void PredictionExon_loadGenomicMapper(Exon *exon, Mapper *mapper, IDType id, int start) {
// NIY Make the Exon_getContig consistent
Mapper_addMapCoordinates( mapper, id, start, start+Exon_getLength(exon)-1,
Exon_getStrand(exon), Slice_getSeqRegionId(PredictionExon_getSlice(exon)),
Exon_getStart(exon), Exon_getEnd(exon) );
}
int main(int argc, char *argv[]) {
initEnsC(argc, argv);
Mapper *mapper = Mapper_new( "rawcontig", "virtualcontig", NULL, NULL );
int nToLoad = loadSGPDump(mapper, 0 );
// loading done successfully
ok(1, nToLoad == 100);
{
// transform a segment entirely within the first rawcontig
int testOutput[][4] = {1, 2, 5, -1};
testTransform (mapper, 627012, 2, 5, -1, "rawcontig", testOutput, NumOutput(testOutput));
}
{
// now a split coord
int testOutput[][4] = {
{314696, 31917, 31937, -1},
{341, 126, 59773, -1},
{315843, 5332, 5963, +1}
};
testTransform (mapper, 1, 383700, 444000, +1, "virtualcontig",testOutput, NumOutput(testOutput));
}
{
// now a simple gap
int testOutput[][4] = {
{ 627011, 7447, 7507, +1 },
{ 1, 273762, 273781, 0 }
};
testTransform (mapper, 1, 273701, 273781, +1, "virtualcontig", testOutput, NumOutput(testOutput));
}
//
// check if the mapper can do merging
//
mapper = Mapper_new( "asm1", "asm2", NULL, NULL );
Mapper_addMapCoordinates(mapper, 1, 1, 10, 1, 1, 101, 110 );
Mapper_addMapCoordinates(mapper, 1, 21, 30, 1, 1, 121, 130 );
Mapper_addMapCoordinates(mapper, 1, 11, 20, 1, 1, 111, 120 );
{
int testOutput[][4] = {{ 1, 105, 125, 1 }};
testTransform(mapper, 1, 5, 25, 1, "asm1", testOutput, NumOutput(testOutput));
}
//
// Slightly differnt merge case
//
mapper = Mapper_new( "asm1", "asm2", NULL, NULL );
Mapper_addMapCoordinates(mapper, 1, 1, 10, 1, 1, 101, 110 );
Mapper_addMapCoordinates(mapper, 1, 21, 30, 1, 1, 121, 130 );
Mapper_addMapCoordinates(mapper, 1, 12, 20, 1, 1, 112, 120 );
{
int testOutput[][4] = {
{ 1, 105, 110, 1 },
{ 1, 11, 11, 0 },
{ 1, 112, 125, 1 }
};
testTransform( mapper, 1, 5, 25, 1, "asm1" , testOutput, NumOutput(testOutput));
}
//
// dont merge on wrong orientation
//
mapper = Mapper_new( "asm1", "asm2", NULL, NULL );
Mapper_addMapCoordinates(mapper, 1, 1, 10, 1, 1, 101, 110 );
Mapper_addMapCoordinates(mapper, 1, 21, 30, 1, 1, 121, 130 );
Mapper_addMapCoordinates(mapper, 1, 11, 20, -1, 1, 111, 120 );
{
int testOutput[][4] = {
{ 1, 105, 110, 1 },
{ 1, 111, 120, -1 },
{ 1, 121, 125, 1 }
};
testTransform( mapper, 1, 5, 25, 1, "asm1" , testOutput, NumOutput(testOutput));
}
//
// can reverse strands merge?
