mapToAlignments_early_truncation.R

library(GenomicAlignments)

alignments <- GAlignments(
    seqnames = Rle(factor(rep("chrX", 3))),
    pos = c(37701723L, 37753335L, 37753335L),
    cigar = c(
        "24H6M1I13M2D5M1D12M1I16M3I6M2D20M1D18M1I34M2I116M2D9M1D9M1I30M1D9M1D44M6I3M2I4M2D19M9D7M1I5M1D18M1I17M2D1M1D16M1D32M1D3M1D18M1I3M1D49M2D34M2D8M1D7M2D1M1D5M1I2M5D4M1D2M1I3M2D10M1I21M1D20M2D1M1D2M1D18M2I3M2D74M1D9M1D5M2D34M1D12M2D20M1I2M1I35M1D10M2D16M1I55M3D82M1D6M1I65M2I8M1I30M1D7M2I15M1D15M1D20M1I2M1I14M1D29M3D12M2D3M1D5M1D20M1D21M2D56M1D7M4D2M1I60M2I9M1D49M2I5M2I28M13206H",
        "6994H26M2I6M1I1M1I50M1D15M2I4M4D35M1D9M1D5M2D37M1I54M1D59M3I27M1I3M1D5M1I8M1I4M2I10M1I47M1D25M1I84M1D8M7D8M1D69M1I23M3D6M1D1M1D11M2D8M1I17M1D43M1I17M1D60M1I1M3D17M1D17M2D1M1D4M1I12M1D28M1D13M1D7M2I44M5D30M1D2M2D1M1D20M1D23M1I7M1D22M1D3M2D73M1I4M5D23M3D4M2D23M1D13M1D9M3D12M1I9M1D11M1D1M3I31M2I56M1D5M6461H",
        "308H103M1D16M2D47M1D1M1D18M1D36M1I26M3I51M1D2M1I8M1D9M1D17M3I53M1D15M1D7M3I22M1D60M3I10M2D20M7D8M1D65M2I16M1D12M1D6M1D11M3D4M1D4M1I8M1I31M3I7M2I5M1I10M1D16M2D9M1D10M4I11M1D107M2D22M1I18M1D40M1I1M2D13M1I15M1D15M1D5M1I31M1D6M1D12M1D21M1I52M1D14M2D6M2I17M3D4M1D27M1I11M1D9M1D2M1D5M1D14M1D4M1D3M1D73M1D30M1D9M11706H"
    ),
    strand = Rle(factor(rep("+", 3), levels = c("+","-", "*"))),
    names = c("read1", "read2", "read3")
)

variants <- GRanges(
    seqnames = Rle(factor(rep("chrX", 6))),
    ranges = IRanges(
        start = c(
            37701926L,
            37702423L,
            37703182L,
            37703236L,
            37753664L,
            37753942L
        ),
        width = 1
    ),
    strand = Rle(factor(rep("*", 6), levels = c("+","-", "*"))),
)

names(variants) <- c("read1", "read2", "read3", "read4", "read5", "read6")

mapToAlignments(variants, alignments) # only returns mapping to first alignment
mapToAlignments(variants, alignments[2:3]) # returns mapping for 2nd and 3rd alignments