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; }