//
mapper = Mapper_new( "asm1", "asm2", NULL, NULL );
Mapper_addMapCoordinates(mapper, 1, 1, 10, -1, 1, 121, 130 );
Mapper_addMapCoordinates(mapper, 1, 21, 30, -1, 1, 101, 110 );
Mapper_addMapCoordinates(mapper, 1, 11, 20, -1, 1, 111, 120 );
{
int testOutput[][4] = {{ 1, 106, 126, -1 } };
testTransform( mapper, 1, 5, 25, 1, "asm1", testOutput, NumOutput(testOutput));
}
//
// normal merge, not three
//
mapper = Mapper_new( "asm1", "asm2", NULL, NULL );
Mapper_addMapCoordinates(mapper, 1, 1, 10, 1, 1, 101, 110 );
Mapper_addMapCoordinates(mapper, 1, 11, 20, 1, 1, 111, 120 );
Mapper_addMapCoordinates(mapper, 1, 22, 30, 1, 1, 132, 140 );
Mapper_addMapCoordinates(mapper, 1, 51, 70, 1, 1, 161, 180 );
Mapper_addMapCoordinates(mapper, 1, 31, 35, 1, 1, 141, 145 );
{
int testOutput[][4] = {
{ 1, 105, 120, 1 },
{ 1, 21, 21, 0 },
{ 1, 132, 145, 1 },
{ 1, 36, 45, 0 }
};
testTransform( mapper, 1, 5, 45, 1, "asm1" , testOutput, NumOutput(testOutput));
}
//
// test tranformation of 'insertion' coordinates where end = start -1
//
mapper = Mapper_new("asm1", "asm2", NULL, NULL);
Mapper_addMapCoordinates(mapper,1, 1, 10, 1, 2, 101, 110);
Mapper_addMapCoordinates(mapper,1, 11, 20, -1, 3, 1, 10);
{
// boundary insert, expect 2 edge inserts back
int testOutput[][4] = {
{2, 111, 110, 1},
{3, 11, 10, -1}
};
testTransform(mapper, 1, 11, 10, 1, "asm1", testOutput, NumOutput(testOutput));
}
{
// edge insert, negative strand, expect edge insert negative strand
int testOutput[][4] = {{2, 101, 100, -1}};
testTransform(mapper, 1, 1, 0, -1, "asm1", testOutput, NumOutput(testOutput));
}
{
// normal case, expect single insert in middle
int testOutput[][4] = {{2, 102, 101, 1}};
testTransform(mapper, 1, 2, 1, 1, "asm1", testOutput, NumOutput(testOutput));
}
{
// expect a gap
int testOutput[][4] = {{1, 100, 200, 0}};
testTransform(mapper, 1, 100, 200, 1, "asm1", testOutput, NumOutput(testOutput));
}
return 0;
}
int loadSGPDump(Mapper *mapper, int reverse) {
//chr_id raw_id chr_start chr_end raw_start raw_end raw_ori
long sgpDump[][7] = {
{ 1, 627012, 1, 31276, 1, 31276, 1 },
{ 1, 627010, 31377, 42949, 72250, 83822, -1 },
{ 1, 2768, 42950, 180950, 251, 138251, 1 },
{ 1, 10423, 180951, 266154, 1, 85204, -1 },
{ 1, 627011, 266255, 273761, 1, 7507, 1 },
{ 1, 314698, 273862, 283122, 1, 9261, -1 },
{ 1, 627009, 283223, 331394, 251, 48422, -1 },
{ 1, 314695, 331395, 352162, 1, 20768, -1 },
{ 1, 314697, 352263, 359444, 1, 7182, -1 },
{ 1, 314696, 359545, 383720, 31917, 56092, -1 },
{ 1, 341, 383721, 443368, 126, 59773, -1 },
{ 1, 315843, 443369, 444727, 5332, 6690, 1 },
{ 1, 315844, 444828, 453463, 1, 8636, -1 },
{ 1, 315834, 453564, 456692, 1, 3129, 1 },
{ 1, 315831, 456793, 458919, 1, 2127, 1 },
{ 1, 315827, 459020, 468965, 251, 10196, -1 },
{ 1, 544782, 468966, 469955, 1, 990, -1 },
{ 1, 315837, 470056, 473446, 186, 3576, -1 },
{ 1, 544807, 473447, 474456, 1, 1010, -1 },
{ 1, 315832, 474557, 477289, 1, 2733, 1 },
{ 1, 544806, 477390, 477601, 1086, 1297, -1 },
{ 1, 315840, 477602, 482655, 21, 5074, 1 },
{ 1, 544802, 482656, 483460, 1, 805, -1 },
{ 1, 544811, 483561, 484162, 6599, 7200, -1 },
{ 1, 315829, 484163, 498439, 15, 14291, -1 },
{ 1, 544813, 498440, 500980, 1, 2541, -1 },
{ 1, 544773, 501081, 502190, 1217, 2326, -1 },
{ 1, 315828, 502191, 513296, 72, 11177, 1 },
{ 1, 544815, 513297, 517276, 2179, 6158, 1 },
{ 1, 315836, 517277, 517662, 2958, 3343, 1 },
{ 1, 544805, 517663, 520643, 299, 3279, 1 },
{ 1, 315835, 520744, 521682, 2462, 3400, -1 },
{ 1, 544784, 521683, 526369, 54, 4740, 1 },
