private void TestNewStitchedDirections(string origCigar1, string origDirections, string newCigar,
string expectedNewDirections)
{
var origRead = TestHelpers.CreateBamAlignment(
"ATTTACGGGC",
66214327, 0, 30, false, cigar: new CigarAlignment(origCigar1));
origRead.ReplaceOrAddStringTag("XD", origDirections);
var realignedRead = TestHelpers.CreateBamAlignment(
"ATTTACGGGC",
66214327, 0, 30, false, cigar: new CigarAlignment(newCigar));
var newXd = StitchedRealignmentHelpers.GetUpdatedXdForRealignedStitchedRead(origRead, realignedRead);
Assert.Equal(expectedNewDirections, newXd);
}
public void GetUpdatedXdForRealignedStitchedRead()
{
// Add a deletion in single-direction region
// MMMMMMMM MM // Orig Cigar
// FFSSSSSR RR // Orig Directions
// MMMMMMMMDMM // New Cigar
// FFSSSSSRRRR // New Directions
TestNewStitchedDirections("10M", "2F5S3R", "8M1D2M", "2F5S4R");
// Add a deletion in stitched region
// MMMMMMMM MM // Orig Cigar
// FFSSSSSS SR // Orig Directions
// MMMMMMMMDMM // New Cigar
// FFSSSSSSSSR // New Directions
TestNewStitchedDirections("10M", "2F7S1R", "8M1D2M", "2F8S1R");
// Add a deletion in border region
// MMMMMMMM MM // Orig Cigar
// FFSSSSSS RR // Orig Directions
// MMMMMMMMDMM // New Cigar
// FFSSSSSS?RR // New Directions
// TODO not clear what the right thing to do is here, we're just going with the later one for now
TestNewStitchedDirections("10M", "2F6S2R", "8M1D2M", "2F6S3R");
// Add a deletion in border region - early border
// MM MMMMMMMM // Orig Cigar
// FF SSSSSSRR // Orig Directions
// MMDMMMMMMMM // New Cigar
// FF?SSSSSSRR // New Directions
// TODO - we just take the direction after the deletion and apply it to the entire deletion. There may be a more nuanced answer? Unclear, and fairly low priority
TestNewStitchedDirections("10M", "2F6S2R", "2M1D8M", "2F7S2R");
// Add a deletion in border region
// MMMMMMMM MM // Orig Cigar
// FFFFFFFS RR // Orig Directions
// MMMMMMMMDMM // New Cigar
// FFFFFFFS?RR // New Directions
// TODO - we just take the direction after the deletion and apply it to the entire deletion. There may be a more nuanced answer? Unclear, and fairly low priority
TestNewStitchedDirections("10M", "7F1S2R", "8M1D2M", "7F1S3R");
// Add a deletion at the very end
// MMMMMMMMMM // Orig Cigar
// FFSSSSSSRR // Orig Directions
// MMMMMMMMMMDD // New Cigar
// FFSSSSSSRRRR // New Directions
TestNewStitchedDirections("10M", "2F6S2R", "10M2D", "2F6S4R");
// Add a deletion at the very beginning
// MMMMMMMMMM // Orig Cigar
// FFSSSSSSRR // Orig Directions
// DDMMMMMMMMMM // New Cigar
// FFFFSSSSSSRR // New Directions
TestNewStitchedDirections("10M", "2F6S2R", "2D10M", "4F6S2R");
// Remove a deletion in single-direction region
// MMMMMMMMDMM // Orig Cigar
// FFSSSSSRRRR // Orig Directions
// MMMMMMMM MM // New Cigar
// FFSSSSSR RR // New Directions
TestNewStitchedDirections("8M1D2M", "2F5S4R", "10M", "2F5S3R");
// Remove a deletion in stitched region
// MMMMMMMMDMM // Orig Cigar
// FFSSSSSSSSR // Orig Directions
// MMMMMMMM MM // New Cigar
// FFSSSSSS SR // New Directions
TestNewStitchedDirections("8M1D2M", "2F8S1R", "10M", "2F7S1R");
// Remove a deletion in border region
// MMMMMMMMDMM // Orig Cigar
// FFSSSSSSRRR // Orig Directions
// MMMMMMMM MM // New Cigar
// FFSSSSSS RR // New Directions
TestNewStitchedDirections("8M1D2M", "2F6S3R", "10M", "2F6S2R");
// Remove a deletion at the very end
// MMMMMMMMMMDD // Orig Cigar
// FFSSSSSSRRRR // Orig Directions
// MMMMMMMMMM // New Cigar
// FFSSSSSSRR // New Directions
TestNewStitchedDirections("10M2D", "2F6S4R", "10M", "2F6S2R");
