = -1, mL = 0;
//Create an end matched pair, which is used to ensure the alignment has the correct end indels.
struct List *opList = constructEmptyList(0, (void (*)(void *)) destructAlignmentOperation);
stList_append(alignedPairs, stIntTuple_construct2(length1, length2));
for (int64_t i = 0; i < stList_length(alignedPairs); i++) {
stIntTuple *alignedPair = stList_get(alignedPairs, i);
int64_t x = stIntTuple_get(alignedPair, 0);
int64_t y = stIntTuple_get(alignedPair, 1);
assert(x - pX > 0);
assert(y - pY > 0);
if (x - pX > 0 && y - pY > 0) { //This is a hack for filtering
if (x - pX > 1) { //There is an indel.
if (mL > 0) {
listAppend(opList, constructAlignmentOperation(PAIRWISE_MATCH, mL, 0));
mL = 0;
}
listAppend(opList, constructAlignmentOperation(PAIRWISE_INDEL_X, x - pX - 1, 0));
}
if (y - pY > 1) {
if (mL > 0) {
listAppend(opList, constructAlignmentOperation(PAIRWISE_MATCH, mL, 0));
mL = 0;
}
listAppend(opList, constructAlignmentOperation(PAIRWISE_INDEL_Y, y - pY - 1, 0));
}
mL++;
pX = x;
pY = y;
}
}
//Deal with a trailing match, but exclude the final match
if (mL > 1) {
listAppend(opList, constructAlignmentOperation(PAIRWISE_MATCH, mL - 1, 0));
}
stIntTuple_destruct(stList_pop(alignedPairs));
//Construct the alignment
struct PairwiseAlignment *pA = constructPairwiseAlignment(seqName1, 0, length1, 1, seqName2, 0, length2, 1, score,
opList);
return pA;
}