{ 1, 544796, 526470, 527698, 1, 1229, 1 },
{ 1, 315833, 527799, 528303, 2530, 3034, -1 },
{ 1, 544803, 528304, 531476, 1, 3173, -1 },
{ 1, 544821, 531577, 532691, 1, 1115, 1 },
{ 1, 544810, 532792, 533843, 1, 1052, 1 },
{ 1, 544800, 533944, 535249, 1, 1306, 1 },
{ 1, 544786, 535350, 536652, 1, 1303, 1 },
{ 1, 544814, 536753, 538358, 1, 1606, 1 },
{ 1, 544812, 538459, 540004, 1, 1546, 1 },
{ 1, 544818, 540105, 541505, 1, 1401, 1 },
{ 1, 544816, 541606, 542693, 1, 1088, 1 },
{ 1, 544778, 542794, 544023, 1, 1230, 1 },
{ 1, 544779, 544124, 545709, 1, 1586, 1 },
{ 1, 544804, 545810, 547660, 1, 1851, 1 },
{ 1, 544774, 547761, 550105, 1, 2345, 1 },
{ 1, 544817, 550206, 552105, 1, 1900, 1 },
{ 1, 544781, 552206, 553640, 1, 1435, 1 },
{ 1, 315830, 553741, 555769, 1, 2029, -1 },
{ 1, 544819, 555870, 558904, 1, 3035, -1 },
{ 1, 544777, 559005, 560670, 1, 1666, 1 },
{ 1, 544795, 560771, 563092, 1, 2322, 1 },
{ 1, 544809, 563193, 565523, 1, 2331, 1 },
{ 1, 544808, 565624, 568113, 1, 2490, 1 },
{ 1, 544798, 568214, 570324, 1, 2111, 1 },
{ 1, 544783, 570425, 574640, 1, 4216, 1 },
{ 1, 544824, 574741, 578101, 1, 3361, 1 },
{ 1, 544775, 578202, 580180, 1, 1979, -1 },
{ 1, 544825, 580281, 581858, 1, 1578, -1 },
{ 1, 544772, 581959, 585312, 1, 3354, 1 },
{ 1, 544793, 585413, 588740, 1, 3328, 1 },
{ 1, 544785, 588841, 591656, 1, 2816, -1 },
{ 1, 544791, 591757, 594687, 1, 2931, 1 },
{ 1, 544820, 594788, 597671, 1, 2884, 1 },
{ 1, 544790, 597772, 601587, 1, 3816, 1 },
{ 1, 544794, 601688, 603324, 1, 1637, -1 },
{ 1, 544823, 603425, 607433, 1, 4009, 1 },
{ 1, 544789, 607534, 610856, 1, 3323, 1 },
{ 1, 544799, 610957, 614618, 1, 3662, 1 },
{ 1, 544776, 614719, 618674, 1, 3956, -1 },
{ 1, 544797, 618775, 624522, 1, 5748, -1 },
{ 1, 544787, 624623, 629720, 1, 5098, -1 },
{ 1, 544792, 629821, 637065, 1, 7245, 1 },
{ 1, 622020, 837066, 851064, 1, 13999, -1 },
{ 1, 622021, 851165, 854101, 1, 2937, -1 },
{ 1, 622016, 854202, 856489, 1, 2288, -1 },
{ 1, 625275, 856590, 888524, 420, 32354, -1 },
{ 1, 622015, 888525, 891483, 1, 2959, -1 },
{ 1, 622024, 891584, 896208, 8871, 13495, -1 },
{ 1, 625537, 896209, 952170, 1, 55962, -1 },
{ 1, 625538, 952271, 1051812, 251, 99792, -1 },
{ 1, 625277, 1051813, 1055193, 1, 3381, -1 },
{ 1, 625266, 1055294, 1062471, 1, 7178, -1 },
{ 1, 598266, 1062572, 1086504, 11, 23943, -1 },
{ 1, 625271, 1086505, 1096571, 3943, 14009, 1 },
{ 1, 625265, 1096572, 1100161, 2436, 6025, -1 },
{ 1, 173125, 1100162, 1106067, 3329, 9234, -1 },
{ 1, 598265, 1106068, 1112101, 286, 6319, 1 },
{ 1, 625360, 1112102, 1172572, 251, 60721, 1 },
{ 1, 173111, 1172573, 1172716, 1, 144, -1 },
{ 1, 173103, 1172817, 1173945, 1, 1129, 1 },
{ 1, 170531, 1174046, 1174188, 8791, 8933, -1 },
{ 1, 625363, 1174189, 1183590, 67, 9468, 1 },
{ 1, 173120, 1183591, 1183929, 153, 491, -1 },
{ 1, 170509, 1183930, 1184112, 864, 1046, 1 },
{ 1, 173119, 1184213, 1189703, 1, 5491, -1 },
{ 1, 625357, 1189804, 1213915, 1, 24112, 1 },
{ 1, 625359, 1214016, 1216330, 1, 2315, 1 }
};
int nRange = sizeof(sgpDump)/(sizeof(long) *7);
printf("Have %d ranges\n",nRange);
int inc = 1;
int pos = 0;
if (reverse) {
inc = -1;
pos = nRange-1;
}
int count=0;
while (count < nRange) {
int chrId = sgpDump[pos][0];
int contigId = sgpDump[pos][1];
int chrStart = sgpDump[pos][2];
int chrEnd = sgpDump[pos][3];
int contigStart= sgpDump[pos][4];
int contigEnd = sgpDump[pos][5];
int contigOri = sgpDump[pos][6];
Mapper_addMapCoordinates(mapper, contigId, contigStart, contigEnd, contigOri, chrId, chrStart, chrEnd);
count++;
pos+=inc;
}
return nRange;
}