// Remove a deletion at the very beginning
// DDMMMMMMMMMM // Orig Cigar
// FFFFSSSSSSRR // Orig Directions
// MMMMMMMMMM // New Cigar
// FFSSSSSSRR // New Directions
TestNewStitchedDirections("2D10M", "4F6S2R", "10M", "2F6S2R");
// Move deletion
// MMMMM MMMDMM // Orig Cigar
// FFSSS SSSRRR // Orig Directions
// MMMMMDMMM MM // New Cigar
// FFSSSSSSS RR // New Directions
TestNewStitchedDirections("8M1D2M", "2F6S3R", "5M1D5M", "2F7S2R");
// Same deletion
// MMMMMMMMDMM // Orig Cigar
// FFSSSSSSRRR // Orig Directions
// MMMMMMMMDMM // New Cigar
// FFSSSSSSRRR // New Directions
TestNewStitchedDirections("8M1D2M", "2F6S3R", "8M1D2M", "2F6S3R");
// Deletion at same spot but different length - gets longer
// MMMMMMMMD MM // Orig Cigar
// FFSSSSSSR RR // Orig Directions
// MMMMMMMMDDMM // New Cigar
// FFSSSSSSRRRR // New Directions
TestNewStitchedDirections("8M1D2M", "2F6S3R", "8M2D2M", "2F6S4R");
// Deletion at same spot but different length - gets shorter
// MMMMMMMMDDMM // Orig Cigar
// FFSSSSSSRRRR // Orig Directions
// MMMMMMMMD MM // New Cigar
// FFSSSSSSR RR // New Directions
TestNewStitchedDirections("8M2D2M", "2F6S4R", "8M1D2M", "2F6S3R");
// Insertion instead
// MMMMMMMMDMM // Orig Cigar
// FFSSSSSSRRR // Orig Directions
// MMMMMMMM IM // New Cigar
// FFSSSSSS RR // New Directions
TestNewStitchedDirections("8M1D2M", "2F6S3R", "9M1I", "2F6S2R");
// Add multiple deletions
// MMMM MMMM MM // Orig Cigar
// FFSS SSSR RR // Orig Directions
// MMMMDMMMMDMM // New Cigar
// FFSSSSSSRRRR // New Directions
TestNewStitchedDirections("10M", "2F5S3R", "4M1D4M1D2M", "2F6S4R");
// Add deletion in addition to one already there
// MMMM MMMMDMM // Orig Cigar
// FFSS SSSRRRR // Orig Directions
// MMMMDMMMMDMM // New Cigar
// FFSSSSSSRRRR // New Directions
TestNewStitchedDirections("8M1D2M", "2F5S4R", "4M1D4M1D2M", "2F6S4R");
// Add a multi-base deletion in single-direction region
// MMMMMMMM MM // Orig Cigar
// FFSSSSSR RR // Orig Directions
// MMMMMMMMDDDDDDMM // New Cigar
// FFSSSSSRRRRRRRRR // New Directions
TestNewStitchedDirections("10M", "2F5S3R", "8M6D2M", "2F5S9R");
// Remove multiple deletions
// MMMMDMMMMDMM // Orig Cigar
// FFSSSSSSRRRR // Orig Directions
// MMMM MMMM MM // New Cigar
// FFSS SSSR RR // New Directions
TestNewStitchedDirections("4M1D4M1D2M", "2F6S4R", "10M", "2F5S3R");
// Remove only one of multiple deletions
// MMMMDMMMMDMM // Orig Cigar
// FFSSSSSSRRRR // Orig Directions
// MMMMDMMMM MM // New Cigar
// FFSSSSSSR RR // New Directions
TestNewStitchedDirections("4M1D4M1D2M", "2F6S4R", "4M1D6M", "2F6S3R");
// Start with multiple deletions, change size of one
// MMMMDMMMMD MM // Orig Cigar
// FFSSSSSSRR RR // Orig Directions
// MMMMDMMMMDDDMM // New Cigar
// FFSSSSSSRRRRRR // New Directions
TestNewStitchedDirections("4M1D4M1D2M", "2F6S4R", "4M1D4M3D2M", "2F6S6R");
// Add multi-base deletion on border of different regions
// MMMMMMMM MM // Orig Cigar
// FFSSSSSS RR // Orig Directions
// MMMMMMMMDDDMM // New Cigar
// FFSSSSSSRRRRR // New Directions
TestNewStitchedDirections("10M", "2F6S2R", "8M3D2M", "2F6S5R");
// Lengthen deletion on border of different regions
// MMMMMMMMD MM // Orig Cigar
// FFSSSSSSS RR // Orig Directions
// MMMMMMMMDDDMM // New Cigar
// FFSSSSSSRRRRR // New Directions
TestNewStitchedDirections("8M1D2M", "2F7S2R", "8M3D2M", "2F6S5R");
// Lengthen multi-base deletion spanning different regions
// MMMMMMMMDDMM // Orig Cigar
// FFSSSSSSSRRR // Orig Directions
// MMMMMMMMDDDMM // New Cigar
// FFSSSSSSRRRRR // New Directions
// FFSSSSSSSRRRR // New Directions - other option?
// TODO - we just take the right-most one and apply it to the entire deletion. There may be a better answer? Maybe just apply it to the part that is extended? Unclear, and low priority
//TestNewStitchedDirections("8M2D2M", "2F7S3R", "8M3D2M", "2F7S4R");
TestNewStitchedDirections("8M2D2M", "2F7S3R", "8M3D2M", "2F6S5R");
// Remove multi-base deletion spanning different regions
// MMMMMMMMDDDMM // Orig Cigar
// FFSSSSSSSRRRR // Orig Directions
// MMMMMMMM MM // New Cigar
// FFSSSSSS RR // New Directions
TestNewStitchedDirections("8M3D2M", "2F7S4R", "10M", "2F6S2R");
// Shorten multi-base deletion spanning different regions so that it only spans one?
// MMMMMMMMDDDMM // Orig Cigar
// FFSSSSSSSRRRR // Orig Directions
// MMMMMMMMD MM // New Cigar
// FFSSSSSSS RR // New Directions
// TODO - we just take the right-most one and apply it to the entire deletion. There may be a better answer? Maybe just trim down the part that is "removed"? Unclear, and low priority
TestNewStitchedDirections("8M3D2M", "2F7S4R", "8M1D2M", "2F6S3R");
// For read-spanning stuff - insertion, softclip, match - directions should stay the same
// Assumes same number of bases... but it should never be possible to be a diff number of bases
TestNewStitchedDirections("10M", "2F5S3R", "9M1I", "2F5S3R");
TestNewStitchedDirections("10M", "2F5S3R", "1S3M1I5M1S", "2F5S3R");
TestNewStitchedDirections("9M1I", "2F5S3R", "10M", "2F5S3R");
TestNewStitchedDirections("1S3M1I5M1S", "2F5S3R", "10M", "2F5S3R");
// Real example
var origRead = TestHelpers.CreateBamAlignment(
"ATTGACATTAACTTAATTGTTTTTACTGACATTCTTAATTGCTTTTTGGAATTCATTAGCTGGTATAATACTAAAGTAATAAATACGTTGTGTTTTTCTAAAGGCATCTGAAATAGTGGAGCTAAATACTAAAACTGGGATAAAAATAATGGTAATTTTAGCTTACAAATAAACA",
66214327, 0, 30, false, cigar: new CigarAlignment("175M"));
origRead.ReplaceOrAddStringTag("XD", "74F25S76R");
var realignedRead = TestHelpers.CreateBamAlignment(
"ATTGACATTAACTTAATTGTTTTTACTGACATTCTTAATTGCTTTTTGGAATTCATTAGCTGGTATAATACTAAAGTAATAAATACGTTGTGTTTTTCTAAAGGCATCTGAAATAGTGGAGCTAAATACTAAAACTGGGATAAAAATAATGGTAATTTTAGCTTACAAATAAACA",
66214327, 0, 30, false, cigar: new CigarAlignment("170M6D5M"));
var newXd = StitchedRealignmentHelpers.GetUpdatedXdForRealignedStitchedRead(origRead, realignedRead);
Assert.Equal("74F25S82R", newXd);
}
